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Mihindukulasuriya KA, Mars RAT, Johnson AJ, Ward T, Priya S, Lekatz HR, Kalari KR, Droit L, Zheng T, Blekhman R, D'Amato M, Farrugia G, Knights D, Handley SA, Kashyap PC. Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome. Gastroenterology 2021; 161:1194-1207.e8. [PMID: 34245762 PMCID: PMC8463486 DOI: 10.1053/j.gastro.2021.06.077] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/21/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The gut virome includes eukaryotic viruses and bacteriophages that can shape the gut bacterial community and elicit host responses. The virome can be implicated in diseases, such as irritable bowel syndrome (IBS), where gut bacteria play an important role in pathogenesis. We provide a comprehensive and longitudinal characterization of the virome, including DNA and RNA viruses and paired multi-omics data in a cohort of healthy subjects and patients with IBS. METHODS We selected 2 consecutive stool samples per subject from a longitudinal study cohort and performed metagenomic sequencing on DNA and RNA viruses after enriching for viral-like particles. Viral sequence abundance was evaluated over time, as well as in the context of diet, bacterial composition and function, metabolite levels, colonic gene expression, host genetics, and IBS subsets. RESULTS We found that the gut virome was temporally stable and correlated with the colonic transcriptome. We identified IBS-subset-specific changes in phage populations; Microviridae, Myoviridae, and Podoviridae species were elevated in diarrhea-predominant IBS, and other Microviridae and Myoviridae species were elevated in constipation-predominant IBS compared to healthy controls. We identified correlations between subsets of the virome and bacterial composition (unclassifiable "dark matter" and phages) and diet (eukaryotic viruses). CONCLUSIONS We found that the gut virome is stable over time but varies among subsets of patients with IBS. It can be affected by diet and potentially influences host function via interactions with gut bacteria and/or altering host gene expression.
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Affiliation(s)
| | - Ruben A T Mars
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Tonya Ward
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Heather R Lekatz
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Lindsay Droit
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Tenghao Zheng
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Mauro D'Amato
- Gastrointestinal Genetics Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Derio, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Gianrico Farrugia
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Dan Knights
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri.
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Medicine and Physiology, Mayo Clinic, Rochester, Minnesota.
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Mars RAT, Yang Y, Ward T, Houtti M, Priya S, Lekatz HR, Tang X, Sun Z, Kalari KR, Korem T, Bhattarai Y, Zheng T, Bar N, Frost G, Johnson AJ, van Treuren W, Han S, Ordog T, Grover M, Sonnenburg J, D'Amato M, Camilleri M, Elinav E, Segal E, Blekhman R, Farrugia G, Swann JR, Knights D, Kashyap PC. Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. Cell 2020; 183:1137-1140. [PMID: 33186523 DOI: 10.1016/j.cell.2020.10.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Mars RAT, Yang Y, Ward T, Houtti M, Priya S, Lekatz HR, Tang X, Sun Z, Kalari KR, Korem T, Bhattarai Y, Zheng T, Bar N, Frost G, Johnson AJ, van Treuren W, Han S, Ordog T, Grover M, Sonnenburg J, D'Amato M, Camilleri M, Elinav E, Segal E, Blekhman R, Farrugia G, Swann JR, Knights D, Kashyap PC. Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. Cell 2020; 182:1460-1473.e17. [PMID: 32916129 DOI: 10.1016/j.cell.2020.08.007] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/25/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022]
Abstract
The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease has been difficult due to apparent disconnects between animal and human studies and lack of an integrated multi-omics view of disease-specific physiological changes. We integrated longitudinal multi-omics data from the gut microbiome, metabolome, host epigenome, and transcriptome in the context of irritable bowel syndrome (IBS) host physiology. We identified IBS subtype-specific and symptom-related variation in microbial composition and function. A subset of identified changes in microbial metabolites correspond to host physiological mechanisms that are relevant to IBS. By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential. Our study highlights the importance of longitudinal sampling and integrating complementary multi-omics data to identify functional mechanisms that can serve as therapeutic targets in a comprehensive treatment strategy for chronic GI diseases. VIDEO ABSTRACT.
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Affiliation(s)
- Ruben A T Mars
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yi Yang
- Department of Metabolism, Digestion and Reproduction, Imperial College, London SW7 2AZ, UK
| | - Tonya Ward
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mo Houtti
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Heather R Lekatz
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaojia Tang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Tal Korem
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; CIFAR Azrieli Global Scholars program, CIFAR, Toronto, ON M5G 1M1, Canada
| | - Yogesh Bhattarai
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Tenghao Zheng
- School of Biological Sciences, Monash University, Clayton, 3800 VIC, Australia
| | - Noam Bar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gary Frost
- Department of Metabolism, Digestion and Reproduction, Imperial College, London SW7 2AZ, UK
| | - Abigail J Johnson
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Will van Treuren
- Department of Microbiology and Immunology, Center for Human Microbiome Studies, Stanford University, Stanford, CA 94305, USA
| | - Shuo Han
- Department of Microbiology and Immunology, Center for Human Microbiome Studies, Stanford University, Stanford, CA 94305, USA
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Madhusudan Grover
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Justin Sonnenburg
- Department of Microbiology and Immunology, Center for Human Microbiome Studies, Stanford University, Stanford, CA 94305, USA
| | - Mauro D'Amato
- School of Biological Sciences, Monash University, Clayton, 3800 VIC, Australia
| | - Michael Camilleri
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel; Division of Cancer-Microbiome Research, DKFZ, 69120 Heidelberg, Germany
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gianrico Farrugia
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Jonathan R Swann
- Department of Metabolism, Digestion and Reproduction, Imperial College, London SW7 2AZ, UK; School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA.
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Kashyap PC, Johnson S, Geno DM, Lekatz HR, Lavey C, Alexander JA, Chen J, Katzka DA. A decreased abundance of clostridia characterizes the gut microbiota in eosinophilic esophagitis. Physiol Rep 2020; 7:e14261. [PMID: 31650712 PMCID: PMC6813259 DOI: 10.14814/phy2.14261] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 08/10/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 01/14/2023] Open
Abstract
Abnormalities in the gut microbiome are associated with suppressed Th2 response (Belizario et al., 2018 Mediators Inflamm. 2018:2037838) and predisposition to atopic disease such as asthma and eczema. We investigated if this applies to eosinophilic esophagitis (EoE). Stool bacterial DNA was extracted and followed by 16S rRNA amplification from 12 patients with eosinophilic esophagitis and 12 controls. Alpha‐ and beta‐diversity were analyzed. Only two patients had asthma or atopy and one patient was on budesonide. No patients were on PPIs. Patients with EoE had lower gut microbiota alpha diversity (species richness, P = 0.09; Shannon index, P = 0.01). The microbial composition was distinct as evidenced by significantly different beta diversity (P = 0.03) when compared to healthy controls. There were also significant differences in relative abundance at multiple taxonomic levels when comparing the two communities; at the phylum level, we observed a marked decrease in Firmicutes and increase in Bacteroidetes and at the order and family level there were significant decreases in Clostridia and Clostridiales in patients with EoE (q ≤ 0.1). We conclude that there are significant differences in microbial community structure, microbial richness, and evenness and a significant decrease in taxa within the Clostridia in patients with EoE. Our data suggest that Clostridia based interventions could be tested as adjuncts to current therapeutic strategies in EoE.
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Affiliation(s)
- Purna C Kashyap
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.,Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
| | - Stephen Johnson
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Debra M Geno
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Heather R Lekatz
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Crystal Lavey
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Jun Chen
- Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
| | - David A Katzka
- Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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Saffouri GB, Shields-Cutler RR, Chen J, Yang Y, Lekatz HR, Hale VL, Cho JM, Battaglioli EJ, Bhattarai Y, Thompson KJ, Kalari KK, Behera G, Berry JC, Peters SA, Patel R, Schuetz AN, Faith JJ, Camilleri M, Sonnenburg JL, Farrugia G, Swann JR, Grover M, Knights D, Kashyap PC. Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders. Nat Commun 2019; 10:2012. [PMID: 31043597 PMCID: PMC6494866 DOI: 10.1038/s41467-019-09964-7] [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: 10/04/2018] [Accepted: 04/03/2019] [Indexed: 12/18/2022] Open
Abstract
Small intestinal bacterial overgrowth (SIBO) has been implicated in symptoms associated with functional gastrointestinal disorders (FGIDs), though mechanisms remain poorly defined and treatment involves non-specific antibiotics. Here we show that SIBO based on duodenal aspirate culture reflects an overgrowth of anaerobes, does not correspond with patient symptoms, and may be a result of dietary preferences. Small intestinal microbial composition, on the other hand, is significantly altered in symptomatic patients and does not correspond with aspirate culture results. In a pilot interventional study we found that switching from a high fiber diet to a low fiber, high simple sugar diet triggered FGID-related symptoms and decreased small intestinal microbial diversity while increasing small intestinal permeability. Our findings demonstrate that characterizing small intestinal microbiomes in patients with gastrointestinal symptoms may allow a more targeted antibacterial or a diet-based approach to treatment.
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Affiliation(s)
- George B Saffouri
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Robin R Shields-Cutler
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Biology, Macalester College, Saint Paul, MN, 55105, USA
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55902, USA
| | - Yi Yang
- Computational and Systems Medicine Section of the Department of Surgery and Cancer, Imperial College, (London), UK
| | - Heather R Lekatz
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Vanessa L Hale
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Janice M Cho
- Division of Internal Medicine, Mayo Clinic, Rochester, MN, 55902, USA
| | - Eric J Battaglioli
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Yogesh Bhattarai
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Kevin J Thompson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55902, USA
| | - Krishna K Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55902, USA
| | - Gaurav Behera
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Jonathan C Berry
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Stephanie A Peters
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Audrey N Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Jeremiah J Faith
- Department of Genetics and Genomic Sciences, Medicine, and Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Camilleri
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55902, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - Gianrico Farrugia
- Division of Gastroenterology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Jonathan R Swann
- Computational and Systems Medicine Section of the Department of Surgery and Cancer, Imperial College, (London), UK
| | - Madhusudan Grover
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55902, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA.
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55902, USA.
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