1
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Li C, Stražar M, Mohamed AMT, Pacheco JA, Walker RL, Lebar T, Zhao S, Lockart J, Dame A, Thurimella K, Jeanfavre S, Brown EM, Ang QY, Berdy B, Sergio D, Invernizzi R, Tinoco A, Pishchany G, Vasan RS, Balskus E, Huttenhower C, Vlamakis H, Clish C, Shaw SY, Plichta DR, Xavier RJ. Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria. Cell 2024; 187:1834-1852.e19. [PMID: 38569543 PMCID: PMC11071153 DOI: 10.1016/j.cell.2024.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 01/23/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
Accumulating evidence suggests that cardiovascular disease (CVD) is associated with an altered gut microbiome. Our understanding of the underlying mechanisms has been hindered by lack of matched multi-omic data with diagnostic biomarkers. To comprehensively profile gut microbiome contributions to CVD, we generated stool metagenomics and metabolomics from 1,429 Framingham Heart Study participants. We identified blood lipids and cardiovascular health measurements associated with microbiome and metabolome composition. Integrated analysis revealed microbial pathways implicated in CVD, including flavonoid, γ-butyrobetaine, and cholesterol metabolism. Species from the Oscillibacter genus were associated with decreased fecal and plasma cholesterol levels. Using functional prediction and in vitro characterization of multiple representative human gut Oscillibacter isolates, we uncovered conserved cholesterol-metabolizing capabilities, including glycosylation and dehydrogenation. These findings suggest that cholesterol metabolism is a broad property of phylogenetically diverse Oscillibacter spp., with potential benefits for lipid homeostasis and cardiovascular health.
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Affiliation(s)
- Chenhao Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ahmed M T Mohamed
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Tina Lebar
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Shijie Zhao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Lockart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrea Dame
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Qi Yan Ang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Dallis Sergio
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rachele Invernizzi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Antonio Tinoco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Ramachandran S Vasan
- Boston University and NHLBI's Framingham Heart Study, Framingham, MA, USA; Sections of Preventive Medicine and Epidemiology and Cardiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA; University of Texas School of Public Health, San Antonio, TX, USA
| | - Emily Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stanley Y Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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2
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Bhosle A, Bae S, Zhang Y, Chun E, Avila-Pacheco J, Geistlinger L, Pishchany G, Glickman JN, Michaud M, Waldron L, Clish CB, Xavier RJ, Vlamakis H, Franzosa EA, Garrett WS, Huttenhower C. Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease. Mol Syst Biol 2024; 20:338-361. [PMID: 38467837 PMCID: PMC10987656 DOI: 10.1038/s44320-024-00027-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 03/13/2024] Open
Abstract
Microbial biochemistry is central to the pathophysiology of inflammatory bowel diseases (IBD). Improved knowledge of microbial metabolites and their immunomodulatory roles is thus necessary for diagnosis and management. Here, we systematically analyzed the chemical, ecological, and epidemiological properties of ~82k metabolic features in 546 Integrative Human Microbiome Project (iHMP/HMP2) metabolomes, using a newly developed methodology for bioactive compound prioritization from microbial communities. This suggested >1000 metabolic features as potentially bioactive in IBD and associated ~43% of prevalent, unannotated features with at least one well-characterized metabolite, thereby providing initial information for further characterization of a significant portion of the fecal metabolome. Prioritized features included known IBD-linked chemical families such as bile acids and short-chain fatty acids, and less-explored bilirubin, polyamine, and vitamin derivatives, and other microbial products. One of these, nicotinamide riboside, reduced colitis scores in DSS-treated mice. The method, MACARRoN, is generalizable with the potential to improve microbial community characterization and provide therapeutic candidates.
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Affiliation(s)
- Amrisha Bhosle
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sena Bae
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Yancong Zhang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eunyoung Chun
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Ludwig Geistlinger
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA, USA
| | - Gleb Pishchany
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan N Glickman
- Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Monia Michaud
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Levi Waldron
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
| | - Clary B Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric A Franzosa
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Wendy S Garrett
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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3
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Schirmer M, Stražar M, Avila-Pacheco J, Rojas-Tapias DF, Brown EM, Temple E, Deik A, Bullock K, Jeanfavre S, Pierce K, Jin S, Invernizzi R, Pust MM, Costliow Z, Mack DR, Griffiths AM, Walters T, Boyle BM, Kugathasan S, Vlamakis H, Hyams J, Denson L, Clish CB, Xavier RJ. Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. Cell Host Microbe 2024; 32:209-226.e7. [PMID: 38215740 PMCID: PMC10923022 DOI: 10.1016/j.chom.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/14/2024]
Abstract
Understanding the role of the microbiome in inflammatory diseases requires the identification of microbial effector molecules. We established an approach to link disease-associated microbes to microbial metabolites by integrating paired metagenomics, stool and plasma metabolomics, and culturomics. We identified host-microbial interactions correlated with disease activity, inflammation, and the clinical course of ulcerative colitis (UC) in the Predicting Response to Standardized Colitis Therapy (PROTECT) pediatric inception cohort. In severe disease, metabolite changes included increased dipeptides and tauro-conjugated bile acids (BAs) and decreased amino-acid-conjugated BAs in stool, whereas in plasma polyamines (N-acetylputrescine and N1-acetylspermidine) increased. Using patient samples and Veillonella parvula as a model, we uncovered nitrate- and lactate-dependent metabolic pathways, experimentally linking V. parvula expansion to immunomodulatory tryptophan metabolite production. Additionally, V. parvula metabolizes immunosuppressive thiopurine drugs through xdhA xanthine dehydrogenase, potentially impairing the therapeutic response. Our findings demonstrate that the microbiome contributes to disease-associated metabolite changes, underscoring the importance of these interactions in disease pathology and treatment.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
| | - Martin Stražar
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Eric M Brown
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Emily Temple
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Deik
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Bullock
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Jeanfavre
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kerry Pierce
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shen Jin
- Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | | | - Marie-Madlen Pust
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Zach Costliow
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R Mack
- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Anne M Griffiths
- Division of Gastroenterology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Thomas Walters
- Division of Gastroenterology, Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Brendan M Boyle
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey Hyams
- Connecticut Children's Medical Center, Division of Digestive Diseases, Hartford, CT 06106, USA
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Clary B Clish
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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4
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Gentry EC, Collins SL, Panitchpakdi M, Belda-Ferre P, Stewart AK, Carrillo Terrazas M, Lu HH, Zuffa S, Yan T, Avila-Pacheco J, Plichta DR, Aron AT, Wang M, Jarmusch AK, Hao F, Syrkin-Nikolau M, Vlamakis H, Ananthakrishnan AN, Boland BS, Hemperly A, Vande Casteele N, Gonzalez FJ, Clish CB, Xavier RJ, Chu H, Baker ES, Patterson AD, Knight R, Siegel D, Dorrestein PC. Reverse metabolomics for the discovery of chemical structures from humans. Nature 2024; 626:419-426. [PMID: 38052229 PMCID: PMC10849969 DOI: 10.1038/s41586-023-06906-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/28/2023] [Indexed: 12/07/2023]
Abstract
Determining the structure and phenotypic context of molecules detected in untargeted metabolomics experiments remains challenging. Here we present reverse metabolomics as a discovery strategy, whereby tandem mass spectrometry spectra acquired from newly synthesized compounds are searched for in public metabolomics datasets to uncover phenotypic associations. To demonstrate the concept, we broadly synthesized and explored multiple classes of metabolites in humans, including N-acyl amides, fatty acid esters of hydroxy fatty acids, bile acid esters and conjugated bile acids. Using repository-scale analysis1,2, we discovered that some conjugated bile acids are associated with inflammatory bowel disease (IBD). Validation using four distinct human IBD cohorts showed that cholic acids conjugated to Glu, Ile/Leu, Phe, Thr, Trp or Tyr are increased in Crohn's disease. Several of these compounds and related structures affected pathways associated with IBD, such as interferon-γ production in CD4+ T cells3 and agonism of the pregnane X receptor4. Culture of bacteria belonging to the Bifidobacterium, Clostridium and Enterococcus genera produced these bile amidates. Because searching repositories with tandem mass spectrometry spectra has only recently become possible, this reverse metabolomics approach can now be used as a general strategy to discover other molecules from human and animal ecosystems.
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Affiliation(s)
- Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Stephanie L Collins
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, San Diego, CA, USA
| | - Allison K Stewart
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | | | - Hsueh-Han Lu
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Tingting Yan
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Fuhua Hao
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Mashette Syrkin-Nikolau
- Division of Gastroenterology, Department of Pediatrics, Rady Children's Hospital University of California San Diego, La Jolla, CA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Brigid S Boland
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Amy Hemperly
- Division of Gastroenterology, Department of Pediatrics, Rady Children's Hospital University of California San Diego, La Jolla, CA, USA
| | - Niels Vande Casteele
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
- CU-UCSD, Center for Mucosal Immunology, Allergy and Vaccine Development, University of California, San Diego, La Jolla, California, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew D Patterson
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, San Diego, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, San Diego, CA, USA
- Department of Bioengineering, University of California, San Diego, San Diego, California, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
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5
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McPherson RL, Isabella CR, Walker RL, Sergio D, Bae S, Gaca T, Raman S, Nguyen LTT, Wesener DA, Halim M, Wuo MG, Dugan A, Kerby R, Ghosh S, Rey FE, Dhennezel C, Pishchany G, Lensch V, Vlamakis H, Alm EJ, Xavier RJ, Kiessling LL. Lectin-Seq: A method to profile lectin-microbe interactions in native communities. Sci Adv 2023; 9:eadd8766. [PMID: 37506208 PMCID: PMC10381928 DOI: 10.1126/sciadv.add8766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
Soluble human lectins are critical components of innate immunity. Genetic models suggest that lectins influence host-resident microbiota, but their specificity for commensal and mutualist species is understudied. Elucidating lectins' roles in regulating microbiota requires an understanding of which microbial species they bind within native communities. To profile human lectin recognition, we developed Lectin-Seq. We apply Lectin-Seq to human fecal microbiota using the soluble mannose-binding lectin (MBL) and intelectin-1 (hItln1). Although each lectin binds a substantial percentage of the samples (10 to 20%), the microbial interactomes of MBL and hItln1 differ markedly in composition and diversity. MBL binding is highly selective for a small subset of species commonly associated with humans. In contrast, hItln1's interaction profile encompasses a broad range of lower-abundance species. Our data uncover stark differences in the commensal recognition properties of human lectins.
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Affiliation(s)
- Robert L. McPherson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christine R. Isabella
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Dallis Sergio
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sunhee Bae
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tony Gaca
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Smrithi Raman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Le Thanh Tu Nguyen
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Darryl A. Wesener
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Melanie Halim
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael G. Wuo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amanda Dugan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert Kerby
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Soumi Ghosh
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Catherine Dhennezel
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Gleb Pishchany
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Valerie Lensch
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hera Vlamakis
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric J. Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Ramnik J. Xavier
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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6
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Scheid JF, Eraslan B, Hudak A, Brown EM, Sergio D, Delorey TM, Phillips D, Lefkovith A, Jess AT, Duck LW, Elson CO, Vlamakis H, Plichta DR, Deguine J, Ananthakrishnan AN, Graham DB, Regev A, Xavier RJ. Remodeling of colon plasma cell repertoire within ulcerative colitis patients. J Exp Med 2023; 220:e20220538. [PMID: 36752797 PMCID: PMC9949229 DOI: 10.1084/jem.20220538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 10/03/2022] [Accepted: 01/11/2023] [Indexed: 02/09/2023] Open
Abstract
Plasma cells (PCs) constitute a significant fraction of colonic mucosal cells and contribute to inflammatory infiltrates in ulcerative colitis (UC). While gut PCs secrete bacteria-targeting IgA antibodies, their role in UC pathogenesis is unknown. We performed single-cell V(D)J- and RNA-seq on sorted B cells from the colon of healthy individuals and patients with UC. A large fraction of B cell clones is shared between different colon regions, but inflammation in UC broadly disrupts this landscape, causing transcriptomic changes characterized by an increase in the unfolded protein response (UPR) and antigen presentation genes, clonal expansion, and isotype skewing from IgA1 and IgA2 to IgG1. We also directly expressed and assessed the specificity of 152 mAbs from expanded PC clones. These mAbs show low polyreactivity and autoreactivity and instead target both shared bacterial antigens and specific bacterial strains. Altogether, our results characterize the microbiome-specific colon PC response and how its disruption might contribute to inflammation in UC.
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Affiliation(s)
- Johannes F. Scheid
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Basak Eraslan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew Hudak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric M. Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dallis Sergio
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Toni M. Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Alison T. Jess
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lennard W. Duck
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Charles O. Elson
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Ashwin N. Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniel B. Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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7
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Vatanen T, Jabbar KS, Ruohtula T, Honkanen J, Avila-Pacheco J, Siljander H, Stražar M, Oikarinen S, Hyöty H, Ilonen J, Mitchell CM, Yassour M, Virtanen SM, Clish CB, Plichta DR, Vlamakis H, Knip M, Xavier RJ. Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism. Cell 2022; 185:4921-4936.e15. [PMID: 36563663 PMCID: PMC9869402 DOI: 10.1016/j.cell.2022.11.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 12/24/2022]
Abstract
The perinatal period represents a critical window for cognitive and immune system development, promoted by maternal and infant gut microbiomes and their metabolites. Here, we tracked the co-development of microbiomes and metabolomes from late pregnancy to 1 year of age using longitudinal multi-omics data from a cohort of 70 mother-infant dyads. We discovered large-scale mother-to-infant interspecies transfer of mobile genetic elements, frequently involving genes associated with diet-related adaptations. Infant gut metabolomes were less diverse than maternal but featured hundreds of unique metabolites and microbe-metabolite associations not detected in mothers. Metabolomes and serum cytokine signatures of infants who received regular-but not extensively hydrolyzed-formula were distinct from those of exclusively breastfed infants. Taken together, our integrative analysis expands the concept of vertical transmission of the gut microbiome and provides original insights into the development of maternal and infant microbiomes and metabolomes during late pregnancy and early life.
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Affiliation(s)
- Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - Terhi Ruohtula
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland
| | - Jarno Honkanen
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland
| | | | - Heli Siljander
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland; Centre for Military Medicine, Finnish Defence Forces, Riihimäki, Finland
| | - Martin Stražar
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sami Oikarinen
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Heikki Hyöty
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Fimlab Laboratories, Tampere, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Caroline M Mitchell
- Vincent Obstetrics & Gynecology Department, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Moran Yassour
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel; The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Suvi M Virtanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland; Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland; Center for Child Health Research and Development and Innovation Center, Tampere University Hospital, Tampere, Finland
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Damian R Plichta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA
| | - Mikael Knip
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; New Children's Hospital, Helsinki University Hospital, Helsinki, Finland; Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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8
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Pedersen TK, Brown EM, Plichta DR, Johansen J, Twardus SW, Delorey TM, Lau H, Vlamakis H, Moon JJ, Xavier RJ, Graham DB. The CD4 + T cell response to a commensal-derived epitope transitions from a tolerant to an inflammatory state in Crohn's disease. Immunity 2022; 55:1909-1923.e6. [PMID: 36115338 PMCID: PMC9890645 DOI: 10.1016/j.immuni.2022.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/19/2022] [Accepted: 08/24/2022] [Indexed: 02/03/2023]
Abstract
Reciprocal interactions between host T helper cells and gut microbiota enforce local immunological tolerance and modulate extra-intestinal immunity. However, our understanding of antigen-specific tolerance to the microbiome is limited. Here, we developed a systematic approach to predict HLA class-II-specific epitopes using the humanized bacteria-originated T cell antigen (hBOTA) algorithm. We identified a diverse set of microbiome epitopes spanning all major taxa that are compatible with presentation by multiple HLA-II alleles. In particular, we uncovered an immunodominant epitope from the TonB-dependent receptor SusC that was universally recognized and ubiquitous among Bacteroidales. In healthy human subjects, SusC-reactive T cell responses were characterized by IL-10-dominant cytokine profiles, whereas in patients with active Crohn's disease, responses were associated with elevated IL-17A. Our results highlight the potential of targeted antigen discovery within the microbiome to reveal principles of tolerance and functional transitions during inflammation.
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Affiliation(s)
- Thomas K Pedersen
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Disease Systems Immunology, Department of Biotechnology and Biomedicine, Section for Protein Science and Biotherapeutics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Eric M Brown
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Damian R Plichta
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joachim Johansen
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Shaina W Twardus
- Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Toni M Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Helena Lau
- Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - James J Moon
- Center for Immunology and Inflammatory Diseases and Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Daniel B Graham
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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9
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Ma S, Shungin D, Mallick H, Schirmer M, Nguyen LH, Kolde R, Franzosa E, Vlamakis H, Xavier R, Huttenhower C. Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin. Genome Biol 2022; 23:208. [PMID: 36192803 PMCID: PMC9531436 DOI: 10.1186/s13059-022-02753-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/19/2022] [Indexed: 01/19/2023] Open
Abstract
Microbiome studies of inflammatory bowel diseases (IBD) have achieved a scale for meta-analysis of dysbioses among populations. To enable microbial community meta-analyses generally, we develop MMUPHin for normalization, statistical meta-analysis, and population structure discovery using microbial taxonomic and functional profiles. Applying it to ten IBD cohorts, we identify consistent associations, including novel taxa such as Acinetobacter and Turicibacter, and additional exposure and interaction effects. A single gradient of dysbiosis severity is favored over discrete types to summarize IBD microbiome population structure. These results provide a benchmark for characterization of IBD and a framework for meta-analysis of any microbial communities.
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Affiliation(s)
- Siyuan Ma
- grid.38142.3c000000041936754XHarvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Dmitry Shungin
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Himel Mallick
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Melanie Schirmer
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Long H. Nguyen
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA USA
| | - Raivo Kolde
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Eric Franzosa
- grid.38142.3c000000041936754XHarvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Hera Vlamakis
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Ramnik Xavier
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Curtis Huttenhower
- grid.38142.3c000000041936754XHarvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA USA
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10
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Rojas-Tapias DF, Brown EM, Temple ER, Onyekaba MA, Mohamed AMT, Duncan K, Schirmer M, Walker RL, Mayassi T, Pierce KA, Ávila-Pacheco J, Clish CB, Vlamakis H, Xavier RJ. Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine. Nat Microbiol 2022; 7:1673-1685. [PMID: 36138166 PMCID: PMC9728153 DOI: 10.1038/s41564-022-01224-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 08/03/2022] [Indexed: 12/13/2022]
Abstract
Colonization of the intestine by oral microbes has been linked to multiple diseases such as inflammatory bowel disease and colon cancer, yet mechanisms allowing expansion in this niche remain largely unknown. Veillonella parvula, an asaccharolytic, anaerobic, oral microbe that derives energy from organic acids, increases in abundance in the intestine of patients with inflammatory bowel disease. Here we show that nitrate, a signature metabolite of inflammation, allows V. parvula to transition from fermentation to anaerobic respiration. Nitrate respiration, through the narGHJI operon, boosted Veillonella growth on organic acids and also modulated its metabolic repertoire, allowing it to use amino acids and peptides as carbon sources. This metabolic shift was accompanied by changes in carbon metabolism and ATP production pathways. Nitrate respiration was fundamental for ectopic colonization in a mouse model of colitis, because a V. parvula narG deletion mutant colonized significantly less than a wild-type strain during inflammation. These results suggest that V. parvula harness conditions present during inflammation to colonize in the intestine.
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Affiliation(s)
- Daniel F Rojas-Tapias
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Agricultural Microbiology, Colombian Corporation for Agricultural Research-Agrosavia, Bogotá, Colombia
| | - Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Ahmed M T Mohamed
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Kellyanne Duncan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Melanie Schirmer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Emmy Noether Group, ZIEL-Institute for Food and Health, Technical University of Munich, Freising, Germany
| | | | - Toufic Mayassi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Kerry A Pierce
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Clary B Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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11
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Martin VM, Virkud YV, Dahan E, Seay HL, Itzkovits D, Vlamakis H, Xavier R, Shreffler WG, Yuan Q, Yassour M. Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis. Microbiome 2022; 10:154. [PMID: 36138438 PMCID: PMC9503280 DOI: 10.1186/s40168-022-01322-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/02/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Complex interactions between the gut microbiome and immune cells in infancy are thought to be part of the pathogenesis for the marked rise in pediatric allergic diseases, particularly food allergies. Food protein-induced allergic proctocolitis (FPIAP) is commonly the earliest recognized non-immunoglobulin E (IgE)-mediated food allergy in infancy and is associated with atopic dermatitis and subsequent IgE-mediated food allergy later in childhood. Yet, a large prospective longitudinal study of the microbiome of infants with FPIAP, including samples prior to symptom onset, has not been done. RESULTS Here, we analyzed 954 longitudinal samples from 160 infants in a nested case-control study (81 who developed FPIAP and 79 matched controls) from 1 week to 1 year of age by 16S rRNA ribosomal gene sequencing as part of the Gastrointestinal Microbiome and Allergic Proctocolitis (GMAP) study. We found key differences in the microbiome of infants with FPIAP, most strongly a higher abundance of a genus of Enterobacteriaceae and a lower abundance of a family of Clostridiales during the symptomatic period. We saw some of these significant taxonomic differences even prior to symptom onset. There were no consistent longitudinal differences in richness or stability diversity metrics between infants with FPIAP and healthy controls. CONCLUSIONS This study is the first to identify differences in the infant gut microbiome in children who develop FPIAP, some even before they develop symptoms, and provides a foundation for more mechanistic investigation into the pathogenesis of FPIAP and subsequent food allergic diseases in childhood. Video abstract.
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Affiliation(s)
- Victoria M. Martin
- Food Allergy Center, Massachusetts General Hospital, Boston, MA USA
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Massachusetts General Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
- Food Allergy Science Initiative of the Broad Institute, Cambridge, MA USA
| | - Yamini V. Virkud
- Food Allergy Center, Massachusetts General Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
- Food Allergy Science Initiative of the Broad Institute, Cambridge, MA USA
- Division of Pediatric Allergy and Immunology, Massachusetts General Hospital, Boston, MA USA
| | - Ehud Dahan
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hannah L. Seay
- Division of Pediatric Allergy and Immunology, Massachusetts General Hospital, Boston, MA USA
| | - Dvir Itzkovits
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hera Vlamakis
- Microbiome and Infectious Diseases, The Broad Institute of MIT and Harvard University, Cambridge, MA USA
| | - Ramnik Xavier
- Food Allergy Science Initiative of the Broad Institute, Cambridge, MA USA
- Microbiome and Infectious Diseases, The Broad Institute of MIT and Harvard University, Cambridge, MA USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Wayne G. Shreffler
- Food Allergy Center, Massachusetts General Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
- Food Allergy Science Initiative of the Broad Institute, Cambridge, MA USA
- Division of Pediatric Allergy and Immunology, Massachusetts General Hospital, Boston, MA USA
| | - Qian Yuan
- Food Allergy Center, Massachusetts General Hospital, Boston, MA USA
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Massachusetts General Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
- Food Allergy Science Initiative of the Broad Institute, Cambridge, MA USA
- Pediatrics at Newton Wellesley, P.C, Newton, MA USA
| | - Moran Yassour
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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12
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Bae M, Cassilly CD, Liu X, Park SM, Tusi BK, Chen X, Kwon J, Filipčík P, Bolze AS, Liu Z, Vlamakis H, Graham DB, Buhrlage SJ, Xavier RJ, Clardy J. Akkermansia muciniphila phospholipid induces homeostatic immune responses. Nature 2022; 608:168-173. [PMID: 35896748 PMCID: PMC9328018 DOI: 10.1038/s41586-022-04985-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/16/2022] [Indexed: 12/12/2022]
Abstract
Multiple studies have established associations between human gut bacteria and host physiology, but determining the molecular mechanisms underlying these associations has been challenging1-3. Akkermansia muciniphila has been robustly associated with positive systemic effects on host metabolism, favourable outcomes to checkpoint blockade in cancer immunotherapy and homeostatic immunity4-7. Here we report the identification of a lipid from A. muciniphila's cell membrane that recapitulates the immunomodulatory activity of A. muciniphila in cell-based assays8. The isolated immunogen, a diacyl phosphatidylethanolamine with two branched chains (a15:0-i15:0 PE), was characterized through both spectroscopic analysis and chemical synthesis. The immunogenic activity of a15:0-i15:0 PE has a highly restricted structure-activity relationship, and its immune signalling requires an unexpected toll-like receptor TLR2-TLR1 heterodimer9,10. Certain features of the phospholipid's activity are worth noting: it is significantly less potent than known natural and synthetic TLR2 agonists; it preferentially induces some inflammatory cytokines but not others; and, at low doses (1% of EC50) it resets activation thresholds and responses for immune signalling. Identifying both the molecule and an equipotent synthetic analogue, its non-canonical TLR2-TLR1 signalling pathway, its immunomodulatory selectivity and its low-dose immunoregulatory effects provide a molecular mechanism for a model of A. muciniphila's ability to set immunological tone and its varied roles in health and disease.
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Affiliation(s)
- Munhyung Bae
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
- College of Pharmacy, Gachon University, Incheon, South Korea
| | - Chelsi D Cassilly
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
| | - Xiaoxi Liu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sung-Moo Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Betsabeh Khoramian Tusi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiangjun Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jaeyoung Kwon
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Ganeung, South Korea
| | - Pavel Filipčík
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- SBGrid Consortium, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
| | | | - Zehua Liu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara J Buhrlage
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA.
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13
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Zhang Y, Bhosle A, Bae S, McIver LJ, Pishchany G, Accorsi EK, Thompson KN, Arze C, Wang Y, Subramanian A, Kearney SM, Pawluk A, Plichta DR, Rahnavard A, Shafquat A, Xavier RJ, Vlamakis H, Garrett WS, Krueger A, Huttenhower C, Franzosa EA. Discovery of bioactive microbial gene products in inflammatory bowel disease. Nature 2022; 606:754-760. [PMID: 35614211 PMCID: PMC9913614 DOI: 10.1038/s41586-022-04648-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/15/2022] [Indexed: 01/26/2023]
Abstract
Microbial communities and their associated bioactive compounds1-3 are often disrupted in conditions such as the inflammatory bowel diseases (IBD)4. However, even in well-characterized environments (for example, the human gastrointestinal tract), more than one-third of microbial proteins are uncharacterized and often expected to be bioactive5-7. Here we systematically identified more than 340,000 protein families as potentially bioactive with respect to gut inflammation during IBD, about half of which have not to our knowledge been functionally characterized previously on the basis of homology or experiment. To validate prioritized microbial proteins, we used a combination of metagenomics, metatranscriptomics and metaproteomics to provide evidence of bioactivity for a subset of proteins that are involved in host and microbial cell-cell communication in the microbiome; for example, proteins associated with adherence or invasion processes, and extracellular von Willebrand-like factors. Predictions from high-throughput data were validated using targeted experiments that revealed the differential immunogenicity of prioritized Enterobacteriaceae pilins and the contribution of homologues of von Willebrand factors to the formation of Bacteroides biofilms in a manner dependent on mucin levels. This methodology, which we term MetaWIBELE (workflow to identify novel bioactive elements in the microbiome), is generalizable to other environmental communities and human phenotypes. The prioritized results provide thousands of candidate microbial proteins that are likely to interact with the host immune system in IBD, thus expanding our understanding of potentially bioactive gene products in chronic disease states and offering a rational compendium of possible therapeutic compounds and targets.
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Affiliation(s)
- Yancong Zhang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Amrisha Bhosle
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sena Bae
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Lauren J. McIver
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Gleb Pishchany
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Emma K. Accorsi
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Kelsey N. Thompson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Cesar Arze
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ya Wang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ayshwarya Subramanian
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sean M. Kearney
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - April Pawluk
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Damian R. Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ali Rahnavard
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Afrah Shafquat
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ramnik J. Xavier
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wendy S. Garrett
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andy Krueger
- Takeda Pharmaceutical Company Limited, Cambridge, MA, USA
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Eric A. Franzosa
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,These authors jointly supervised this work: Curtis Huttenhower & Eric A. Franzosa
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14
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Vadaq N, Schirmer M, Tunjungputri RN, Vlamakis H, Chiriac C, Ardiansyah E, Gasem MH, Joosten LAB, de Groot PG, Xavier RJ, Netea MG, van der Ven AJ, de Mast Q. Untargeted Plasma Metabolomics and Gut Microbiome Profiling Provide Novel Insights into the Regulation of Platelet Reactivity in Healthy Individuals. Thromb Haemost 2022; 122:529-539. [PMID: 34192775 DOI: 10.1055/a-1541-3706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND Considerable variation exists in platelet reactivity to stimulation among healthy individuals. Various metabolites and metabolic pathways influence platelet reactivity, but a comprehensive overview of these associations is missing. The gut microbiome has a strong influence on the plasma metabolome. Here, we investigated the association of platelet reactivity with results of untargeted plasma metabolomics and gut microbiome profiling. METHODS We used data from a cohort of 534 healthy adult Dutch volunteers (the 500 Functional Genomics study). Platelet activation and reactivity were measured by the expression of the alpha-granule protein P-selectin and the binding of fibrinogen to the activated integrin αIIbβ3, both in unstimulated blood and after ex vivo stimulation with platelet agonists. Plasma metabolome was measured using an untargeted metabolic profiling approach by quadrupole time-of-flight mass spectrometry. Gut microbiome data were measured by shotgun metagenomic sequencing from stool samples. RESULTS Untargeted metabolomics yielded 1,979 metabolites, of which 422 were identified to play a role in a human metabolic pathway. Overall, 92/422 (21.8%) metabolites were significantly associated with at least one readout of platelet reactivity. The majority of associations involved lipids, especially members of eicosanoids, including prostaglandins and leukotrienes. Dietary-derived polyphenols were also found to inhibit platelet reactivity. Validation of metabolic pathways with functional microbial profiles revealed two overlapping metabolic pathways ("alanine, aspartate, and glutamate metabolism" and "arginine biosynthesis") that were associated with platelet reactivity. CONCLUSION This comprehensive overview is an resource for understanding the regulation of platelet reactivity by the plasma metabolome and the possible contribution of the gut microbiota.
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Affiliation(s)
- Nadira Vadaq
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Center for Tropical and Infectious Diseases, Faculty of Medicine, Diponegoro University-Dr. Kariadi Hospital, Semarang, Indonesia
| | - Melanie Schirmer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
| | - Rahajeng N Tunjungputri
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Center for Tropical and Infectious Diseases, Faculty of Medicine, Diponegoro University-Dr. Kariadi Hospital, Semarang, Indonesia
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States.,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, Massachusetts, United States
| | - Cecilia Chiriac
- National Institute of Research and Development for Biological Sciences, Institute of Biological Research, Cluj-Napoca, Romania.,Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Edwin Ardiansyah
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M Hussein Gasem
- Center for Tropical and Infectious Diseases, Faculty of Medicine, Diponegoro University-Dr. Kariadi Hospital, Semarang, Indonesia.,Department of Internal Medicine, Faculty of Medicine Diponegoro University-Dr. Kariadi Hospital, Semarang, Indonesia
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Philip G de Groot
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States.,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, Massachusetts, United States
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Andre J van der Ven
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Quirijn de Mast
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
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15
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Paik D, Yao L, Zhang Y, Bae S, D'Agostino GD, Zhang M, Kim E, Franzosa EA, Avila-Pacheco J, Bisanz JE, Rakowski CK, Vlamakis H, Xavier RJ, Turnbaugh PJ, Longman RS, Krout MR, Clish CB, Rastinejad F, Huttenhower C, Huh JR, Devlin AS. Human gut bacteria produce Τ Η17-modulating bile acid metabolites. Nature 2022; 603:907-912. [PMID: 35296854 PMCID: PMC9132548 DOI: 10.1038/s41586-022-04480-z] [Citation(s) in RCA: 176] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/27/2022] [Indexed: 01/14/2023]
Abstract
The microbiota modulates gut immune homeostasis. Bacteria influence the development and function of host immune cells, including T helper cells expressing interleukin-17A (TH17 cells). We previously reported that the bile acid metabolite 3-oxolithocholic acid (3-oxoLCA) inhibits TH17 cell differentiation1. Although it was suggested that gut-residing bacteria produce 3-oxoLCA, the identity of such bacteria was unknown, and it was unclear whether 3-oxoLCA and other immunomodulatory bile acids are associated with inflammatory pathologies in humans. Here we identify human gut bacteria and corresponding enzymes that convert the secondary bile acid lithocholic acid into 3-oxoLCA as well as the abundant gut metabolite isolithocholic acid (isoLCA). Similar to 3-oxoLCA, isoLCA suppressed TH17 cell differentiation by inhibiting retinoic acid receptor-related orphan nuclear receptor-γt, a key TH17-cell-promoting transcription factor. The levels of both 3-oxoLCA and isoLCA and the 3α-hydroxysteroid dehydrogenase genes that are required for their biosynthesis were significantly reduced in patients with inflammatory bowel disease. Moreover, the levels of these bile acids were inversely correlated with the expression of TH17-cell-associated genes. Overall, our data suggest that bacterially produced bile acids inhibit TH17 cell function, an activity that may be relevant to the pathophysiology of inflammatory disorders such as inflammatory bowel disease.
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Affiliation(s)
- Donggi Paik
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Lina Yao
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Yancong Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sena Bae
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Gabriel D D'Agostino
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Minghao Zhang
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eunha Kim
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Jordan E Bisanz
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | | | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Randy S Longman
- Jill Roberts Center for IBD, Weill Cornell Medicine, New York, NY, USA
| | - Michael R Krout
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fraydoon Rastinejad
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jun R Huh
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
| | - A Sloan Devlin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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16
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Walker RL, Vlamakis H, Lee JWJ, Besse LA, Xanthakis V, Vasan RS, Shaw SY, Xavier RJ. Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease. Genome Med 2021; 13:188. [PMID: 34915914 PMCID: PMC8680346 DOI: 10.1186/s13073-021-01007-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/01/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The human gut harbors trillions of microbes that play dynamic roles in health. While the microbiome contributes to many cardiometabolic traits by modulating host inflammation and metabolism, there is an incomplete understanding regarding the extent that and mechanisms by which individual microbes impact risk and development of cardiovascular disease (CVD). The Framingham Heart Study (FHS) is a multi-generational observational study following participants over decades to identify risk factors for CVD by correlating genetic and phenotypic factors with clinical outcomes. As a large-scale population-based cohort with extensive clinical phenotyping, FHS provides a rich landscape to explore the relationships between the gut microbiome and cardiometabolic traits. METHODS We performed 16S rRNA gene sequencing on stool from 1423 participants of the FHS Generation 3, OMNI2, and New Offspring Spouse cohorts. Data processing and taxonomic assignment were performed with the 16S bioBakery workflow using the UPARSE pipeline. We conducted statistical analyses to investigate trends in overall microbiome composition and diversity in relation to disease states and systematically examined taxonomic associations with a variety of clinical traits, disease phenotypes, clinical blood markers, and medications. RESULTS We demonstrate that overall microbial diversity decreases with increasing 10-year CVD risk and body mass index measures. We link lifestyle factors, especially diet and exercise, to microbial diversity. Our association analyses reveal both known and unreported microbial associations with CVD and diabetes, related prescription medications, as well as many anthropometric and blood test measurements. In particular, we observe a set of microbial species that demonstrate significant associations with CVD risk, metabolic syndrome, and type 2 diabetes as well as a number of shared associations between microbial species and cardiometabolic subphenotypes. CONCLUSIONS The identification of significant microbial taxa associated with prevalent CVD and diabetes, as well as risk for developing CVD, adds to increasing evidence that the microbiome may contribute to CVD pathogenesis. Our findings support new hypothesis generation around shared microbe-mediated mechanisms that influence metabolic syndrome, diabetes, and CVD risk. Further investigation of the gut microbiomes of CVD patients in a targeted manner may elucidate microbial mechanisms with diagnostic and therapeutic implications.
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Affiliation(s)
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jonathan Wei Jie Lee
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Gastroenterology and Hepatology, National University Health System, Singapore, Singapore
| | - Luke A Besse
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vanessa Xanthakis
- Boston University and NHLBI's Framingham Heart Study, Framingham, MA, USA
- Department of Medicine, Section of Preventive Medicine and Epidemiology, Boston University School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ramachandran S Vasan
- Boston University and NHLBI's Framingham Heart Study, Framingham, MA, USA
- Department of Medicine, Section of Preventive Medicine and Epidemiology, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Cardiology, Boston University School of Medicine, Boston, MA, USA
| | - Stanley Y Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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17
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Ke X, You K, Pichaud M, Haiser HJ, Graham DB, Vlamakis H, Porter JA, Xavier RJ. Gut bacterial metabolites modulate endoplasmic reticulum stress. Genome Biol 2021; 22:292. [PMID: 34654459 PMCID: PMC8518294 DOI: 10.1186/s13059-021-02496-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/10/2021] [Indexed: 12/26/2022] Open
Abstract
Background The endoplasmic reticulum (ER) is a membranous organelle that maintains proteostasis and cellular homeostasis, controlling the fine balance between health and disease. Dysregulation of the ER stress response has been implicated in intestinal inflammation associated with inflammatory bowel disease (IBD), a chronic condition characterized by changes to the mucosa and alteration of the gut microbiota. While the microbiota and microbially derived metabolites have also been implicated in ER stress, examples of this connection remain limited to a few observations from pathogenic bacteria. Furthermore, the mechanisms underlying the effects of bacterial metabolites on ER stress signaling have not been well established. Results Utilizing an XBP1s-GFP knock-in reporter colorectal epithelial cell line, we screened 399 microbiome-related metabolites for ER stress pathway modulation. We find both ER stress response inducers (acylated dipeptide aldehydes and bisindole methane derivatives) and suppressors (soraphen A) and characterize their activities on ER stress gene transcription and translation. We further demonstrate that these molecules modulate the ER stress pathway through protease inhibition or lipid metabolism interference. Conclusions Our study identified novel links between classes of gut microbe-derived metabolites and the ER stress response, suggesting the potential for these metabolites to contribute to gut ER homeostasis and providing insight into the molecular mechanisms by which gut microbes impact intestinal epithelial cell homeostasis. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02496-8.
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Affiliation(s)
- Xiaobo Ke
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Novartis Institute for Biomedical Research Inc., Cambridge, MA, 02139, USA
| | - Kwontae You
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Matthieu Pichaud
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Novartis Institute for Biomedical Research Inc., Cambridge, MA, 02139, USA
| | - Henry J Haiser
- Novartis Institute for Biomedical Research Inc., Cambridge, MA, 02139, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard School of Medicine, Boston, Massachusetts, 02114, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jeffrey A Porter
- Novartis Institute for Biomedical Research Inc., Cambridge, MA, 02139, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard School of Medicine, Boston, Massachusetts, 02114, USA. .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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18
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Stražar M, Temba GS, Vlamakis H, Kullaya VI, Lyamuya F, Mmbaga BT, Joosten LAB, van der Ven AJAM, Netea MG, de Mast Q, Xavier RJ. Author Correction: Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations. Nat Commun 2021; 12:5818. [PMID: 34588450 PMCID: PMC8481251 DOI: 10.1038/s41467-021-26145-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
| | - Godfrey S Temba
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vesla I Kullaya
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Department of Respiratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Furaha Lyamuya
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Blandina T Mmbaga
- Department of Pediatrics, Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andre J A M van der Ven
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands. .,Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Quirijn de Mast
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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19
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Stražar M, Mourits VP, Koeken VACM, de Bree LCJ, Moorlag SJCFM, Joosten LAB, van Crevel R, Vlamakis H, Netea MG, Xavier RJ. The influence of the gut microbiome on BCG-induced trained immunity. Genome Biol 2021; 22:275. [PMID: 34551799 PMCID: PMC8456614 DOI: 10.1186/s13059-021-02482-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 08/30/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The bacillus Calmette-Guérin (BCG) vaccine protects against tuberculosis and heterologous infections but elicits high inter-individual variation in specific and nonspecific, or trained, immune responses. While the gut microbiome is increasingly recognized as an important modulator of vaccine responses and immunity in general, its potential role in BCG-induced protection is largely unknown. RESULTS Stool and blood were collected from 321 healthy adults before BCG vaccination, followed by blood sampling after 2 weeks and 3 months. Metagenomics based on de novo genome assembly reveals 43 immunomodulatory taxa. The nonspecific, trained immune response is detected by altered production of cytokines IL-6, IL-1β, and TNF-α upon ex vivo blood restimulation with Staphylococcus aureus and negatively correlates with abundance of Roseburia. The specific response, measured by IFN-γ production upon Mycobacterium tuberculosis stimulation, is associated positively with Ruminococcus and Eggerthella lenta. The identified immunomodulatory taxa also have the strongest effects on circulating metabolites, with Roseburia affecting phenylalanine metabolism. This is corroborated by abundances of relevant enzymes, suggesting alternate phenylalanine metabolism modules are activated in a Roseburia species-dependent manner. CONCLUSIONS Variability in cytokine production after BCG vaccination is associated with the abundance of microbial genomes, which in turn affect or produce metabolites in circulation. Roseburia is found to alter both trained immune responses and phenylalanine metabolism, revealing microbes and microbial products that may alter BCG-induced immunity. Together, our findings contribute to the understanding of specific and trained immune responses after BCG vaccination.
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Affiliation(s)
| | - Vera P Mourits
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Valerie A C M Koeken
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM) & TWINCORE, Joint Ventures Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - L Charlotte J de Bree
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
- Odense Patient Data Explorative Network, University of Southern Denmark/Odense University Hospital, Odense, Denmark
| | - Simone J C F M Moorlag
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Reinout van Crevel
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands.
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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20
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Brown EM, Arellano-Santoyo H, Temple ER, Costliow ZA, Pichaud M, Hall AB, Liu K, Durney MA, Gu X, Plichta DR, Clish CA, Porter JA, Vlamakis H, Xavier RJ. Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors. Cell Host Microbe 2021; 29:1351-1365.e11. [PMID: 34403684 DOI: 10.1016/j.chom.2021.07.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 06/23/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022]
Abstract
Bacterial ADP-ribosyltransferases (ADPRTs) have been described as toxins involved in pathogenesis through the modification of host proteins. Here, we report that ADPRTs are not pathogen restricted but widely prevalent in the human gut microbiome and often associated with phage elements. We validated their biochemical activity in a large clinical isolate collection and further examined Bxa, a highly abundant ADPRT in Bacteroides. Bxa is expressed, secreted, and enzymatically active in Bacteroides and can ADP-ribosylate non-muscle myosin II proteins. Addition of Bxa to epithelial cells remodeled the actin cytoskeleton and induced secretion of inosine. Bxa-encoding B. stercoris can use inosine as a carbon source and colonizes the gut to significantly greater numbers than a bxa-deleted strain in germ-free and altered Schaedler flora (ASF) mice. Colonization correlated with increased inosine concentrations in the feces and tissues. Altogether, our results show that ADPRTs are abundant in the microbiome and act as bacterial fitness factors.
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Affiliation(s)
- Eric M Brown
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hugo Arellano-Santoyo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novartis Institutes for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Emily R Temple
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Matthieu Pichaud
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novartis Institutes for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - A Brantley Hall
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kai Liu
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Xiebin Gu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Clary A Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey A Porter
- Novartis Institutes for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ramnik J Xavier
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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21
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Petersen AØ, Jokinen M, Plichta DR, Liebisch G, Gronwald W, Dettmer K, Oefner PJ, Vlamakis H, Chung DC, Ranki A, Xavier RJ. Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1. J Allergy Clin Immunol 2021; 148:876-888. [PMID: 33819509 PMCID: PMC8429070 DOI: 10.1016/j.jaci.2021.03.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/23/2021] [Accepted: 03/24/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND Gastrointestinal dysfunction is a frequent and disabling manifestation of autoimmune polyendocrine syndrome type 1 (APS-1), a rare monogenic multiorgan autoimmune disease caused by the loss of central AIRE-controlled immune tolerance. OBJECTIVES This study aimed to understand the role of the gut microbiome in APS-1 symptoms and potentially alleviate common gastrointestinal symptoms by probiotic intervention. METHODS This study characterized the fecal microbiomes of 28 patients with APS-1 and searched for associations with gastrointestinal symptoms, circulating anti-cytokine autoantibodies, and tryptophan-related metabolites. Additionally, daily doses of the probiotic Lactobacillus rhamnosus GG were administered for 3 months. RESULTS Of 581 metagenomic operational taxonomic units (mOTUs) characterized in total, 14 were significantly associated with patients with APS-1 compared with healthy controls, with 6 mOTUs depleted and 8 enriched in patients with APS-1. Four overabundant mOTUs were significantly associated with severity of constipation. Phylogenetically conserved microbial associations with autoantibodies against cytokines were observed. After the 3-month intervention with the probiotic L rhamnosus GG, a subset of gastrointestinal symptoms were alleviated. L rhamnosus GG abundance was increased postintervention and corresponded with decreased abundances of Alistipes onderdonkii and Collinsella aerofaciens, 2 species positively associated with severity of diarrhea in patients with APS-1. CONCLUSIONS The APS-1 microbiome correlates with several APS-1 symptoms, some of which are alleviated after a 3-month L rhamnosus GG intervention. Autoantibodies against cytokines appear to shape the gut microbiome by positively correlating with a taxonomically consistent group of bacteria.
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Affiliation(s)
- Anders Ø Petersen
- Broad Institute of MIT and Harvard, Cambridge, Mass; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Mass; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Martta Jokinen
- Department of Dermatology and Allergology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Damian R Plichta
- Broad Institute of MIT and Harvard, Cambridge, Mass; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Mass
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Wolfram Gronwald
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Katja Dettmer
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, Mass; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Mass
| | - Daniel C Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Mass
| | - Annamari Ranki
- Department of Dermatology and Allergology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Mass; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Mass; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Mass.
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22
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Stražar M, Temba GS, Vlamakis H, Kullaya VI, Lyamuya F, Mmbaga BT, Joosten LAB, van der Ven AJAM, Netea MG, de Mast Q, Xavier RJ. Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations. Nat Commun 2021; 12:4845. [PMID: 34381036 PMCID: PMC8357928 DOI: 10.1038/s41467-021-25213-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/30/2021] [Indexed: 12/18/2022] Open
Abstract
The human gut microbiota is increasingly recognized as an important factor in modulating innate and adaptive immunity through release of ligands and metabolites that translocate into circulation. Urbanizing African populations harbor large intestinal diversity due to a range of lifestyles, providing the necessary variation to gauge immunomodulatory factors. Here, we uncover a gradient of intestinal microbial compositions from rural through urban Tanzanian, towards European samples, manifested both in relative abundance and genomic variation observed in stool metagenomics. The rural population shows increased Bacteroidetes, led by Prevotella copri, but also presence of fungi. Measured ex vivo cytokine responses were significantly associated with 34 immunomodulatory microbes, which have a larger impact on circulating metabolites than non-significant microbes. Pathway effects on cytokines, notably TNF-α and IFN-γ, differential metabolome analysis and enzyme copy number enrichment converge on histidine and arginine metabolism as potential immunomodulatory pathways mediated by Bifidobacterium longum and Akkermansia muciniphila. The authors profile stool metagenomics and plasma metabolomics in Tanzanian individuals and uncover a gradient of gut microbial profiles, from rural through urban Tanzania towards Western populations. Integration with ex vivo blood microbial stimulations reveals immune responses associated with histidine and arginine pathways, mediated by Bifidobacterium longum and Akkermansia muciniphila.
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Affiliation(s)
| | - Godfrey S Temba
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vesla I Kullaya
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Department of Respiratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Furaha Lyamuya
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Blandina T Mmbaga
- Department of Pediatrics, Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andre J A M van der Ven
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands. .,Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Quirijn de Mast
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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23
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Lee JWJ, Plichta D, Hogstrom L, Borren NZ, Lau H, Gregory SM, Tan W, Khalili H, Clish C, Vlamakis H, Xavier RJ, Ananthakrishnan AN. Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. Cell Host Microbe 2021; 29:1294-1304.e4. [PMID: 34297922 DOI: 10.1016/j.chom.2021.06.019] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/01/2021] [Accepted: 06/24/2021] [Indexed: 12/26/2022]
Abstract
The intestinal microbiome is a key determinant of responses to biologic therapy in inflammatory bowel disease (IBD). However, diverse therapeutics and variable responses among IBD patients have posed challenges in predicting clinical therapeutic success. In this prospective study, we profiled baseline stool and blood in patients with moderate-to-severe Crohn's disease or ulcerative colitis initiating anti-cytokine therapy (anti-TNF or -IL12/23) or anti-integrin therapy. Patients were assessed at 14 weeks for clinical remission and 52 weeks for clinical and endoscopic remission. Baseline microbial richness indicated preferential responses to anti-cytokine therapy and correlated with the abundance of microbial species capable of 7α/β-dehydroxylation of primary to secondary bile acids. Serum signatures of immune proteins reflecting microbial diversity identified patients more likely to achieve remission with anti-cytokine therapy. Remission-associated multi-omic profiles were unique to each therapeutic class. These profiles may facilitate a priori determination of optimal therapeutics for patients and serve as targets for newer therapies.
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Affiliation(s)
- Jonathan Wei Jie Lee
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, Singapore 119228, Singapore; Division of Gastroenterology and Hepatology, National University Health System, Singapore University Medical Center, 5 Lower Kent Ridge Rd, Singapore 119074, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), 14 Medical Drive, MD6-Centre for Translational Medicine, Singapore 117599, Singapore
| | - Damian Plichta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Larson Hogstrom
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nynke Z Borren
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Helena Lau
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sara M Gregory
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - William Tan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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24
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Pagan JD, Vlamakis H, Gaca A, Xavier RJ, Anthony RM. Modulating T Follicular Cells In Vivo Enhances Antigen-Specific Humoral Immunity. J Immunol 2021; 206:2583-2595. [PMID: 34011521 DOI: 10.4049/jimmunol.2001434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/22/2021] [Indexed: 11/19/2022]
Abstract
Generation of high-affinity IgG is essential for defense against infections and cancer, which is the intended consequence of many vaccines, but can cause autoimmune and inflammatory diseases when inappropriately directed against self. The interplay of T follicular helper (TFH) cells and T follicular regulatory (TFR) cells is critical for the production of high-affinity IgG of a specific subclass. In this study, we sought to improve Ag-specific IgG responses with two interventions intended to transiently diminish TFR cell influence. First, adult mice were administered an antibiotic mixture (ABX) for an extended period to deplete the immunoregulatory intestinal microbiota. This intriguingly increased TFH cell and reduced TFR cell numbers. 2,4,6-Trinitrophenyl hapten conjugated to keyhole limpet hemocyanin immunization resulted in higher affinity 2,4,6-trinitrophenyl hapten-specific IgG1 in ABX mice compared with controls. In a model of IgG-driven inflammatory nephritis, ABX mice had significantly worse nephritis accompanied by higher affinity Ag-specific IgG2b and enriched TFH cells compared with controls. Second, we sought to functionally manipulate TFH and TFR cells, which both express the checkpoint inhibitory molecule, PD-1, by administration of anti-PD-1 during immunization. This intervention enhanced the affinity of Ag-specific IgG of the appropriate subclass and increased in TFH cells following 2,4,6-trinitrophenyl hapten conjugated to keyhole limpet hemocyanin immunization and nephritis induction. These results suggest that altering TFH and TFR cell ratios during immunization is an appealing strategy to qualitatively improve Ag- and subclass-specific IgG responses.
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Affiliation(s)
- Jose D Pagan
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA
| | - Hera Vlamakis
- Broad Immunology, Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA; and.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA
| | - Anthony Gaca
- Broad Immunology, Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA; and
| | - Ramnik J Xavier
- Broad Immunology, Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA; and.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA
| | - Robert M Anthony
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA;
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25
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Henke MT, Brown EM, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J. Capsular polysaccharide correlates with immune response to the human gut microbe Ruminococcus gnavus. Proc Natl Acad Sci U S A 2021; 118:e2007595118. [PMID: 33972416 PMCID: PMC8157926 DOI: 10.1073/pnas.2007595118] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Active inflammatory bowel disease (IBD) often coincides with increases of Ruminococcus gnavus, a gut microbe found in nearly everyone. It was not known how, or if, this correlation contributed to disease. We investigated clinical isolates of R. gnavus to identify molecular mechanisms that would link R. gnavus to inflammation. Here, we show that only some isolates of R. gnavus produce a capsular polysaccharide that promotes a tolerogenic immune response, whereas isolates lacking functional capsule biosynthetic genes elicit robust proinflammatory responses in vitro. Germ-free mice colonized with an isolate of R. gnavus lacking a capsule show increased measures of gut inflammation compared to those colonized with an encapsulated isolate in vivo. These observations in the context of our earlier identification of an inflammatory cell-wall polysaccharide reveal how some strains of R. gnavus could drive the inflammatory responses that characterize IBD.
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Affiliation(s)
- Matthew T Henke
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Eric M Brown
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Chelsi D Cassilly
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Hera Vlamakis
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Ramnik J Xavier
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114
| | - Jon Clardy
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;
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26
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Borren NZ, Plichta D, Joshi AD, Bonilla G, Peng V, Colizzo FP, Luther J, Khalili H, Garber JJ, Janneke van der Woude C, Sadreyev R, Vlamakis H, Xavier RJ, Ananthakrishnan AN. Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases. Clin Gastroenterol Hepatol 2021; 19:519-527.e5. [PMID: 32184182 DOI: 10.1016/j.cgh.2020.03.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/24/2020] [Accepted: 03/02/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Fatigue is frequent and disabling in patients with inflammatory bowel diseases (IBD) but its mechanisms are poorly understood. We investigated alterations in fecal microbiomes and serum metabolomes and proteomes in patients with quiescent IBD, with vs without fatigue. METHODS We performed a prospective observational study of patients (44% women; mean age, 39.8 y) with clinically and endoscopically quiescent Crohn's disease (n = 106) or ulcerative colitis (n = 60) at a tertiary hospital, from March 2016 through December 2018. Fatigue was assessed using the functional assessment of chronic illness therapy-fatigue scoring system and defined as a score of 43 or less. We performed metabolomic analysis of serum samples using liquid chromatography-mass spectrometry methods and proteomic analysis using multiplex proximity extension assay (PEA) technology. Stool samples were obtained from 50 patients and analyzed by shotgun metagenomic sequencing on Illumina HiSeq platform. RESULTS Of the 166 study participants, 91 (55%) were fatigued. Serum samples from patients with fatigue (n = 59) did not have significant increases in levels of inflammatory cytokines compared with serum samples from nonfatigued patients (n = 72). We found a statistically significant difference in a cluster of 18 serum metabolites between patients with fatigue (n = 84) vs without fatigue (n = 72) (P = .033); serum samples from patients with fatigue had significant reductions in levels of methionine (P = .020), tryptophan (P = .042), proline (P = .017), and sarcosine (P = .047). Fecal samples from patients with fatigue had a less diverse gut microbiome, with significant reductions in butyrate-producing bacteria, including Faecalibacterium prausnitzii (P = .0002, q =.007) and Roseburia hominis (P = .0079, q = 0.105). This fatigue-like microbiome was associated with fatigue scales and correlated with progressive depletion of metabolites from serum samples. CONCLUSIONS In an analysis of fecal and serum samples from 166 patients with IBD, we found alterations in serum metabolites and fecal microbes that were associated with fatigue.
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Affiliation(s)
- Nienke Z Borren
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Damian Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Amit D Joshi
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gracia Bonilla
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Vincent Peng
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St Louis, Missouri
| | - Francis P Colizzo
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jay Luther
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - John J Garber
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - C Janneke van der Woude
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ramnik J Xavier
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
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27
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Plichta DR, Somani J, Pichaud M, Wallace ZS, Fernandes AD, Perugino CA, Lähdesmäki H, Stone JH, Vlamakis H, Chung DC, Khanna D, Pillai S, Xavier RJ. Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis. Genome Med 2021; 13:35. [PMID: 33648559 PMCID: PMC7919092 DOI: 10.1186/s13073-021-00853-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/11/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Immunoglobulin G4-related disease (IgG4-RD) and systemic sclerosis (SSc) are rare autoimmune diseases characterized by the presence of CD4+ cytotoxic T cells in the blood as well as inflammation and fibrosis in various organs, but they have no established etiologies. Similar to other autoimmune diseases, the gut microbiome might encode disease-triggering or disease-sustaining factors. METHODS The gut microbiomes from IgG4-RD and SSc patients as well as healthy individuals with no recent antibiotic treatment were studied by metagenomic sequencing of stool DNA. De novo assembly-based taxonomic and functional characterization, followed by association and accessory gene set enrichment analysis, were applied to describe microbiome changes associated with both diseases. RESULTS Microbiomes of IgG4-RD and SSc patients distinctly separated from those of healthy controls: numerous opportunistic pathogenic Clostridium and typically oral Streptococcus species were significantly overabundant, while Alistipes, Bacteroides, and butyrate-producing species were depleted in the two diseases compared to healthy controls. Accessory gene content analysis in these species revealed an enrichment of Th17-activating Eggerthella lenta strains in IgG4-RD and SSc and a preferential colonization of a homocysteine-producing strain of Clostridium bolteae in SSc. Overabundance of the classical mevalonate pathway, hydroxyproline dehydratase, and fibronectin-binding protein in disease microbiomes reflects potential functional differences in host immune recognition and extracellular matrix utilization associated with fibrosis. Strikingly, the majority of species that were differentially abundant in IgG4-RD and SSc compared to controls showed the same directionality in both diseases. Compared with multiple sclerosis and rheumatoid arthritis, the gut microbiomes of IgG4-RD and SSc showed similar signatures; in contrast, the most differentially abundant taxa were not the facultative anaerobes consistently identified in inflammatory bowel diseases, suggesting the microbial signatures of IgG4-RD and SSc do not result from mucosal inflammation and decreased anaerobism. CONCLUSIONS These results provide an initial characterization of gut microbiome ecology in fibrosis-prone IgG4-RD and SSc and reveal microbial functions that offer insights into the pathophysiology of these rare diseases.
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Affiliation(s)
| | - Juhi Somani
- Department of Computer Science, Aalto University, 02150, Espoo, Finland
| | | | - Zachary S Wallace
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
- Clinical Epidemiology Program and Rheumatology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ana D Fernandes
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Cory A Perugino
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, 02150, Espoo, Finland
| | - John H Stone
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel C Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Risk Assessment, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dinesh Khanna
- University of Michigan Scleroderma Program, Ann Arbor, MI, USA
| | - Shiv Pillai
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.
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28
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Wang Y, Yan Y, Thompson KN, Bae S, Accorsi EK, Zhang Y, Shen J, Vlamakis H, Hartmann EM, Huttenhower C. Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. Microbiome 2021; 9:17. [PMID: 33478576 PMCID: PMC7819323 DOI: 10.1186/s40168-020-00961-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/06/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at scale. There is as yet not one best solution to this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular profiling (e.g., qPCR or sequencing). While these studies have met with moderate success, most of them focused on the resulting "viable" communities without systematic evaluations of the technique. Here, we present our work to rigorously benchmark "PMA-seq" (PMA treatment followed by 16S rRNA gene amplicon sequencing) for viability assessment in synthetic and realistic microbial communities. RESULTS PMA-seq was able to successfully reconstruct simple synthetic communities comprising viable/heat-killed Escherichia coli and Streptococcus sanguinis. However, in realistically complex communities (computer screens, computer mice, soil, and human saliva) with E. coli spike-in controls, PMA-seq did not accurately quantify viability (even relative to variability in amplicon sequencing), with its performance largely affected by community properties such as initial biomass, sample types, and compositional diversity. We then applied this technique to environmental swabs from the Boston subway system. Several taxa differed significantly after PMA treatment, while not all microorganisms responded consistently. To elucidate the "PMA-responsive" microbes, we compared our results with previous PMA-based studies and found that PMA responsiveness varied widely when microbes were sourced from different ecosystems but were reproducible within similar environments across studies. CONCLUSIONS This study provides a comprehensive evaluation of PMA-seq exploring its quantitative potential in synthetic and complex microbial communities, where the technique was effective for semi-quantitative purposes in simple synthetic communities but provided only qualitative assessments in realistically complex community samples. Video abstract.
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Affiliation(s)
- Ya Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Kelsey N. Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Sena Bae
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Emma K. Accorsi
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
| | - Yancong Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
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Jackson DR, Cassilly CD, Plichta DR, Vlamakis H, Liu H, Melville SB, Xavier RJ, Clardy J. Plasmalogen Biosynthesis by Anaerobic Bacteria: Identification of a Two-Gene Operon Responsible for Plasmalogen Production in Clostridium perfringens. ACS Chem Biol 2021; 16:6-13. [PMID: 33350306 PMCID: PMC7812594 DOI: 10.1021/acschembio.0c00673] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Plasmalogens are vinyl ether-containing
lipids produced by mammals
and bacteria. The aerobic biosynthetic pathway in eukaryotes and bacteria
is known, but the anaerobic pathway has remained a mystery. Here,
we describe a two-gene operon (plasmalogen synthase, pls) responsible for plasmalogen production in the anaerobic bacterium Clostridium perfringens. While aerobic plasmalogen biosynthesis
involves an oxidative conversion of an ether to a vinyl ether, anaerobic
plasmalogen biosynthesis uses the reductive conversion of an ester
to an aldehyde equivalent. Heterologous expression of the C. perfringens pls operon in E. coli conferred
the ability to produce plasmalogens. The pls operon
is predicted to encode a multidomain complex similar to benzoyl-CoA
reductase/hydroxylacyl-CoA dehydratase (BCR/HAD) enzymes. Versions
of this operon can be found in a wide range of obligate and facultative
anaerobic bacteria, including many human gut microbes.
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Affiliation(s)
- David R. Jackson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston Massachusetts 02115, United States
| | - Chelsi D. Cassilly
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston Massachusetts 02115, United States
| | - Damian R. Plichta
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Hualan Liu
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Stephen B. Melville
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston Massachusetts 02115, United States
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Mitchell CM, Mazzoni C, Hogstrom L, Bryant A, Bergerat A, Cher A, Pochan S, Herman P, Carrigan M, Sharp K, Huttenhower C, Lander ES, Vlamakis H, Xavier RJ, Yassour M. Delivery Mode Affects Stability of Early Infant Gut Microbiota. Cell Rep Med 2020; 1:100156. [PMID: 33377127 PMCID: PMC7762768 DOI: 10.1016/j.xcrm.2020.100156] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 09/29/2020] [Accepted: 11/19/2020] [Indexed: 01/07/2023]
Abstract
Mode of delivery strongly influences the early infant gut microbiome. Children born by cesarean section (C-section) lack Bacteroides species until 6–18 months of age. One hypothesis is that these differences stem from lack of exposure to the maternal vaginal microbiome. Here, we re-evaluate this hypothesis by comparing the microbial profiles of 75 infants born vaginally or by planned versus emergent C-section. Multiple children born by C-section have a high abundance of Bacteroides in their first few days of life, but at 2 weeks, both C-section groups lack Bacteroides (primarily according to 16S sequencing), despite their difference in exposure to the birth canal. Finally, a comparison of microbial strain profiles between infants and maternal vaginal or rectal samples finds evidence for mother-to-child transmission of rectal rather than vaginal strains. These results suggest differences in colonization stability as an important factor in infant gut microbiome composition rather than birth canal exposure. Week 1 gut microbiota does not differ between infants born vaginally versus C-section Week 2 gut microbiota of C-section infants lacks Bacteroides Microbiota of infants born by C-section after labor resembles scheduled C-section Bacterial strains in infants match maternal rectal rather than vaginal strains
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Affiliation(s)
- Caroline M Mitchell
- Vincent Obstetrics & Gynecology Department, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Chiara Mazzoni
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Larson Hogstrom
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Allison Bryant
- Vincent Obstetrics & Gynecology Department, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Agnes Bergerat
- Vincent Obstetrics & Gynecology Department, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Avital Cher
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Shawna Pochan
- Vincent Obstetrics & Gynecology Department, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Penelope Herman
- Vincent Obstetrics & Gynecology Department, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Maureen Carrigan
- Vincent Obstetrics & Gynecology Department, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Karen Sharp
- Vincent Obstetrics & Gynecology Department, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA 02125, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Moran Yassour
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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31
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Kong L, Lloyd-Price J, Vatanen T, Seksik P, Beaugerie L, Simon T, Vlamakis H, Sokol H, Xavier RJ. Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn's Disease. Gastroenterology 2020; 159:2193-2202.e5. [PMID: 32860788 PMCID: PMC7725862 DOI: 10.1053/j.gastro.2020.08.045] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/02/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Crohn's disease (CD) is a chronic gastrointestinal disease resulting from the dysfunctional interplay between genetic susceptibility, the immune system, and commensal intestinal microbiota. Emerging evidence suggests that treatment by suppression of the immune response and replacement of the microbiota through fecal microbiota transplantation (FMT) is a promising approach for the treatment of CD. METHODS We obtained stool metagenomes from CD patients in remission and assessed gut microbiome composition before and after FMT at the species and strain levels. Longitudinal follow-up evaluation allowed us to identify the gain, loss, and strain replacement of specific species and link these events to the maintenance of remission in CD. RESULTS We found that FMT had a significant long-term effect on patient microbial compositions, although this was primarily driven by the engraftment of donor species, which remained at low abundance. Thirty-eight percent of FMT-driven changes were strain replacements, emphasizing the importance of detailed profiling methods, such as metagenomics. Several instances of long-term coexistence between donor and patient strains were also observed. Engraftment of some Actinobacteria, and engraftment or loss of Proteobacteria, were related to better disease outcomes in CD patients who received FMT, and transmission of Bacteroidetes was deleterious. CONCLUSIONS Our results suggest clades that may be beneficial to transmit/eliminate through FMT, and provide criteria that may help identify personalized FMT donors to more effectively maintain remission in CD patients. The framework established here creates a foundation for future studies centered around the application of FMT and defined microbial communities as a therapeutic approach for treating CD.
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Affiliation(s)
- Lingjia Kong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Philippe Seksik
- Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint Antoine, Service de Gastroenterologie, Sorbonne Université, Inserm, 75012, Paris, France.,Department of Gastroenterology, Saint Antoine Hospital, Assistance Publique-Hopitaux de Paris (APHP), 184 rue du Faubourg Saint-Antoine, 75571, Paris, CEDEX 12, France.,French Group of Fecal Transplantation (GFTF), Paris, France.,Paris Center for Microbiome Medicine (FHU PaCeMM), Paris, France
| | - Laurent Beaugerie
- Department of Gastroenterology, Saint Antoine Hospital, Assistance Publique-Hopitaux de Paris (APHP), 184 rue du Faubourg Saint-Antoine, 75571, Paris, CEDEX 12, France.,Paris Center for Microbiome Medicine (FHU PaCeMM), Paris, France
| | - Tabassome Simon
- Clinical Research Platform (URC-CRC-CRB), AP-HP Saint-Antoine Hospital, Paris, France.,Department of Clinical Pharmacology, APHP, Saint Antoine Hospital, Paris, France
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Harry Sokol
- Centre de Recherche Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Hôpital Saint Antoine, Service de Gastroenterologie, Sorbonne Université, INSERM 75012, Paris, France; Department of Gastroenterology, Saint Antoine Hospital, Assistance Publique-Hopitaux de Paris, Paris, France; French Group of Fecal Transplantation, Paris, France; Paris Center for Microbiome Medicine, Paris, France.
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA,Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Correspondence:;
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32
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Turner D, Bishai J, Reshef L, Abitbol G, Focht G, Marcus D, Ledder O, Lev-Tzion R, Orlanski-Meyer E, Yerushalmi B, Aloi M, Griffiths AM, Albenberg L, Kolho KL, Assa A, Cohen S, Gophna U, Vlamakis H, Lurz E, Levine A. Antibiotic Cocktail for Pediatric Acute Severe Colitis and the Microbiome: The PRASCO Randomized Controlled Trial. Inflamm Bowel Dis 2020; 26:1733-1742. [PMID: 31833543 DOI: 10.1093/ibd/izz298] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Indexed: 01/01/2023]
Abstract
BACKGROUND Alterations in the microbiome have been postulated to drive inflammation in IBD. In this pilot randomized controlled trial, we evaluated the effectiveness of quadruple antibiotic cocktail in addition to intravenous-corticosteroids (IVCSs) in acute severe colitis (ASC). METHODS Hospitalized children with ASC (pediatric ulcerative colitis activity index [PUCAI] ≥65) were randomized into 2 arms: the first received antibiotics in addition to IVCS (amoxicillin, vancomycin, metronidazole, doxycycline/ciprofloxacin [IVCS+AB]), whereas the other received only IVCS for 14 days. The primary outcome was disease activity (PUCAI) at day 5. Microbiome was analyzed using 16S rRNA gene and metagenome. RESULTS Twenty-eight children were included: 16 in the AB + IVCS arm and 12 in the IVCS arm (mean age 13.9 ± 4.1 years and 23 [82%] with extensive colitis). The mean day-5 PUCAI was 25 ± 16.7 vs 40.4 ± 20.4, respectively (P = 0.037). Only 3 and 2 children, respectively, required colectomy during 1-year follow-up (P = 0.89). Microbiome data at time of admission were analyzed for 25 children, of whom 17 (68%) had a predominant bacterial species (>33% abundance); response was not associated with the specific species, whereas decreased microbiome diversity at admission was associated with day-5 response in the IVCS arm. CONCLUSION Patients with ASC have alterations in the microbiome characterized by loss of diversity and presence of predominant bacterial species. Quadruple therapy in addition to IVCS improved disease activity on day 5, but larger studies are needed to determine whether this is associated with improved long-term outcomes (clinicaltrials.gov NCT02033408).
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Affiliation(s)
- Dan Turner
- Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Jason Bishai
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Leah Reshef
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Guila Abitbol
- Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Gili Focht
- Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Dana Marcus
- Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Oren Ledder
- Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Raffi Lev-Tzion
- Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | | | - Baruch Yerushalmi
- Pediatric Gastroenterology Unit, Soroka University Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | | | - Lindsey Albenberg
- The Children's Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
| | - Kaija-Leena Kolho
- Hospital for Children and Adolescents, Children´s Hospital, Helsinki University, Helsinki, Finland
| | - Amit Assa
- Schneider Children's Medical Center, Petah Tikvah, Israel
| | - Shlomi Cohen
- Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Uri Gophna
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Arie Levine
- Dr. von Hauner Children's Hospital, Ludwig Maximilians-University, Munich, Germany
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33
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Borren NZ, Plichta D, Joshi AD, Bonilla G, Sadreyev R, Vlamakis H, Xavier RJ, Ananthakrishnan AN. Multi-"-Omics" Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse. Inflamm Bowel Dis 2020; 26:1524-1532. [PMID: 32766830 PMCID: PMC7500522 DOI: 10.1093/ibd/izaa183] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Inflammatory bowel diseases (IBD) are characterized by intermittent relapses, and their course is heterogeneous and unpredictable. Our aim was to determine the ability of protein, metabolite, or microbial biomarkers to predict relapse in patients with quiescent disease. METHODS This prospective study enrolled patients with quiescent Crohn disease and ulcerative colitis, defined as the absence of clinical symptoms (Harvey-Bradshaw Index ≤ 4, Simple Clinical Colitis Activity Index ≤ 2) and endoscopic remission within the prior year. The primary outcome was relapse within 2 years, defined as symptomatic worsening accompanied by elevated inflammatory markers resulting in a change in therapy or IBD-related hospitalization or surgery. Biomarkers were tested in a derivation cohort, and their performance was examined in an independent validation cohort. RESULTS Our prospective cohort study included 164 patients with IBD (108 with Crohn disease, 56 with ulcerative colitis). Upon follow-up for a median of 1 year, 22 patients (13.4%) experienced a relapse. Three protein biomarkers (interleukin-10, glial cell line-derived neurotrophic factor, and T-cell surface glycoprotein CD8 alpha chain) and 4 metabolomic markers (propionyl-L-carnitine, carnitine, sarcosine, and sorbitol) were associated with relapse in multivariable models. Proteomic and metabolomic risk scores independently predicted relapse with a combined area under the curve of 0.83. A high proteomic risk score (odds ratio = 9.11; 95% confidence interval, 1.90-43.61) or metabolomic risk score (odds ratio = 5.79; 95% confidence interval, 1.24-27.11) independently predicted a higher risk of relapse over 2 years. Fecal metagenomics showed an increased abundance of Proteobacteria (P = 0.0019, q = 0.019) and Fusobacteria (P = 0.0040, q = 0.020) and at the species level Lachnospiraceae_bacterium_2_1_58FAA (P = 0.000008, q = 0.0009) among the relapses. CONCLUSIONS Proteomic, metabolomic, and microbial biomarkers identify a proinflammatory state in quiescent IBD that predisposes to clinical relapse.
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Affiliation(s)
- Nienke Z Borren
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA,Department of Gastroenterology & Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Damian Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Amit D Joshi
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Gracia Bonilla
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ramnik J Xavier
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA,Address correspondence to: Ashwin N. Ananthakrishnan, MD, MPH, Massachusetts General Hospital Crohn’s and Colitis Center, 165 Cambridge Street, 9 Floor, Boston, MA 02114 ()
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Mills KI, Albert BD, Bechard LJ, Duggan CP, Kaza A, Rakoff-Nahoum S, Vlamakis H, Sleeper LA, Newburger JW, Priebe GP, Mehta NM. Stress ulcer prophylaxis versus placebo-a blinded randomized control trial to evaluate the safety of two strategies in critically ill infants with congenital heart disease (SUPPRESS-CHD). Trials 2020; 21:590. [PMID: 32600393 PMCID: PMC7322718 DOI: 10.1186/s13063-020-04513-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/15/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Critically ill infants with congenital heart disease (CHD) are often prescribed stress ulcer prophylaxis (SUP) to prevent upper gastrointestinal bleeding, despite the low incidence of stress ulcers and limited data on the safety and efficacy of SUP in infants. Recently, SUP has been associated with an increased incidence of hospital-acquired infections, community-acquired pneumonia, and necrotizing enterocolitis. The objective of this pilot study is to investigate the feasibility of performing a randomized controlled trial to assess the safety and efficacy of withholding SUP in infants with congenital heart disease admitted to the cardiac intensive care unit. METHODS A single center, prospective, double-blinded, randomized placebo-controlled pilot feasibility trial will be performed in infants with CHD admitted to the cardiac intensive care unit and anticipated to require respiratory support for > 24 h. Patients will be randomized to receive a histamine-2 receptor antagonist (H2RA) or placebo until they are discontinued from respiratory support. Randomization will be performed within 2 strata defined by admission type (medical or surgical) and age (neonate, age < 30 days, or infant, 1 month to 1 year). Allocation will be a 1:1 ratio using permuted blocks to ensure balanced allocations across the two treatment groups within each stratum. The primary outcomes include feasibility of screening, consent, timely allocation of study drug, and protocol adherence. The primary safety outcome is the rate of clinically significant upper gastrointestinal bleeding. The secondary outcomes are the difference in the relative and absolute abundance of the gut microbiota and functional microbial profiles between the two study groups. We plan to enroll 100 patients in this pilot study. DISCUSSION Routine use of SUP to prevent upper gastrointestinal bleeding in infants is controversial due to a low incidence of bleeding events and concern for adverse effects. The role of SUP in infants with CHD has not been examined, and there is equipoise on the risks and benefits of withholding this therapy. In addition, this therapy has been discontinued in other neonatal populations due to the concern for hospital-acquired infections and necrotizing enterocolitis. Furthermore, exploring changes to the microbiome after exposure to SUP may highlight the mechanisms by which SUP impacts potential microbial dysbiosis of the gut and its association with hospital-acquired infections. Assessment of the feasibility of a trial of withholding SUP in critically ill infants with CHD will facilitate planning of a larger multicenter trial of safety and efficacy of SUP in this vulnerable population. TRIAL REGISTRATION ClinicalTrials.gov , NCT03667703. Registered 12 September 2018, https://clinicaltrials.gov/ct2/show/NCT03667703?term=SUPPRESS+CHD&draw=2&rank=1 . All WHO Trial Registration Data Set Criteria are met in this manuscript.
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Affiliation(s)
- Kimberly I. Mills
- grid.2515.30000 0004 0378 8438Department of Cardiology, Boston Children’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Ben D. Albert
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Division of Critical Care Medicine, Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA USA
| | - Lori J. Bechard
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Division of Critical Care Medicine, Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA USA
| | - Christopher P. Duggan
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Center for Nutrition, Boston Children’s Hospital, Boston, MA USA
| | - Aditya Kaza
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Department of Cardiac Surgery, Boston Children’s Hospital, Boston, MA USA
| | - Seth Rakoff-Nahoum
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Department of Pediatrics, Boston Children’s Hospital, Boston, MA USA
| | - Hera Vlamakis
- grid.66859.34Broad Institute of MIT and Harvard, Boston, MA USA
| | - Lynn A. Sleeper
- grid.2515.30000 0004 0378 8438Department of Cardiology, Boston Children’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Jane W. Newburger
- grid.2515.30000 0004 0378 8438Department of Cardiology, Boston Children’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Gregory P. Priebe
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Division of Critical Care Medicine, Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA USA
| | - Nilesh M. Mehta
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Division of Critical Care Medicine, Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA USA ,grid.2515.30000 0004 0378 8438Center for Nutrition, Boston Children’s Hospital, Boston, MA USA
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35
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Kenny DJ, Plichta DR, Shungin D, Koppel N, Hall AB, Fu B, Vasan RS, Shaw SY, Vlamakis H, Balskus EP, Xavier RJ. Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level. Cell Host Microbe 2020; 28:245-257.e6. [PMID: 32544460 PMCID: PMC7435688 DOI: 10.1016/j.chom.2020.05.013] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/01/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
The human microbiome encodes extensive metabolic capabilities, but our understanding of the mechanisms linking gut microbes to human metabolism remains limited. Here, we focus on the conversion of cholesterol to the poorly absorbed sterol coprostanol by the gut microbiota to develop a framework for the identification of functional enzymes and microbes. By integrating paired metagenomics and metabolomics data from existing cohorts with biochemical knowledge and experimentation, we predict and validate a group of microbial cholesterol dehydrogenases that contribute to coprostanol formation. These enzymes are encoded by ismA genes in a clade of uncultured microorganisms, which are prevalent in geographically diverse human cohorts. Individuals harboring coprostanol-forming microbes have significantly lower fecal cholesterol levels and lower serum total cholesterol with effects comparable to those attributed to variations in lipid homeostasis genes. Thus, cholesterol metabolism by these microbes may play important roles in reducing intestinal and serum cholesterol concentrations, directly impacting human health. Bioinformatics enabled discovery of ismA, a microbial cholesterol dehydrogenase Metagenomic species with ismA genes form coprostanol in microbial communities ismA+ species are associated with decreased fecal and serum cholesterol in humans Effect sizes of ismA+ species on serum cholesterol are on par with human genetics
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Affiliation(s)
- Douglas J Kenny
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Dmitry Shungin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Odontology, Umeå University, Umeå, Sweden
| | - Nitzan Koppel
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Beverly Fu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ramachandran S Vasan
- Boston University and NHLBI's Framingham Heart Study, Framingham, MA, USA; Sections of Preventive Medicine and Epidemiology and Cardiovascular Medicine, Departments of Medicine and Epidemiology, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - Stanley Y Shaw
- Harvard Medical School, Boston, MA, USA; HMS and Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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36
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Abstract
Perturbations in the intestinal microbiome are implicated in inflammatory bowel disease (IBD). Studies of treatment-naive patients have identified microbial taxa associated with disease course and treatment efficacy. To gain a mechanistic understanding of how the microbiome affects gastrointestinal health, we need to move from census to function. Bacteria, including those that adhere to epithelial cells as well as several Clostridium species, can alter differentiation of T helper 17 cells and regulatory T cells. Similarly, microbial products such as short-chain fatty acids and sphingolipids also influence immune responses. Metagenomics and culturomics have identified strains of Ruminococcus gnavus and adherent invasive Escherichia coli that are linked to IBD and gut inflammation. Integrated analysis of multiomics data, including metagenomics, metatranscriptomics and metabolomics, with measurements of host response and culturomics, have great potential in understanding the role of the microbiome in IBD. In this Review, we highlight current knowledge of gut microbial factors linked to IBD pathogenesis and discuss how multiomics data from large-scale population studies in health and disease have been used to identify specific microbial strains, transcriptional changes and metabolic alterations associated with IBD.
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Affiliation(s)
| | - Ashley Garner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.
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37
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Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC. Global chemical effects of the microbiome include new bile-acid conjugations. Nature 2020; 579:123-129. [PMID: 32103176 PMCID: PMC7252668 DOI: 10.1038/s41586-020-2047-9] [Citation(s) in RCA: 266] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/03/2020] [Indexed: 12/26/2022]
Abstract
A mosaic of cross-phylum chemical interactions occurs between all metazoans and their microbiomes. A number of molecular families that are known to be produced by the microbiome have a marked effect on the balance between health and disease1-9. Considering the diversity of the human microbiome (which numbers over 40,000 operational taxonomic units10), the effect of the microbiome on the chemistry of an entire animal remains underexplored. Here we use mass spectrometry informatics and data visualization approaches11-13 to provide an assessment of the effects of the microbiome on the chemistry of an entire mammal by comparing metabolomics data from germ-free and specific-pathogen-free mice. We found that the microbiota affects the chemistry of all organs. This included the amino acid conjugations of host bile acids that were used to produce phenylalanocholic acid, tyrosocholic acid and leucocholic acid, which have not previously been characterized despite extensive research on bile-acid chemistry14. These bile-acid conjugates were also found in humans, and were enriched in patients with inflammatory bowel disease or cystic fibrosis. These compounds agonized the farnesoid X receptor in vitro, and mice gavaged with the compounds showed reduced expression of bile-acid synthesis genes in vivo. Further studies are required to confirm whether these compounds have a physiological role in the host, and whether they contribute to gut diseases that are associated with microbiome dysbiosis.
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Affiliation(s)
- Robert A Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Alison Vrbanac
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Ting Fu
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Kathryn A Patras
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Mitchell P Christy
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Zsolt Bodai
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Anupriya Tripathi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Lawton K Chung
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Ryan D Welch
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Melissa Quinn
- Department of Kinesiology, Michigan State University, East Lansing, MI, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,UCSD Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA
| | - Alexander Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Ricardo da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | | | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sena Bae
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Himel Mallick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jason Lloyd-Price
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Robert Bussell
- Department of Radiology, University of California San Diego, San Diego, CA, USA
| | - Taren Thron
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrew T Nelson
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Eric Leszczynski
- Department of Kinesiology, Michigan State University, East Lansing, MI, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Emily Gentry
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Timothy D Arthur
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA, USA
| | - Orit Poulsen
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - John T Chang
- Division of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - William J Sandborn
- Division of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Meerana Lim
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.,Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA
| | - Julie C Lumeng
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Ruchi Jain
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Marie Egan
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Kyung E Rhee
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - David Ferguson
- Department of Kinesiology, Michigan State University, East Lansing, MI, USA
| | - Manuela Raffatellu
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriel G Haddad
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Dionicio Siegel
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, San Diego, CA, USA
| | - Victor Nizet
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,UCSD Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,UCSD Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.,Department of Engineering, University of California San Diego, San Diego, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA. .,Department of Pediatrics, University of California San Diego, San Diego, CA, USA. .,UCSD Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA.
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38
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Brown EM, Ke X, Hitchcock D, Jeanfavre S, Avila-Pacheco J, Nakata T, Arthur TD, Fornelos N, Heim C, Franzosa EA, Watson N, Huttenhower C, Haiser HJ, Dillow G, Graham DB, Finlay BB, Kostic AD, Porter JA, Vlamakis H, Clish CB, Xavier RJ. Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis. Cell Host Microbe 2019; 25:668-680.e7. [PMID: 31071294 DOI: 10.1016/j.chom.2019.04.002] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/19/2019] [Accepted: 04/02/2019] [Indexed: 12/28/2022]
Abstract
Sphingolipids are structural membrane components and important eukaryotic signaling molecules. Sphingolipids regulate inflammation and immunity and were recently identified as the most differentially abundant metabolite in stool from inflammatory bowel disease (IBD) patients. Commensal bacteria from the Bacteroidetes phylum also produce sphingolipids, but the impact of these metabolites on host pathways is largely uncharacterized. To determine whether bacterial sphingolipids modulate intestinal health, we colonized germ-free mice with a sphingolipid-deficient Bacteroides thetaiotaomicron strain. A lack of Bacteroides-derived sphingolipids resulted in intestinal inflammation and altered host ceramide pools in mice. Using lipidomic analysis, we described a sphingolipid biosynthesis pathway and revealed a variety of Bacteroides-derived sphingolipids including ceramide phosphoinositol and deoxy-sphingolipids. Annotating Bacteroides sphingolipids in an IBD metabolomic dataset revealed lower abundances in IBD and negative correlations with inflammation and host sphingolipid production. These data highlight the role of bacterial sphingolipids in maintaining homeostasis and symbiosis in the gut.
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Affiliation(s)
- Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xiaobo Ke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novartis Institute for Biomedical Research Inc., Cambridge, MA 02139, USA
| | | | - Sarah Jeanfavre
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Toru Nakata
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Nadine Fornelos
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cortney Heim
- Novartis Institute for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Nicki Watson
- W. M. Keck Microscopy Facility, The Whitehead Institute, Cambridge, MA 02142, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Henry J Haiser
- Novartis Institute for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Glen Dillow
- Novartis Institute for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Aleksandar D Kostic
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Microbiology and Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey A Porter
- Novartis Institute for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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39
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Jiang X, Hall AB, Arthur TD, Plichta DR, Covington CT, Poyet M, Crothers J, Moses PL, Tolonen AC, Vlamakis H, Alm EJ, Xavier RJ. Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. Science 2019; 363:181-187. [PMID: 30630933 DOI: 10.1126/science.aau5238] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022]
Abstract
Phase variation, the reversible alternation between genetic states, enables infection by pathogens and colonization by commensals. However, the diversity of phase variation remains underexplored. We developed the PhaseFinder algorithm to quantify DNA inversion-mediated phase variation. A systematic search of 54,875 bacterial genomes identified 4686 intergenic invertible DNA regions (invertons), revealing an enrichment in host-associated bacteria. Invertons containing promoters often regulate extracellular products, underscoring the importance of surface diversity for gut colonization. We found invertons containing promoters regulating antibiotic resistance genes that shift to the ON orientation after antibiotic treatment in human metagenomic data and in vitro, thereby mitigating the cost of antibiotic resistance. We observed that the orientations of some invertons diverge after fecal microbiota transplant, potentially as a result of individual-specific selective forces.
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Affiliation(s)
- Xiaofang Jiang
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - A Brantley Hall
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Damian R Plichta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Christian T Covington
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Mathilde Poyet
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jessica Crothers
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT 05401, USA
| | - Peter L Moses
- Division of Gastroenterology and Hepatology, University of Vermont, Burlington, VT 05401, USA
| | - Andrew C Tolonen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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40
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Mallick H, Franzosa EA, Mclver LJ, Banerjee S, Sirota-Madi A, Kostic AD, Clish CB, Vlamakis H, Xavier RJ, Huttenhower C. Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. Nat Commun 2019; 10:3136. [PMID: 31316056 PMCID: PMC6637180 DOI: 10.1038/s41467-019-10927-1] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 06/06/2019] [Indexed: 02/07/2023] Open
Abstract
Microbial community metabolomics, particularly in the human gut, are beginning to provide a new route to identify functions and ecology disrupted in disease. However, these data can be costly and difficult to obtain at scale, while amplicon or shotgun metagenomic sequencing data are readily available for populations of many thousands. Here, we describe a computational approach to predict potentially unobserved metabolites in new microbial communities, given a model trained on paired metabolomes and metagenomes from the environment of interest. Focusing on two independent human gut microbiome datasets, we demonstrate that our framework successfully recovers community metabolic trends for more than 50% of associated metabolites. Similar accuracy is maintained using amplicon profiles of coral-associated, murine gut, and human vaginal microbiomes. We also provide an expected performance score to guide application of the model in new samples. Our results thus demonstrate that this 'predictive metabolomic' approach can aid in experimental design and provide useful insights into the thousands of community profiles for which only metagenomes are currently available.
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Affiliation(s)
- Himel Mallick
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Lauren J Mclver
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Soumya Banerjee
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Alexandra Sirota-Madi
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Aleksandar D Kostic
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA.
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41
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Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 2019; 569:655-662. [PMID: 31142855 PMCID: PMC6650278 DOI: 10.1038/s41586-019-1237-9] [Citation(s) in RCA: 1352] [Impact Index Per Article: 270.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/16/2019] [Indexed: 12/11/2022]
Abstract
Inflammatory bowel diseases, which include Crohn’s disease and ulcerative colitis, affect several million individuals worldwide. Crohn’s disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study’s infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi’omics Database (http://ibdmdb.org), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases. The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.
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Affiliation(s)
- Jason Lloyd-Price
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Cesar Arze
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Melanie Schirmer
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Tiffany W Poon
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nadim J Ajami
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kevin S Bonham
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
| | - David Casero
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Holly Courtney
- Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Thomas G Graeber
- Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA
| | - A Brantley Hall
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathleen Lake
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carol J Landers
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Himel Mallick
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Damian R Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mahadev Prasad
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Gholamali Rahnavard
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jenny Sauk
- Vatche and Tamar Manoukian Division of Digestive Diseases, University of California Los Angeles, Los Angeles, CA, USA
| | - Dmitry Shungin
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Odontology, Umeå University, Umeå, Sweden
| | - Yoshiki Vázquez-Baeza
- Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Richard A White
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
| | | | - Jonathan Braun
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lee A Denson
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | | | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joseph F Petrosino
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | | | - Harland S Winter
- Department of Pediatrics, MassGeneral Hospital for Children, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Clary B Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Gastroenterology, Massachusetts General Hospital, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ. Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol 2019; 4:898. [PMID: 30971771 DOI: 10.1038/s41564-019-0442-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the Supplementary Tables 2, 4 and 6 originally published with this Article, the authors mistakenly included sample identifiers in the form of UMCGs rather than UMCG IBDs in the validation cohort; this has now been amended.
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Affiliation(s)
- Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | | | | | | | - Henry J Haiser
- Novartis Institute for Biomedical Research Inc, Cambridge, MA, USA
| | - Stefan Reinker
- Novartis Institute for Biomedical Research Inc, Cambridge, MA, USA
| | - Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Himel Mallick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Lauren J McIver
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Jenny S Sauk
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Robin G Wilson
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Betsy W Stevens
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Kerry Pierce
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy A Deik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kevin Bullock
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Jeffrey A Porter
- Novartis Institute for Biomedical Research Inc, Basel, Switzerland
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.,Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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43
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Ramos Y, Rocha J, Hael AL, van Gestel J, Vlamakis H, Cywes-Bentley C, Cubillos-Ruiz JR, Pier GB, Gilmore MS, Kolter R, Morales DK. PolyGlcNAc-containing exopolymers enable surface penetration by non-motile Enterococcus faecalis. PLoS Pathog 2019; 15:e1007571. [PMID: 30742693 PMCID: PMC6386517 DOI: 10.1371/journal.ppat.1007571] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/22/2019] [Accepted: 01/08/2019] [Indexed: 11/20/2022] Open
Abstract
Bacterial pathogens have evolved strategies that enable them to invade tissues and spread within the host. Enterococcus faecalis is a leading cause of local and disseminated multidrug-resistant hospital infections, but the molecular mechanisms used by this non-motile bacterium to penetrate surfaces and translocate through tissues remain largely unexplored. Here we present experimental evidence indicating that E. faecalis generates exopolysaccharides containing β-1,6-linked poly-N-acetylglucosamine (polyGlcNAc) as a mechanism to successfully penetrate semisolid surfaces and translocate through human epithelial cell monolayers. Genetic screening and molecular analyses of mutant strains identified glnA, rpiA and epaX as genes critically required for optimal E. faecalis penetration and translocation. Mechanistically, GlnA and RpiA cooperated to generate uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) that was utilized by EpaX to synthesize polyGlcNAc-containing polymers. Notably, exogenous supplementation with polymeric N-acetylglucosamine (PNAG) restored surface penetration by E. faecalis mutants devoid of EpaX. Our study uncovers an unexpected mechanism whereby the RpiA-GlnA-EpaX metabolic axis enables production of polyGlcNAc-containing polysaccharides that endow E. faecalis with the ability to penetrate surfaces. Hence, targeting carbohydrate metabolism or inhibiting biosynthesis of polyGlcNAc-containing exopolymers may represent a new strategy to more effectively confront enterococcal infections in the clinic. Enterococcus faecalis is a microbial inhabitant of the human gastrointestinal tract that can cause lethal infections. Typically classified as a non-motile bacterium, E. faecalis can readily migrate and translocate across epithelial barriers to invade distant organs. Nevertheless, the molecular pathways driving enterococcal invasive attributes remain poorly understood. In this study, we uncover that E. faecalis produces a polyGlcNAc-containing extracellular glycopolymer to efficiently migrate into semisolid surfaces and translocate through human epithelial cell monolayers. Our work provides evidence that non-motile bacterial pathogens can exploit endogenous carbohydrate metabolic pathways to penetrate surfaces. Thus, targeting glycopolymer biosynthetic programs might be useful to control infections by Gram-positive cocci in the clinic.
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Affiliation(s)
- Yusibeska Ramos
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States of America
| | - Jorge Rocha
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Ana L. Hael
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Hera Vlamakis
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Colette Cywes-Bentley
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Juan R. Cubillos-Ruiz
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States of America
| | - Gerald B. Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Michael S. Gilmore
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
- Department of Ophthalmology, Harvard Medical School, Boston, MA, United States of America
| | - Roberto Kolter
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Diana K. Morales
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States of America
- * E-mail:
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44
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Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol 2019; 4:293-305. [PMID: 30531976 PMCID: PMC6342642 DOI: 10.1038/s41564-018-0306-4] [Citation(s) in RCA: 890] [Impact Index Per Article: 178.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 10/25/2018] [Indexed: 12/13/2022]
Abstract
The inflammatory bowel diseases (IBDs), which include Crohn's disease (CD) and ulcerative colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome-the molecular interface between host and microbiota-are less well understood. To address this gap, we performed untargeted metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n = 155) and validation (n = 65) cohorts of CD, UC and non-IBD control patients. Metabolomic and metagenomic profiles were broadly correlated with faecal calprotectin levels (a measure of gut inflammation). Across >8,000 measured metabolite features, we identified chemicals and chemical classes that were differentially abundant in IBD, including enrichments for sphingolipids and bile acids, and depletions for triacylglycerols and tetrapyrroles. While > 50% of differentially abundant metabolite features were uncharacterized, many could be assigned putative roles through metabolomic 'guilt by association' (covariation with known metabolites). Differentially abundant species and functions from the metagenomic profiles reflected adaptation to oxidative stress in the IBD gut, and were individually consistent with previous findings. Integrating these data, however, we identified 122 robust associations between differentially abundant species and well-characterized differentially abundant metabolites, indicating possible mechanistic relationships that are perturbed in IBD. Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly accurate and, like the vast majority of individual trends, generalized well to the independent validation cohort. Our findings thus provide an improved understanding of perturbations of the microbiome-metabolome interface in IBD, including identification of many potential diagnostic and therapeutic targets.
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Affiliation(s)
- Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | | | | | | | - Henry J Haiser
- Novartis Institute for Biomedical Research Inc., Cambridge, MA, USA
| | - Stefan Reinker
- Novartis Institute for Biomedical Research Inc., Cambridge, MA, USA
| | - Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Himel Mallick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Lauren J McIver
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Jenny S Sauk
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Robin G Wilson
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Betsy W Stevens
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Kerry Pierce
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy A Deik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kevin Bullock
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Jeffrey A Porter
- Novartis Institute for Biomedical Research Inc., Basel, Switzerland
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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45
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Lavoie S, Conway KL, Lassen KG, Jijon HB, Pan H, Chun E, Michaud M, Lang JK, Gallini Comeau CA, Dreyfuss JM, Glickman JN, Vlamakis H, Ananthakrishnan A, Kostic A, Garrett WS, Xavier RJ. The Crohn's disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response. eLife 2019; 8:39982. [PMID: 30666959 PMCID: PMC6342529 DOI: 10.7554/elife.39982] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/20/2018] [Indexed: 12/15/2022] Open
Abstract
Inflammatory bowel disease (IBD) is driven by dysfunction between host genetics, the microbiota, and immune system. Knowledge gaps remain regarding how IBD genetic risk loci drive gut microbiota changes. The Crohn's disease risk allele ATG16L1 T300A results in abnormal Paneth cells due to decreased selective autophagy, increased cytokine release, and decreased intracellular bacterial clearance. To unravel the effects of ATG16L1 T300A on the microbiota and immune system, we employed a gnotobiotic model using human fecal transfers into ATG16L1 T300A knock-in mice. We observed increases in Bacteroides ovatus and Th1 and Th17 cells in ATG16L1 T300A mice. Association of altered Schaedler flora mice with B. ovatus specifically increased Th17 cells selectively in ATG16L1 T300A knock-in mice. Changes occur before disease onset, suggesting that ATG16L1 T300A contributes to dysbiosis and immune infiltration prior to disease symptoms. Our work provides insight for future studies on IBD subtypes, IBD patient treatment and diagnostics.
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Affiliation(s)
- Sydney Lavoie
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | - Kara L Conway
- Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
| | - Kara G Lassen
- Broad Institute of Harvard and MIT, Cambridge, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
| | - Humberto B Jijon
- Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
| | - Hui Pan
- Joslin Diabetes Center, Boston, United States
| | - Eunyoung Chun
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | - Monia Michaud
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | - Jessica K Lang
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | - Carey Ann Gallini Comeau
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | | | - Jonathan N Glickman
- Department of Pathology, Harvard Medical School, Boston, United States.,Beth Israel Deaconess Medical Center, Boston, United States
| | - Hera Vlamakis
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Ashwin Ananthakrishnan
- Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
| | - Aleksander Kostic
- Joslin Diabetes Center, Boston, United States.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States.,Department and Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Ramnik J Xavier
- Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
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46
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Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJ. Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nat Microbiol 2018; 4:470-479. [PMID: 30559407 PMCID: PMC6384140 DOI: 10.1038/s41564-018-0321-5] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022]
Abstract
The human gut microbiome matures toward the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on gut microbiome development using integrated early childhood datasets collected in the DIABIMMUNE study in Finland, Estonia and Russian Karelia. We show that gut microbial diversity is associated with household location and linear growth of children. Single nucleotide polymorphism (SNP)- and metagenomic assembly-based strain tracking revealed large and highly dynamic microbial pangenomes, especially in the genus Bacteroides, in which we identified evidence of variability deriving from Bacteroides-targeting bacteriophages. Our analyses revealed functional consequences of strain diversity; only 10% of Finnish infants harbored Bifidobacterium longum subsp. infantis, a subspecies specialized in human milk metabolism, whereas Russian infants commonly maintained a probiotic Bifidobacterium bifidum strain in infancy. Groups of bacteria contributing to diverse, characterized metabolic pathways converged to highly subject-specific configurations over the first two years of life. This longitudinal study extends the current view of early gut microbial community assembly based on strain-level genomic variation.
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Affiliation(s)
- Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Juhi Somani
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Philipp C Münch
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, Brunswick, Germany.,Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, Munich, Germany
| | | | | | - Sabine Rudolf
- Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Edward J Oakeley
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Xiaobo Ke
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Rachel A Young
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Henry J Haiser
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Raivo Kolde
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moran Yassour
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kristiina Luopajärvi
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Heli Siljander
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.,Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Suvi M Virtanen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland.,Faculty of Social Sciences/Health Sciences, University of Tampere, Tampere, Finland.,Science Centre, Pirkanmaa Hospital District and Research Center for Child Health, University Hospital, Tampere, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku, Turku, Finland.,Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Raivo Uibo
- Department of Immunology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Vallo Tillmann
- Department of Pediatrics, University of Tartu and Tartu University Hospital, Tartu, Estonia
| | - Sergei Mokurov
- Ministry of Health and Social Development, Karelian Republic of the Russian Federation, Petrozavodsk, Russia
| | - Natalya Dorshakova
- Petrozavodsk State University, Department of Family Medicine, Petrozavodsk, Russia
| | - Jeffrey A Porter
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Alice C McHardy
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, Brunswick, Germany
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mikael Knip
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.,Department of Pediatrics, Tampere University Hospital, Tampere, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Gastrointestinal Unit, and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.
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47
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Schirmer M, Denson L, Vlamakis H, Franzosa EA, Thomas S, Gotman NM, Rufo P, Baker SS, Sauer C, Markowitz J, Pfefferkorn M, Oliva-Hemker M, Rosh J, Otley A, Boyle B, Mack D, Baldassano R, Keljo D, LeLeiko N, Heyman M, Griffiths A, Patel AS, Noe J, Kugathasan S, Walters T, Huttenhower C, Hyams J, Xavier RJ. Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course. Cell Host Microbe 2018; 24:600-610.e4. [PMID: 30308161 PMCID: PMC6277984 DOI: 10.1016/j.chom.2018.09.009] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/28/2018] [Accepted: 09/03/2018] [Indexed: 12/11/2022]
Abstract
Evaluating progression risk and determining optimal therapy for ulcerative colitis (UC) is challenging as many patients exhibit incomplete responses to treatment. As part of the PROTECT (Predicting Response to Standardized Colitis Therapy) Study, we evaluated the role of the gut microbiome in disease course for 405 pediatric, new-onset, treatment-naive UC patients. Patients were monitored for 1 year upon treatment initiation, and microbial taxonomic composition was analyzed from fecal samples and rectal biopsies. Depletion of core gut microbes and expansion of bacteria typical of the oral cavity were associated with baseline disease severity. Remission and refractory disease were linked to species-specific temporal changes that may be implicative of therapy efficacy, and a pronounced increase in microbiome variability was observed prior to colectomy. Finally, microbial associations with disease-associated serological markers suggest host-microbial interactions in UC. These insights will help improve existing treatments and develop therapeutic approaches guiding optimal medical care.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Infectious Disease and Microbiome, Cambridge, MA 02142, USA; Harvard T.H. Chan School of Public Health, Biostatistics Department, Boston, MA 02115, USA
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Infectious Disease and Microbiome, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eric A Franzosa
- The Broad Institute of MIT and Harvard, Infectious Disease and Microbiome, Cambridge, MA 02142, USA; Harvard T.H. Chan School of Public Health, Biostatistics Department, Boston, MA 02115, USA
| | - Sonia Thomas
- Collaborative Studies Coordinating Center, Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27516, USA; RTI International, Biostatistics and Epidemiology Division, Research Triangle Park, NC 27709, USA
| | - Nathan M Gotman
- Collaborative Studies Coordinating Center, Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27516, USA
| | - Paul Rufo
- Children's Hospital Boston, Boston, MA 02115, USA
| | - Susan S Baker
- Women and Children's Hospital of Buffalo WCHOB, Buffalo, NY 14222, USA
| | - Cary Sauer
- Emory Children's Center, Atlanta, GA 30322, USA
| | - James Markowitz
- Cohen Children's Medical Center, Pediatric Gastroenterology, New York, NY 11040, USA
| | - Marian Pfefferkorn
- Riley Children's Hospital Indiana University, School of Medicine, Section of Gastroenterology/Hepatology/Nutrition, Indianapolis, IN 46202, USA
| | - Maria Oliva-Hemker
- Johns Hopkins Children's Center, Department of Pediatrics, Baltimore, MD 21287, USA
| | - Joel Rosh
- Goryeb Children's Hospital/Atlantic Health, Pediatric Gastroenterology, Morristown, NJ 07960, USA
| | - Anthony Otley
- IWK Health Centre, Division of Gastroenterology and Nutrition, Halifax, NS B3K 6R8, Canada
| | - Brendan Boyle
- Nationwide Children's Hospital, Pediatrics, Columbus, OH 43205, USA
| | - David Mack
- Children's Hospital of Eastern Ontario and University of Ottawa, Department of Pediatrics, Ottawa, ON K1H 8L1, Canada
| | - Robert Baldassano
- Children's Hospital of Philadelphia CHOP, Pediatric Gastroenterologist, Philadelphia, PA 19104, USA
| | - David Keljo
- UPMC Children's Hospital of Pittsburgh, Department of Pediatrics, Pittsburgh, PA 15224, USA
| | - Neal LeLeiko
- Hasbro Children's Hospital, Pediatric Gastroenterology, Providence, RI 02903, USA
| | - Melvin Heyman
- University of California at San Francisco, Pediatric Gastroenterology, San Francisco, CA 94158, USA
| | - Anne Griffiths
- Sickkids Hospital, University of Toronto, Gastroenterology, Hepatology and Nutrition, Toronto, ON M5G 1X8, Canada
| | - Ashish S Patel
- UT Southwestern, Department of Pediatrics, Dallas, TX 75390, USA
| | - Joshua Noe
- Medical College of Wisconsin, Gastroenterology, Milwaukee, WI 53226, USA
| | | | - Thomas Walters
- Sickkids Hospital, University of Toronto, Gastroenterology, Hepatology and Nutrition, Toronto, ON M5G 1X8, Canada
| | - Curtis Huttenhower
- The Broad Institute of MIT and Harvard, Infectious Disease and Microbiome, Cambridge, MA 02142, USA; Harvard T.H. Chan School of Public Health, Biostatistics Department, Boston, MA 02115, USA
| | - Jeffrey Hyams
- Connecticut Children's Medical Center, Division of Digestive Diseases, Hartford, CT 06106, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Infectious Disease and Microbiome, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
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48
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Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ. The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature 2018; 562:589-594. [PMID: 30356183 PMCID: PMC6296767 DOI: 10.1038/s41586-018-0620-2] [Citation(s) in RCA: 456] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 09/06/2018] [Indexed: 12/12/2022]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that targets pancreatic islet beta cells and incorporates genetic and environmental factors1, including complex genetic elements2, patient exposures3 and the gut microbiome4. Viral infections5 and broader gut dysbioses6 have been identified as potential causes or contributing factors; however, human studies have not yet identified microbial compositional or functional triggers that are predictive of islet autoimmunity or T1D. Here we analyse 10,913 metagenomes in stool samples from 783 mostly white, non-Hispanic children. The samples were collected monthly from three months of age until the clinical end point (islet autoimmunity or T1D) in the The Environmental Determinants of Diabetes in the Young (TEDDY) study, to characterize the natural history of the early gut microbiome in connection to islet autoimmunity, T1D diagnosis, and other common early life events such as antibiotic treatments and probiotics. The microbiomes of control children contained more genes that were related to fermentation and the biosynthesis of short-chain fatty acids, but these were not consistently associated with particular taxa across geographically diverse clinical centres, suggesting that microbial factors associated with T1D are taxonomically diffuse but functionally more coherent. When we investigated the broader establishment and development of the infant microbiome, both taxonomic and functional profiles were dynamic and highly individualized, and dominated in the first year of life by one of three largely exclusive Bifidobacterium species (B. bifidum, B. breve or B. longum) or by the phylum Proteobacteria. In particular, the strain-specific carriage of genes for the utilization of human milk oligosaccharide within a subset of B. longum was present specifically in breast-fed infants. These analyses of TEDDY gut metagenomes provide, to our knowledge, the largest and most detailed longitudinal functional profile of the developing gut microbiome in relation to islet autoimmunity, T1D and other early childhood events. Together with existing evidence from human cohorts7,8 and a T1D mouse model9, these data support the protective effects of short-chain fatty acids in early-onset human T1D.
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Affiliation(s)
- Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Randall Schwager
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Kendra Vehik
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital SUS, Malmo, Sweden
| | | | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Munich, Germany
- Forschergruppe Diabetes, Technische Universität München, Klinikum Rechts der Isar, Munich, Germany
- Forschergruppe Diabetes e.V. at Helmholtz Zentrum München, Munich, Germany
| | - Beena Akolkar
- National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD, USA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Dirk Gevers
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Janssen Human Microbiome Institute, Janssen Research and Development, Cambridge, MA, USA
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, and Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.
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49
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Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Duranti S, Lugli GA, Mancabelli L, Turroni F, Ferrario C, Milani C, Mangifesta M, Anzalone R, Viappiani A, Yassour M, Vlamakis H, Xavier R, Collado CM, Koren O, Tateo S, Soffiati M, Pedrotti A, Ventura M, Huttenhower C, Bork P, Segata N. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. Cell Host Microbe 2018; 24:133-145.e5. [PMID: 30001516 PMCID: PMC6716579 DOI: 10.1016/j.chom.2018.06.005] [Citation(s) in RCA: 640] [Impact Index Per Article: 106.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/17/2018] [Accepted: 06/14/2018] [Indexed: 02/08/2023]
Abstract
The acquisition and development of the infant microbiome are key to establishing a healthy host-microbiome symbiosis. The maternal microbial reservoir is thought to play a crucial role in this process. However, the source and transmission routes of the infant pioneering microbes are poorly understood. To address this, we longitudinally sampled the microbiome of 25 mother-infant pairs across multiple body sites from birth up to 4 months postpartum. Strain-level metagenomic profiling showed a rapid influx of microbes at birth followed by strong selection during the first few days of life. Maternal skin and vaginal strains colonize only transiently, and the infant continues to acquire microbes from distinct maternal sources after birth. Maternal gut strains proved more persistent in the infant gut and ecologically better adapted than those acquired from other sources. Together, these data describe the mother-to-infant microbiome transmission routes that are integral in the development of the infant microbiome.
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Affiliation(s)
- Pamela Ferretti
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy; European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Edoardo Pasolli
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Adrian Tett
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesco Asnicar
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | | | - Sabina Fedi
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Federica Armanini
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Duy Tin Truong
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Serena Manara
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Moreno Zolfo
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesco Beghini
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Roberto Bertorelli
- NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Veronica De Sanctis
- NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | | | - Rosarita Canto
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | | | - Marina Cologna
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Tiziana Crifò
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | | | | | | | - Caterina Masè
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Daniela Postai
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Daniela Savoi
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; GenProbio srl, 43124 Parma, Italy
| | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | | | - Moran Yassour
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carmen Maria Collado
- Institute of Agrochemistry and Food Technology, National Research Council, Paterna, 46980 Valencia, Spain
| | - Omry Koren
- Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Saverio Tateo
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | | | - Anna Pedrotti
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy.
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50
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Verma MS, Fink MJ, Salmon GL, Fornelos N, Ohara TE, Ryu SH, Vlamakis H, Xavier RJ, Stappenbeck TS, Whitesides GM. A Common Mechanism Links Activities of Butyrate in the Colon. ACS Chem Biol 2018; 13:1291-1298. [PMID: 29584955 DOI: 10.1021/acschembio.8b00073] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Two biological activities of butyrate in the colon (suppression of proliferation of colonic epithelial stem cells and inflammation) correlate with inhibition of the activity of histone deacetylases. Cellular and biochemical studies of molecules similar in structure to butyrate, but different in molecular details (functional groups, chain-length, deuteration, oxidation level, fluorination, or degree of unsaturation), demonstrated that these activities were sensitive to molecular structure, and were compatible with the hypothesis that butyrate acts by binding to the Zn2+ in the catalytic site of histone deacetylases. Structure-activity relationships drawn from a set of 36 compounds offer a starting point for the design of new compounds targeting the inhibition of histone deacetylases. The observation that butyrate was more potent than other short-chain fatty acids is compatible with the hypothesis that crypts evolved (at least in part), to separate stem cells at the base of crypts from butyrate produced by commensal bacteria.
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Affiliation(s)
- Mohit S. Verma
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Michael J. Fink
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Gabriel L. Salmon
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Nadine Fornelos
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Takahiro E. Ohara
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Stacy H. Ryu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ramnik J. Xavier
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- The Center for Microbiome Informatics & Therapeutics, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thaddeus S. Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, United States
- Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, United States
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