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Bethlehem L, Estevinho MM, Grinspan A, Magro F, Faith JJ, Colombel JF. Microbiota therapeutics for inflammatory bowel disease: the way forward. Lancet Gastroenterol Hepatol 2024; 9:476-486. [PMID: 38604201 DOI: 10.1016/s2468-1253(23)00441-7] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 04/13/2024]
Abstract
Microbiota therapeutics that transplant faecal material from healthy donors to people with mild-to-moderate ulcerative colitis have shown the potential to induce remission in about 30% of participants in small, phase 2 clinical trials. Despite this substantial achievement, the field needs to leverage the insights gained from these trials and progress towards phase 3 clinical trials and drug approval, while identifying the distinct clinical niche for this new therapeutic modality within inflammatory bowel disease (IBD) therapeutics. We describe the lessons that can be learned from past studies of microbiota therapeutics, from full spectrum donor stool to defined products manufactured in vitro. We explore the actionable insights these lessons provide on the design of near-term studies and future trajectories for the integration of microbiota therapeutics in the treatment of IBD. If successful, microbiota therapeutics will provide a powerful orthogonal approach (complementing or in combination with existing immunomodulatory drugs) to raise the therapeutic ceiling for the many non-responders and partial responders within the IBD patient population.
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Affiliation(s)
- Lukas Bethlehem
- Department of Genomics and Genetic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maria Manuela Estevinho
- Department of Gastroenterology, Vila Nova de Gaia Espinho Hospital Center, Vila Nova de Gaia, Portugal; Unit of Pharmacology and Therapeutics, Department of Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Ari Grinspan
- Dr Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fernando Magro
- Unit of Pharmacology and Therapeutics, Department of Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal; CINTESIS@RISE, Department of Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal; Department of Gastroenterology, São João Hospital Center, Porto, Portugal
| | - Jeremiah J Faith
- Department of Genomics and Genetic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Dr Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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2
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Canales-Herrerias P, Uzzan M, Seki A, Czepielewski RS, Verstockt B, Livanos AE, Raso F, Dunn A, Dai D, Wang A, Al-Taie Z, Martin J, Laurent T, Ko HM, Tokuyama M, Tankelevich M, Meringer H, Cossarini F, Jha D, Krek A, Paulsen JD, Taylor MD, Nakadar MZ, Wong J, Erlich EC, Mintz RL, Onufer EJ, Helmink BA, Sharma K, Rosenstein A, Ganjian D, Chung G, Dawson T, Juarez J, Yajnik V, Cerutti A, Faith JJ, Suarez-Farinas M, Argmann C, Petralia F, Randolph GJ, Polydorides AD, Reboldi A, Colombel JF, Mehandru S. Gut-associated lymphoid tissue attrition associates with response to anti-α4β7 therapy in ulcerative colitis. Sci Immunol 2024; 9:eadg7549. [PMID: 38640252 DOI: 10.1126/sciimmunol.adg7549] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/20/2024] [Indexed: 04/21/2024]
Abstract
Vedolizumab (VDZ) is a first-line treatment in ulcerative colitis (UC) that targets the α4β7- mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1) axis. To determine the mechanisms of action of VDZ, we examined five distinct cohorts of patients with UC. A decrease in naïve B and T cells in the intestines and gut-homing (β7+) plasmablasts in circulation of VDZ-treated patients suggested that VDZ targets gut-associated lymphoid tissue (GALT). Anti-α4β7 blockade in wild-type and photoconvertible (KikGR) mice confirmed a loss of GALT size and cellularity because of impaired cellular entry. In VDZ-treated patients with UC, treatment responders demonstrated reduced intestinal lymphoid aggregate size and follicle organization and a reduction of β7+IgG+ plasmablasts in circulation, as well as IgG+ plasma cells and FcγR-dependent signaling in the intestine. GALT targeting represents a previously unappreciated mechanism of action of α4β7-targeted therapies, with major implications for this therapeutic paradigm in UC.
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Affiliation(s)
- Pablo Canales-Herrerias
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mathieu Uzzan
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Paris Est Créteil University UPEC, Assistance Publique-Hôpitaux de Paris (AP-HP), Henri Mondor Hospital, Gastroenterology Department, Fédération Hospitalo-Universitaire TRUE (InnovaTive theRapy for immUne disordErs), Créteil F-94010, France
| | - Akihiro Seki
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rafael S Czepielewski
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bram Verstockt
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Translational Research in Gastrointestinal Disorders, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Alexandra E Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fiona Raso
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Alexandra Dunn
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Dai
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Wang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zainab Al-Taie
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerome Martin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nantes Université, CHU Nantes, Inserm, Centre de Recherche Translationelle en Transplantation et Immunologie, UMR 1064, Nantes, France
- CHU Nantes, Nantes Université, Laboratoire d'Immunologie, CIMNA, Nantes, France
| | - Thomas Laurent
- Nantes Université, CHU Nantes, Inserm, Centre de Recherche Translationelle en Transplantation et Immunologie, UMR 1064, Nantes, France
- CHU Nantes, Nantes Université, Laboratoire d'Immunologie, CIMNA, Nantes, France
| | - Huaibin M Ko
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minami Tokuyama
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Tankelevich
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hadar Meringer
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Cossarini
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Divya Jha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John D Paulsen
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D Taylor
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mohammad Zuber Nakadar
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua Wong
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma C Erlich
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel L Mintz
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Emily J Onufer
- Division of Pediatric Surgery, Department of Surgery, St. Louis Children's Hospital, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Beth A Helmink
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Keshav Sharma
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam Rosenstein
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danielle Ganjian
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Grace Chung
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Andrea Cerutti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Translational Clinical Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mayte Suarez-Farinas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gwendalyn J Randolph
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexandros D Polydorides
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrea Reboldi
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jean-Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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3
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Thompson KN, Bonham KS, Ilott NE, Britton GJ, Colmenero P, Bullers SJ, McIver LJ, Ma S, Nguyen LH, Filer A, Brough I, Pearson C, Moussa C, Kumar V, Lam LH, Jackson MA, Pawluk A, Kiriakidis S, Taylor PC, Wedderburn LR, Marsden B, Young SP, Littman DR, Faith JJ, Pratt AG, Bowness P, Raza K, Powrie F, Huttenhower C. Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes. Sci Transl Med 2023; 15:eabn4722. [PMID: 37494472 DOI: 10.1126/scitranslmed.abn4722] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
Musculoskeletal diseases affect up to 20% of adults worldwide. The gut microbiome has been implicated in inflammatory conditions, but large-scale metagenomic evaluations have not yet traced the routes by which immunity in the gut affects inflammatory arthritis. To characterize the community structure and associated functional processes driving gut microbial involvement in arthritis, the Inflammatory Arthritis Microbiome Consortium investigated 440 stool shotgun metagenomes comprising 221 adults diagnosed with rheumatoid arthritis, ankylosing spondylitis, or psoriatic arthritis and 219 healthy controls and individuals with joint pain without an underlying inflammatory cause. Diagnosis explained about 2% of gut taxonomic variability, which is comparable in magnitude to inflammatory bowel disease. We identified several candidate microbes with differential carriage patterns in patients with elevated blood markers for inflammation. Our results confirm and extend previous findings of increased carriage of typically oral and inflammatory taxa and decreased abundance and prevalence of typical gut clades, indicating that distal inflammatory conditions, as well as local conditions, correspond to alterations to the gut microbial composition. We identified several differentially encoded pathways in the gut microbiome of patients with inflammatory arthritis, including changes in vitamin B salvage and biosynthesis and enrichment of iron sequestration. Although several of these changes characteristic of inflammation could have causal roles, we hypothesize that they are mainly positive feedback responses to changes in host physiology and immune homeostasis. By connecting taxonomic alternations to functional alterations, this work expands our understanding of the shifts in the gut ecosystem that occur in response to systemic inflammation during arthritis.
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Affiliation(s)
- Kelsey N Thompson
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kevin S Bonham
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicholas E Ilott
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Graham J Britton
- Marc and Jennifer Lipschultz Precision Immunology Institute and Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paula Colmenero
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Samuel J Bullers
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Lauren J McIver
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Siyuan Ma
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Long H Nguyen
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Andrew Filer
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research and Research Into Inflammatory Arthritis Centre Versus Arthritis, University of Birmingham, Chesterfield S41 7TD, UK
| | - India Brough
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Claire Pearson
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Caroline Moussa
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Vinod Kumar
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Lilian H Lam
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Matthew A Jackson
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - April Pawluk
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Serafim Kiriakidis
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Peter C Taylor
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis, University College London, UCLH, and GOSH, Chesterfield S41 7TD, UK
- NIHR Great Ormond Street Biomedical Research Centre, University College London, London WC1N 1EH, UK
- UCL GOS Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Brian Marsden
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Stephen P Young
- Department of Rheumatology, Sandwell & West Birmingham NHS Trust, West Bromwich B71 4HJ, UK
| | - Dan R Littman
- Howard Hughes Medical Institute and the Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Jeremiah J Faith
- Marc and Jennifer Lipschultz Precision Immunology Institute and Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arthur G Pratt
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Research into Inflammatory Arthritis Centre Versus Arthritis, Newcastle Birmingham, Glasgow, and Oxford, Chesterfield S41 7TD, UK
- Department of Rheumatology, Musculoskeletal Services Directorate, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Paul Bowness
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Karim Raza
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research and Research Into Inflammatory Arthritis Centre Versus Arthritis, University of Birmingham, Chesterfield S41 7TD, UK
- Department of Rheumatology, Sandwell & West Birmingham NHS Trust, West Bromwich B71 4HJ, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Curtis Huttenhower
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
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4
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Louie T, Golan Y, Khanna S, Bobilev D, Erpelding N, Fratazzi C, Carini M, Menon R, Ruisi M, Norman JM, Faith JJ, Olle B, Li M, Silber JL, Pardi DS. VE303, a Defined Bacterial Consortium, for Prevention of Recurrent Clostridioides difficile Infection: A Randomized Clinical Trial. JAMA 2023; 329:1356-1366. [PMID: 37060545 PMCID: PMC10105904 DOI: 10.1001/jama.2023.4314] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/07/2023] [Indexed: 04/16/2023]
Abstract
Importance The effect of rationally defined nonpathogenic, nontoxigenic, commensal strains of Clostridia on prevention of Clostridioides difficile infection (CDI) is unknown. Objective To determine the efficacy of VE303, a defined bacterial consortium of 8 strains of commensal Clostridia, in adults at high risk for CDI recurrence. The primary objective was to determine the recommended VE303 dosing for a phase 3 trial. Design, Setting, and Participants Phase 2, randomized, double-blind, placebo-controlled, dose-ranging study conducted from February 2019 to September 2021 at 27 sites in the US and Canada. The study included 79 participants aged 18 years or older who were diagnosed with laboratory-confirmed CDI with 1 or more prior CDI episodes in the last 6 months and those with primary CDI at high risk for recurrence (defined as aged ≥75 years or ≥65 years with ≥1 risk factors: creatinine clearance <60 mL/min/1.73 m2, proton pump inhibitor use, remote [>6 months earlier] CDI history). Interventions Participants were randomly assigned to high-dose VE303 (8.0 × 109 colony-forming units [CFUs]) (n = 30), low-dose VE303 (1.6 × 109 CFUs) (n = 27), or placebo capsules (n = 22) orally once daily for 14 days. Main Outcomes and Measures The primary efficacy end point was the proportion of participants with CDI recurrence at 8 weeks using a combined clinical and laboratory definition. The primary efficacy end point was analyzed in 3 prespecified analyses, using successively broader definitions for an on-study CDI recurrence: (1) diarrhea consistent with CDI plus a toxin-positive stool sample; (2) diarrhea consistent with CDI plus a toxin-positive, polymerase chain reaction-positive, or toxigenic culture-positive stool sample; and (3) diarrhea consistent with CDI plus laboratory confirmation or (in the absence of a stool sample) treatment with a CDI-targeted antibiotic. Results Baseline characteristics were similar across the high-dose VE303 (n = 29; 1 additional participant excluded from efficacy analysis), low-dose VE303 (n = 27), and placebo (n = 22) groups. The participants' median age was 63.5 years (range, 24-96); 70.5% were female; and 1.3% were Asian, 1.3% Black, 2.6% Hispanic, and 96.2% White. CDI recurrence rates through week 8 (using the efficacy analysis 3 definition) were 13.8% (4/29) for high-dose VE303, 37.0% (10/27) for low-dose VE303, and 45.5% (10/22) for placebo (P = .006, high-dose VE303 vs placebo). Conclusions and Relevance Among adults with laboratory-confirmed CDI with 1 or more prior CDI episodes in the last 6 months and those with primary CDI at high risk for recurrence, high-dose VE303 prevented recurrent CDI compared with placebo. A larger, phase 3 study is needed to confirm these findings. Trial Registration ClinicalTrials.gov Identifier: NCT03788434.
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Affiliation(s)
- Thomas Louie
- University of Calgary and Foothills Medical Centre, Calgary, Alberta, Canada
| | - Yoav Golan
- Tufts Medical Center, Boston, Massachusetts
| | | | - Dmitri Bobilev
- Vedanta Biosciences Inc, Cambridge, Massachusetts
- Fusion Pharmaceuticals, Boston, Massachusetts
| | - Nathalie Erpelding
- Vedanta Biosciences Inc, Cambridge, Massachusetts
- Bicycle Therapeutics, Cambridge, Massachusetts
| | - Candida Fratazzi
- Vedanta Biosciences Inc, Cambridge, Massachusetts
- Boston Biotech Clinical Research, Natick, Massachusetts
| | - Meg Carini
- Vedanta Biosciences Inc, Cambridge, Massachusetts
| | - Rajita Menon
- Vedanta Biosciences Inc, Cambridge, Massachusetts
| | - Mary Ruisi
- Vedanta Biosciences Inc, Cambridge, Massachusetts
- C4 Therapeutics, Watertown, Massachusetts
| | | | | | - Bernat Olle
- Vedanta Biosciences Inc, Cambridge, Massachusetts
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5
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Spindler MP, Mogno I, Suri P, Britton GJ, Faith JJ. Species-specific CD4 + T cells enable prediction of mucosal immune phenotypes from microbiota composition. Proc Natl Acad Sci U S A 2023; 120:e2215914120. [PMID: 36917674 PMCID: PMC10041165 DOI: 10.1073/pnas.2215914120] [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: 09/17/2022] [Accepted: 01/27/2023] [Indexed: 03/16/2023] Open
Abstract
How bacterial strains within a complex human microbiota collectively shape intestinal T cell homeostasis is not well understood. Methods that quickly identify effector strains or species that drive specific mucosal T cell phenotypes are needed to define general principles for how the microbiota modulates host immunity. We colonize germ-free mice with defined communities of cultured strains and profile antigen-specific responses directed toward individual strains ex vivo. We find that lamina propria T cells are specific to bacterial strains at the species level and can discriminate between strains of the same species. Ex vivo restimulations consistently identify the strains within complex communities that induce Th17 responses in vivo, providing the potential to shape baseline immune tone via community composition. Using an adoptive transfer model of colitis, we find that lamina propria T cells respond to different bacterial strains in conditions of inflammation versus homeostasis. Collectively, our approach represents a unique method for efficiently predicting the relative impact of individual bacterial strains within a complex community and for parsing microbiota-dependent phenotypes into component fractions.
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Affiliation(s)
- Matthew P. Spindler
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Ilaria Mogno
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Prerna Suri
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Graham J. Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Jeremiah J. Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
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Plitt T, Faith JJ. Seminars in immunology special issue: Nutrition, microbiota and immunity The unexplored microbes in health and disease. Semin Immunol 2023; 66:101735. [PMID: 36857892 PMCID: PMC10049858 DOI: 10.1016/j.smim.2023.101735] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/17/2023] [Accepted: 02/09/2023] [Indexed: 03/03/2023]
Abstract
Functional characterization of the microbiome's influence on host physiology has been dominated by a few characteristic example strains that have been studied in detail. However, the extensive development of methods for high-throughput bacterial isolation and culture over the past decade is enabling functional characterization of the broader microbiota that may impact human health. Characterizing the understudied majority of human microbes and expanding our functional understanding of the diversity of the gut microbiota could enable new insights into diseases with unknown etiology, provide disease-predictive microbiome signatures, and advance microbial therapeutics. We summarize high-throughput culture-dependent platforms for characterizing bacterial strain function and host-interactions. We elaborate on the importance of these technologies in facilitating mechanistic studies of previously unexplored microbes, highlight new opportunities for large-scale in vitro screens of host-relevant microbial functions, and discuss the potential translational applications for microbiome science.
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Affiliation(s)
- Tamar Plitt
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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7
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Haskey N, Gold SL, Faith JJ, Raman M. To Fiber or Not to Fiber: The Swinging Pendulum of Fiber Supplementation in Patients with Inflammatory Bowel Disease. Nutrients 2023; 15:nu15051080. [PMID: 36904081 PMCID: PMC10005525 DOI: 10.3390/nu15051080] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Evidence-based dietary guidance around dietary fiber in inflammatory bowel disease (IBD) has been limited owing to insufficient reproducibility in intervention trials. However, the pendulum has swung because of our increased understanding of the importance of fibers in maintaining a health-associated microbiome. Preliminary evidence suggests that dietary fiber can alter the gut microbiome, improve IBD symptoms, balance inflammation, and enhance health-related quality of life. Therefore, it is now more vital than ever to examine how fiber could be used as a therapeutic strategy to manage and prevent disease relapse. At present, there is limited knowledge about which fibers are optimal and in what form and quantity they should be consumed to benefit patients with IBD. Additionally, individual microbiomes play a strong role in determining the outcomes and necessitate a more personalized nutritional approach to implementing dietary changes, as dietary fiber may not be as benign as once thought in a dysbiotic microbiome. This review describes dietary fibers and their mechanism of action within the microbiome, details novel fiber sources, including resistant starches and polyphenols, and concludes with potential future directions in fiber research, including the move toward precision nutrition.
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Affiliation(s)
- Natasha Haskey
- Department of Biology, The Irving K. Barber Faculty of Science, University of British Columbia—Okanagan, 3187 University Way, Kelowna, BC V1V 1V7, Canada
- Division of Gastroenterology, Cumming School of Medicine, University of Calgary, 6D33 TRW Building, 3280 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Stephanie L. Gold
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Jeremiah J. Faith
- Precision Immunology Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Maitreyi Raman
- Division of Gastroenterology, Cumming School of Medicine, University of Calgary, 6D33 TRW Building, 3280 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
- Correspondence:
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8
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Bianchimano P, Britton GJ, Wallach DS, Smith EM, Cox LM, Liu S, Iwanowski K, Weiner HL, Faith JJ, Clemente JC, Tankou SK. Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis. Microbiome 2022; 10:174. [PMID: 36253847 PMCID: PMC9575236 DOI: 10.1186/s40168-022-01364-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 07/08/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The gut microbiome plays an important role in autoimmunity including multiple sclerosis and its mouse model called experimental autoimmune encephalomyelitis (EAE). Prior studies have demonstrated that the multiple sclerosis gut microbiota can contribute to disease, hence making it a potential therapeutic target. In addition, antibiotic treatment has been shown to ameliorate disease in the EAE mouse model of multiple sclerosis. Yet, to this date, the mechanisms mediating these antibiotic effects are not understood. Furthermore, there is no consensus on the gut-derived bacterial strains that drive neuroinflammation in multiple sclerosis. RESULTS Here, we characterized the gut microbiome of untreated and vancomycin-treated EAE mice over time to identify bacteria with neuroimmunomodulatory potential. We observed alterations in the gut microbiota composition following EAE induction. We found that vancomycin treatment ameliorates EAE, and that this protective effect is mediated via the microbiota. Notably, we observed increased abundance of bacteria known to be strong inducers of regulatory T cells, including members of Clostridium clusters XIVa and XVIII in vancomycin-treated mice during the presymptomatic phase of EAE, as well as at disease peak. We identified 50 bacterial taxa that correlate with EAE severity. Interestingly, several of these taxa exist in the human gut, and some of them have been implicated in multiple sclerosis including Anaerotruncus colihominis, a butyrate producer, which had a positive correlation with disease severity. We found that Anaerotruncus colihominis ameliorates EAE, and this is associated with induction of RORγt+ regulatory T cells in the mesenteric lymph nodes. CONCLUSIONS We identified vancomycin as a potent modulator of the gut-brain axis by promoting the proliferation of bacterial species that induce regulatory T cells. In addition, our findings reveal 50 gut commensals as regulator of the gut-brain axis that can be used to further characterize pathogenic and beneficial host-microbiota interactions in multiple sclerosis patients. Our findings suggest that elevated Anaerotruncus colihominis in multiple sclerosis patients may represent a protective mechanism associated with recovery from the disease. Video Abstract.
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Affiliation(s)
- Paola Bianchimano
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
| | - Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David S Wallach
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma M Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
| | - Laura M Cox
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Shirong Liu
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Present address: Department of Medical Oncology, Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Kacper Iwanowski
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jose C Clemente
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephanie K Tankou
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA.
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA.
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9
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Spindler MP, Siu S, Mogno I, Li Z, Yang C, Mehandru S, Britton GJ, Faith JJ. Human gut microbiota stimulate defined innate immune responses that vary from phylum to strain. Cell Host Microbe 2022; 30:1481-1498.e5. [PMID: 36099923 PMCID: PMC9588646 DOI: 10.1016/j.chom.2022.08.009] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 06/10/2022] [Accepted: 08/15/2022] [Indexed: 11/03/2022]
Abstract
The potential of commensal bacteria to modulate host immunity remains largely uncharacterized, largely due to the vast number of strains that comprise the human gut microbiota. We have developed a screening platform to measure the innate immune responses of myeloid cells to 277 bacterial strains isolated from the gut microbiota of healthy individuals and those with inflammatory bowel diseases. The innate immune responses to gut-derived bacteria are as strong as those toward pathogenic bacteria, and they vary from phylum to strain. Myeloid cells differentially rely upon innate receptors TLR2 or TLR4 to sense taxa, with differential sensing of Bacteroidetes and Proteobacteria that predict in vivo functions. These innate immune responses can be modeled using combinations of up to 8 Toll-like receptor (TLR) agonists. Furthermore, the immunogenicity of strains is stable over time and following fecal microbiota transplantation into new human recipients. Collectively, this high-throughput approach provides an insight into how commensal microorganisms shape innate immune phenotypes.
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Affiliation(s)
- Matthew P Spindler
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sophia Siu
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ilaria Mogno
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhihua Li
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chao Yang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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10
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Yang C, Chen-Liaw A, Spindler MP, Tortorella D, Moran TM, Cerutti A, Faith JJ. Immunoglobulin A antibody composition is sculpted to bind the self gut microbiome. Sci Immunol 2022; 7:eabg3208. [PMID: 35857580 PMCID: PMC9421563 DOI: 10.1126/sciimmunol.abg3208] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Despite being the most abundantly secreted immunoglobulin isotype, the pattern of reactivity of immunoglobulin A (IgA) antibodies toward each individual's own gut commensal bacteria still remains elusive. By colonizing germ-free mice with defined commensal bacteria, we found that the binding specificity of bulk fecal and serum IgA toward resident gut bacteria resolves well at the species level and has modest strain-level specificity. IgA hybridomas generated from lamina propria B cells of gnotobiotic mice showed that most IgA clones recognized a single bacterial species, whereas a small portion displayed cross-reactivity. Orally administered hybridoma-produced IgAs still retained bacterial antigen binding capability, implying the potential for a new class of therapeutic antibodies. Species-specific IgAs had a range of strain specificities. Given the distinctive bacterial species and strain composition found in each individual's gut, our findings suggest the IgA antibody repertoire is shaped uniquely to bind "self" gut bacteria.
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Affiliation(s)
- Chao Yang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alice Chen-Liaw
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew P. Spindler
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Domenico Tortorella
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Thomas M. Moran
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Therapeutic Antibody Development, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrea Cerutti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona 08003, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona 08003, Spain
| | - Jeremiah J. Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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11
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Centa M, Weinstein EG, Clemente JC, Faith JJ, Fiel MI, Lyallpuri R, Herbin O, Alexandropoulos K. Impaired central tolerance induces changes in the gut microbiota that exacerbate autoimmune hepatitis. J Autoimmun 2022; 128:102808. [PMID: 35276587 PMCID: PMC8963681 DOI: 10.1016/j.jaut.2022.102808] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/10/2022] [Accepted: 02/19/2022] [Indexed: 12/18/2022]
Abstract
Medullary thymic epithelial cells (mTECs) induce T cell tolerance in the thymus through the elimination of self-reactive thymocytes. Commensal bacteria are also critical for shaping T cell responses in the gut and distal organs. We previously showed that mice depleted of mTECs (Traf6ΔTEC) generated autoreactive T cells and developed autoimmune hepatitis (AIH). In this report, we found that Toll-like receptor (TLR)-mediated microbial sensing on liver hematopoietic cells and the gut microbiota contributed to AIH development in Traf6ΔTEC mice. While adoptive transfer of thymic Traf6ΔTEC T cells in immune-deficient mice was sufficient for AIH development, colonization of germ-free mice with Traf6ΔTEC microbiota failed to induce AIH, suggesting that the gut microbiota contributes to but is not sufficient for AIH development. Microbiota-mediated exacerbation of AIH associated with increased numbers of hepatic Foxp3+ T cells and their increase was proportional to the degree of inflammation. The contribution of the gut microbiota to AIH development associated with an altered microbial signature whose composition was influenced by the qualitative nature of the thymic T cell compartment. These results suggest that aberrant selection of T cells in the thymus can induce changes in the gut microbiota that lead to exacerbation of organ-specific autoimmunity and AIH. Our results add to our understanding of the mechanisms of AIH development and create a platform towards developing novel therapeutic approaches for treating this disease.
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Affiliation(s)
- Monica Centa
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Jose C Clemente
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah J Faith
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Isabel Fiel
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robby Lyallpuri
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Konstantina Alexandropoulos
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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12
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Spindler MP, Faith JJ, Wang J, Kenny PJ. Gut clues to weight gain after quitting smoking. Nature 2021; 600:611-612. [PMID: 34880480 DOI: 10.1038/d41586-021-03548-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Despite identification of numerous associations between microbiomes and diseases, the complexity of the human microbiome has hindered identification of individual species and strains that are causative in host phenotype or disease. Uncovering causative microbes is vital to fully understand disease processes and to harness the potential therapeutic benefits of microbiota manipulation. Developments in sequencing technology, animal models, and bacterial culturing have facilitated the discovery of specific microbes that impact the host and are beginning to advance the characterization of host-microbiome interaction mechanisms. We summarize the historical and contemporary experimental approaches taken to uncover microbes from the microbiota that affect host biology and describe examples of commensals that have specific effects on the immune system, inflammation, and metabolism. There is still much to learn, and we lay out challenges faced by the field and suggest potential remedies for common pitfalls encountered in the hunt for causative commensal microbes. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; .,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; .,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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14
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Fan TJ, Goeser L, Lu K, Faith JJ, Hansen JJ. Enterococcus faecalis Glucosamine Metabolism Exacerbates Experimental Colitis. Cell Mol Gastroenterol Hepatol 2021; 12:1373-1389. [PMID: 34246809 PMCID: PMC8479252 DOI: 10.1016/j.jcmgh.2021.06.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS The inflammatory bowel diseases (IBDs), Crohn's disease and ulcerative colitis, are caused in part by aberrant immune responses to resident intestinal bacteria. Certain dietary components, including carbohydrates, are associated with IBDs and alter intestinal bacterial composition. However, the effects of luminal carbohydrates on the composition and colitogenic potential of intestinal bacteria are incompletely understood. We hypothesize that carbohydrate metabolism by resident proinflammatory intestinal bacteria enhances their growth and worsens intestinal inflammation. METHODS We colonized germ-free, wild-type, and colitis-susceptible interleukin-10 knockout mice (Il10-/-) with a consortium of resident intestinal bacterial strains and quantified colon inflammation using blinded histologic scoring and spontaneous secretion of IL12/23p40 by colon explants. We measured luminal bacterial composition using real-time 16S polymerase chain reaction, bacterial gene expression using RNA sequencing and real-time polymerase chain reaction, and luminal glucosamine levels using gas chromatography-mass spectrometry. RESULTS We show that a consortium of 8 bacterial strains induces severe colitis in Il10-/- mice and up-regulates genes associated with carbohydrate metabolism during colitis. Specifically, Enterococcus faecalis strain OG1RF is proinflammatory and strongly up-regulates OG1RF_11616-11610, an operon that encodes genes of a previously undescribed phosphotransferase system that we show imports glucosamine. Experimental colitis is associated with increased levels of luminal glucosamine and OG1RF_11616 causes worse colitis, not by increasing E faecalis numbers, but rather by mechanisms that require the presence of complex microbiota. CONCLUSIONS Further studies of luminal carbohydrate levels and bacterial carbohydrate metabolism during intestinal inflammation will improve our understanding of the pathogenesis of IBDs and may lead to the development of novel therapies for these diseases.
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Affiliation(s)
- Ting-Jia Fan
- Center for Gastrointestinal Biology and Disease, Chapel Hill, North Carolina; Department of Microbiology and Immunology, Chapel Hill, North Carolina
| | - Laura Goeser
- Center for Gastrointestinal Biology and Disease, Chapel Hill, North Carolina
| | - Kun Lu
- Department of Environmental Sciences and Engineering, Chapel Hill, North Carolina
| | - Jeremiah J Faith
- The Precision Immunology Institute, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jonathan J Hansen
- Center for Gastrointestinal Biology and Disease, Chapel Hill, North Carolina; Department of Microbiology and Immunology, Chapel Hill, North Carolina; Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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15
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He Z, Chen L, Catalan-Dibene J, Bongers G, Faith JJ, Suebsuwong C, DeVita RJ, Shen Z, Fox JG, Lafaille JJ, Furtado GC, Lira SA. Food colorants metabolized by commensal bacteria promote colitis in mice with dysregulated expression of interleukin-23. Cell Metab 2021; 33:1358-1371.e5. [PMID: 33989521 PMCID: PMC8266754 DOI: 10.1016/j.cmet.2021.04.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/26/2021] [Accepted: 04/20/2021] [Indexed: 12/26/2022]
Abstract
Both genetic predisposition and environmental factors appear to play a role in inflammatory bowel disease (IBD) development. Genetic studies in humans have linked the interleukin (IL)-23 signaling pathway with IBD, but the environmental factors contributing to disease have remained elusive. Here, we show that the azo dyes Red 40 and Yellow 6, the most abundant food colorants in the world, can trigger an IBD-like colitis in mice conditionally expressing IL-23, or in two additional animal models in which IL-23 expression was augmented. Increased IL-23 expression led to generation of activated CD4+ T cells that expressed interferon-γ and transferred disease to mice exposed to Red 40. Colitis induction was dependent on the commensal microbiota promoting the azo reduction of Red 40 and generation of a metabolite, 1-amino-2-naphthol-6-sulfonate sodium salt. Together these findings suggest that specific food colorants represent novel risk factors for development of colitis in mice with increased IL-23 signaling.
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Affiliation(s)
- Zhengxiang He
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lili Chen
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Jovani Catalan-Dibene
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gerold Bongers
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chalada Suebsuwong
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert J DeVita
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Juan J Lafaille
- Department of Pathology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Glaucia C Furtado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio A Lira
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Britton GJ, Chen-Liaw A, Cossarini F, Livanos AE, Spindler MP, Plitt T, Eggers J, Mogno I, Gonzalez-Reiche AS, Siu S, Tankelevich M, Grinspan LT, Dixon RE, Jha D, van de Guchte A, Khan Z, Martinez-Delgado G, Amanat F, Hoagland DA, tenOever BR, Dubinsky MC, Merad M, van Bakel H, Krammer F, Bongers G, Mehandru S, Faith JJ. Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19. Sci Rep 2021; 11:13308. [PMID: 34172783 PMCID: PMC8233421 DOI: 10.1038/s41598-021-92740-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [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: 01/29/2021] [Accepted: 06/10/2021] [Indexed: 12/20/2022] Open
Abstract
Gastrointestinal symptoms are common in COVID-19 patients but the nature of the gut immune response to SARS-CoV-2 remains poorly characterized, partly due to the difficulty of obtaining biopsy specimens from infected individuals. In lieu of tissue samples, we measured cytokines, inflammatory markers, viral RNA, microbiome composition, and antibody responses in stool samples from a cohort of 44 hospitalized COVID-19 patients. SARS-CoV-2 RNA was detected in stool of 41% of patients and more frequently in patients with diarrhea. Patients who survived had lower fecal viral RNA than those who died. Strains isolated from stool and nasopharynx of an individual were the same. Compared to uninfected controls, COVID-19 patients had higher fecal levels of IL-8 and lower levels of fecal IL-10. Stool IL-23 was higher in patients with more severe COVID-19 disease, and we found evidence of intestinal virus-specific IgA responses associated with more severe disease. We provide evidence for an ongoing humeral immune response to SARS-CoV-2 in the gastrointestinal tract, but little evidence of overt inflammation.
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Affiliation(s)
- Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alice Chen-Liaw
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Francesca Cossarini
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexandra E Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matthew P Spindler
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tamar Plitt
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joseph Eggers
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ilaria Mogno
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ana S Gonzalez-Reiche
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sophia Siu
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Tankelevich
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lauren Tal Grinspan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rebekah E Dixon
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Divya Jha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adriana van de Guchte
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zenab Khan
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gustavo Martinez-Delgado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daisy A Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla C Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Harm van Bakel
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gerold Bongers
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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17
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Livanos AE, Jha D, Cossarini F, Gonzalez-Reiche AS, Tokuyama M, Aydillo T, Parigi TL, Ladinsky MS, Ramos I, Dunleavy K, Lee B, Dixon RE, Chen ST, Martinez-Delgado G, Nagula S, Bruce EA, Ko HM, Glicksberg BS, Nadkarni G, Pujadas E, Reidy J, Naymagon S, Grinspan A, Ahmad J, Tankelevich M, Bram Y, Gordon R, Sharma K, Houldsworth J, Britton GJ, Chen-Liaw A, Spindler MP, Plitt T, Wang P, Cerutti A, Faith JJ, Colombel JF, Kenigsberg E, Argmann C, Merad M, Gnjatic S, Harpaz N, Danese S, Cordon-Cardo C, Rahman A, Schwartz RE, Kumta NA, Aghemo A, Bjorkman PJ, Petralia F, van Bakel H, Garcia-Sastre A, Mehandru S. Intestinal Host Response to SARS-CoV-2 Infection and COVID-19 Outcomes in Patients With Gastrointestinal Symptoms. Gastroenterology 2021; 160:2435-2450.e34. [PMID: 33676971 PMCID: PMC7931673 DOI: 10.1053/j.gastro.2021.02.056] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Given that gastrointestinal (GI) symptoms are a prominent extrapulmonary manifestation of COVID-19, we investigated intestinal infection with SARS-CoV-2, its effect on pathogenesis, and clinical significance. METHODS Human intestinal biopsy tissues were obtained from patients with COVID-19 (n = 19) and uninfected control individuals (n = 10) for microscopic examination, cytometry by time of flight analyses, and RNA sequencing. Additionally, disease severity and mortality were examined in patients with and without GI symptoms in 2 large, independent cohorts of hospitalized patients in the United States (N = 634) and Europe (N = 287) using multivariate logistic regressions. RESULTS COVID-19 case patients and control individuals in the biopsy cohort were comparable for age, sex, rates of hospitalization, and relevant comorbid conditions. SARS-CoV-2 was detected in small intestinal epithelial cells by immunofluorescence staining or electron microscopy in 15 of 17 patients studied. High-dimensional analyses of GI tissues showed low levels of inflammation, including down-regulation of key inflammatory genes including IFNG, CXCL8, CXCL2, and IL1B and reduced frequencies of proinflammatory dendritic cells compared with control individuals. Consistent with these findings, we found a significant reduction in disease severity and mortality in patients presenting with GI symptoms that was independent of sex, age, and comorbid illnesses and despite similar nasopharyngeal SARS-CoV-2 viral loads. Furthermore, there was reduced levels of key inflammatory proteins in circulation in patients with GI symptoms. CONCLUSIONS These data highlight the absence of a proinflammatory response in the GI tract despite detection of SARS-CoV-2. In parallel, reduced mortality in patients with COVID-19 presenting with GI symptoms was observed. A potential role of the GI tract in attenuating SARS-CoV-2-associated inflammation needs to be further examined.
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Affiliation(s)
- Alexandra E Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Divya Jha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Francesca Cossarini
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Minami Tokuyama
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tommaso L Parigi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Irene Ramos
- Department of Neurology and Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Katie Dunleavy
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brian Lee
- Human Immune Monitoring Center (HIMC) Icahn School of Medicine at Mount Sinai New York, New York, New York
| | - Rebekah E Dixon
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Steven T Chen
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gustavo Martinez-Delgado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Satish Nagula
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Emily A Bruce
- Division of Immunobiology, Department of Medicine, University of Vermont, Larner College of Medicine, Burlington, Vermont
| | - Huaibin M Ko
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Girish Nadkarni
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; The Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elisabet Pujadas
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jason Reidy
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Steven Naymagon
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ari Grinspan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jawad Ahmad
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael Tankelevich
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Ronald Gordon
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Keshav Sharma
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jane Houldsworth
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alice Chen-Liaw
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Matthew P Spindler
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tamar Plitt
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrea Cerutti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Catalan Institute for Research and Advanced Studies, Barcelona, Spain; Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jean-Frederic Colombel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ephraim Kenigsberg
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center (HIMC) Icahn School of Medicine at Mount Sinai New York, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sacha Gnjatic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center (HIMC) Icahn School of Medicine at Mount Sinai New York, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Noam Harpaz
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Silvio Danese
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Carlos Cordon-Cardo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Adeeb Rahman
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center (HIMC) Icahn School of Medicine at Mount Sinai New York, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Nikhil A Kumta
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alessio Aghemo
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Adolfo Garcia-Sastre
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
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Carter JK, Bhattacharya D, Borgerding JN, Fiel MI, Faith JJ, Friedman SL. Modeling dysbiosis of human NASH in mice: Loss of gut microbiome diversity and overgrowth of Erysipelotrichales. PLoS One 2021; 16:e0244763. [PMID: 33395434 PMCID: PMC7781477 DOI: 10.1371/journal.pone.0244763] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 10/14/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Background & aim Non-alcoholic steatohepatitis (NASH) is a severe form of non-alcoholic fatty liver disease (NAFLD) that is responsible for a growing fraction of cirrhosis and liver cancer cases worldwide. Changes in the gut microbiome have been implicated in NASH pathogenesis, but the lack of suitable murine models has been a barrier to progress. We have therefore characterized the microbiome in a well-validated murine NASH model to establish its value in modeling human disease. Methods The composition of intestinal microbiota was monitored in mice on a 12- or 24-week NASH protocol consisting of high fat, high sugar Western Diet (WD) plus once weekly i.p injection of low-dose CCl4. Additional mice were subjected to WD-only or CCl4-only conditions to assess the independent effect of these variables on the microbiome. Results There was substantial remodeling of the intestinal microbiome in NASH mice, characterized by declines in both species diversity and bacterial abundance. Based on changes to beta diversity, microbiota from NASH mice clustered separately from controls in principal coordinate analyses. A comparison between WD-only and CCl4-only controls with the NASH model identified WD as the primary driver of early changes to the microbiome, resulting in loss of diversity within the 1st week. A NASH signature emerged progressively at weeks 6 and 12, including, most notably, a reproducible bloom of the Firmicute order Erysipelotrichales. Conclusions We have established a valuable model to study the role of gut microbes in NASH, enabling us to identify a new NASH gut microbiome signature.
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Affiliation(s)
- James K. Carter
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Dipankar Bhattacharya
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Joshua N. Borgerding
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - M. Isabel Fiel
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jeremiah J. Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Scott L. Friedman
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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19
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Britton GJ, Chen-Liaw A, Cossarini F, Livanos AE, Spindler MP, Plitt T, Eggers J, Mogno I, Gonzalez-Reiche AS, Siu S, Tankelevich M, Grinspan LT, Dixon RE, Jha D, van de Guchte A, Khan Z, Martinez-Delgado G, Amanat F, Hoagland DA, tenOever BR, Dubinsky MC, Merad M, van Bakel H, Krammer F, Bongers G, Mehandru S, Faith JJ. Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19. medRxiv 2020:2020.09.03.20183947. [PMID: 32909002 PMCID: PMC7480054 DOI: 10.1101/2020.09.03.20183947] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We sought to characterize the role of the gastrointestinal immune system in the pathogenesis of the inflammatory response associated with COVID-19. We measured cytokines, inflammatory markers, viral RNA, microbiome composition and antibody responses in stool from a cohort of 44 hospitalized COVID-19 patients. SARS-CoV-2 RNA was detected in stool of 41% of patients and more frequently in patients with diarrhea. Patients who survived had lower fecal viral RNA than those who died. Strains isolated from stool and nasopharynx of an individual were the same. Compared to uninfected controls, COVID-19 patients had higher fecal levels of IL-8 and lower levels of fecal IL-10. Stool IL-23 was higher in patients with more severe COVID-19 disease, and we found evidence of intestinal virus-specific IgA responses associated with more severe disease. We provide evidence for an ongoing humeral immune response to SARS-CoV-2 in the gastrointestinal tract, but little evidence of overt inflammation.
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Affiliation(s)
- Graham J. Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Alice Chen-Liaw
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Francesca Cossarini
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Alexandra E. Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Matthew P. Spindler
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Tamar Plitt
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Joseph Eggers
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ilaria Mogno
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Ana S. Gonzalez-Reiche
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Sophia Siu
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Michael Tankelevich
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Lauren Tal Grinspan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Rebekah E. Dixon
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Divya Jha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Adriana van de Guchte
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Zenab Khan
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Gustavo Martinez-Delgado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029
| | - Daisy A. Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Benjamin R. tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla C. Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Harm van Bakel
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gerold Bongers
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jeremiah J. Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
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20
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Livanos AE, Jha D, Cossarini F, Gonzalez-Reiche AS, Tokuyama M, Aydillo T, Parigi TL, Ramos I, Dunleavy K, Lee B, Dixon R, Chen ST, Martinez-Delgado G, Nagula S, Ko HM, Glicksberg BS, Nadkarni G, Pujadas E, Reidy J, Naymagon S, Grinspan A, Ahmad J, Tankelevich M, Gordon R, Sharma K, Houldsworth J, Britton GJ, Chen-Liaw A, Spindler MP, Plitt T, Wang P, Cerutti A, Faith JJ, Colombel JF, Kenigsberg E, Argmann C, Merad M, Gnjatic S, Harpaz N, Danese S, Cordon-Cardo C, Rahman A, Kumta NA, Aghemo A, Petralia F, van Bakel H, Garcia-Sastre A, Mehandru S. Gastrointestinal involvement attenuates COVID-19 severity and mortality. medRxiv 2020. [PMID: 32935117 DOI: 10.1101/2020.09.07.20187666] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Given that gastrointestinal (GI) symptoms are a prominent extrapulmonary manifestation of coronavirus disease 2019 (COVID-19), we investigated intestinal infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its effect on disease pathogenesis. SARS-CoV-2 was detected in small intestinal enterocytes by immunofluorescence staining or electron microscopy, in 13 of 15 patients studied. High dimensional analyses of GI tissues revealed low levels of inflammation in general, including active downregulation of key inflammatory genes such as IFNG, CXCL8, CXCL2 and IL1B and reduced frequencies of proinflammatory dendritic cell subsets. To evaluate the clinical significance of these findings, examination of two large, independent cohorts of hospitalized patients in the United States and Europe revealed a significant reduction in disease severity and mortality that was independent of gender, age, and examined co-morbid illnesses. The observed mortality reduction in COVID-19 patients with GI symptoms was associated with reduced levels of key inflammatory proteins including IL-6, CXCL8, IL-17A and CCL28 in circulation but was not associated with significant differences in nasopharyngeal viral loads. These data draw attention to organ-level heterogeneity in disease pathogenesis and highlight the role of the GI tract in attenuating SARS-CoV-2-associated inflammation with related mortality benefit. One Sentence Summary Intestinal infection with SARS-CoV-2 is associated with a mild inflammatory response and improved clinical outcomes.
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21
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Leonardi I, Paramsothy S, Doron I, Semon A, Kaakoush NO, Clemente JC, Faith JJ, Borody TJ, Mitchell HM, Colombel JF, Kamm MA, Iliev ID. Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis. Cell Host Microbe 2020; 27:823-829.e3. [PMID: 32298656 DOI: 10.1016/j.chom.2020.03.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [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: 01/29/2020] [Revised: 02/10/2020] [Accepted: 03/11/2020] [Indexed: 02/06/2023]
Abstract
Fecal microbiota transplantation (FMT) targeting gut microbiota has recently been successfully applied to ulcerative colitis. However, only a subset of patients responds to FMT, and there is a pressing need for biomarkers of responsiveness. Fungi (the mycobiota) represent a highly immunologically reactive component of the gut microbiota. We analyzed samples from a large randomized controlled trial of FMT for ulcerative colitis (UC). High Candida abundance pre-FMT was associated with a clinical response, whereas decreased Candida abundance post-FMT was indicative of ameliorated disease severity. High pre-FMT Candida was associated with increased bacterial diversity post-FMT, and the presence of genera was linked to FMT responsiveness. Although we detected elevated anti-Candida antibodies in placebo recipients, this increase was abrogated in FMT recipients. Our data suggest that FMT might reduce Candida to contain pro-inflammatory immunity during intestinal disease and highlight the utility of mycobiota-focused approaches to identify FMT responders prior to therapy initiation.
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Affiliation(s)
- Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Sudarshan Paramsothy
- University of New South Wales, Sydney NSW 2052, Australia; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Concord Repatriation General Hospital, Sydney, NSW 2139, Australia
| | - Itai Doron
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Alexa Semon
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | | | - Jose C Clemente
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeremiah J Faith
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | | | - Michael A Kamm
- St. Vincent's Hospital and University of Melbourne, Melbourne, VIC 3065, Australia
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
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22
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Yang C, Mogno I, Contijoch EJ, Borgerding JN, Aggarwala V, Li Z, Siu S, Grasset EK, Helmus DS, Dubinsky MC, Mehandru S, Cerutti A, Faith JJ. Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation. Cell Host Microbe 2020; 27:467-475.e6. [PMID: 32075742 DOI: 10.1016/j.chom.2020.01.016] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [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: 08/23/2019] [Revised: 11/15/2019] [Accepted: 01/21/2020] [Indexed: 02/07/2023]
Abstract
Fecal IgA production depends on colonization by a gut microbiota. However, the bacterial strains that drive gut IgA production remain largely unknown. Here, we assessed the IgA-inducing capacity of a diverse set of human gut microbial strains by monocolonizing mice with each strain. We identified Bacteroides ovatus as the species that best induced gut IgA production. However, this induction varied bimodally across different B. ovatus strains. The high IgA-inducing B. ovatus strains preferentially elicited more IgA production in the large intestine through the T cell-dependent B cell-activation pathway. Remarkably, a low-IgA phenotype in mice could be robustly and consistently converted into a high-IgA phenotype by transplanting a multiplex cocktail of high IgA-inducing B. ovatus strains but not individual ones. Our results highlight the critical importance of microbial strains in driving phenotype variation in the mucosal immune system and provide a strategy to robustly modify a gut immune phenotype, including IgA production.
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Affiliation(s)
- Chao Yang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ilaria Mogno
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eduardo J Contijoch
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua N Borgerding
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Varun Aggarwala
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhihua Li
- Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sophia Siu
- Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emilie K Grasset
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | - Drew S Helmus
- Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Susan and Leonard Feinstein IBD Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marla C Dubinsky
- Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Susan and Leonard Feinstein IBD Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrea Cerutti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona 08003, Spain; Catalan Institute for Advanced Studies (ICREA), Barcelona 08003, Spain
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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23
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Torres J, Hu J, Seki A, Eisele C, Nair N, Huang R, Tarassishin L, Jharap B, Cote-Daigneault J, Mao Q, Mogno I, Britton GJ, Uzzan M, Chen CL, Kornbluth A, George J, Legnani P, Maser E, Loudon H, Stone J, Dubinsky M, Faith JJ, Clemente JC, Mehandru S, Colombel JF, Peter I. Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice. Gut 2020; 69:42-51. [PMID: 31036757 DOI: 10.1136/gutjnl-2018-317855] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [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: 11/02/2018] [Revised: 03/19/2019] [Accepted: 04/09/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Prenatal and early life bacterial colonisation is thought to play a major role in shaping the immune system. Furthermore, accumulating evidence links early life exposures to the risk of developing IBD later in life. We aimed to assess the effect of maternal IBD on the composition of the microbiome during pregnancy and on the offspring's microbiome. METHODS We prospectively examined the diversity and taxonomy of the microbiome of pregnant women with and without IBD and their babies at multiple time points. We evaluated the role of maternal IBD diagnosis, the mode of delivery, antibiotic use and feeding behaviour on the microbiome composition during early life. To assess the effects of IBD-associated maternal and infant microbiota on the enteric immune system, we inoculated germ-free mice (GFM) with the respective stool and profiled adaptive and innate immune cell populations in the murine intestines. RESULTS Pregnant women with IBD and their offspring presented with lower bacterial diversity and altered bacterial composition compared with control women and their babies. Maternal IBD was the main predictor of the microbiota diversity in the infant gut at 7, 14, 30, 60 and 90 days of life. Babies born to mothers with IBD demonstrated enrichment in Gammaproteobacteria and depletion in Bifidobacteria. Finally, GFM inoculated with third trimester IBD mother and 90-day infant stools showed significantly reduced microbial diversity and fewer class-switched memory B cells and regulatory T cells in the colon. CONCLUSION Aberrant gut microbiota composition persists during pregnancy with IBD and alters the bacterial diversity and abundance in the infant stool. The dysbiotic microbiota triggered abnormal imprinting of the intestinal immune system in GFM.
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Affiliation(s)
- Joana Torres
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Department of Gastroenterology, Hospital Beatriz Angelo, Loures, Portugal
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Akihiro Seki
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Caroline Eisele
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Nilendra Nair
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Ruiqi Huang
- Department of Health Evidence and Policy, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Leonid Tarassishin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Bindia Jharap
- Department of Gastroenterology and Hepatology, Meander Medical Center, Amersfoort, The Netherlands
| | - Justin Cote-Daigneault
- Department of Gastroenterology, Centre Hospitalier de L'Universite de Montreal, Montreal, Quebec, Canada
| | - Qixing Mao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Naijing, China
| | - Ilaria Mogno
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Graham J Britton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,The Precision Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Mathieu Uzzan
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Ching-Lynn Chen
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Asher Kornbluth
- Department of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - James George
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Peter Legnani
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Elana Maser
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Holly Loudon
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Joanne Stone
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Marla Dubinsky
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Jeremiah J Faith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Saurabh Mehandru
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Jean-Frederic Colombel
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
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24
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Chen L, Strohmeier V, He Z, Deshpande M, Catalan-Dibene J, Durum SK, Moran TM, Kraus T, Xiong H, Faith JJ, Sodhi CP, Hackam DJ, Lira SA, Furtado GC. Interleukin 22 disrupts pancreatic function in newborn mice expressing IL-23. Nat Commun 2019; 10:4517. [PMID: 31586069 PMCID: PMC6778080 DOI: 10.1038/s41467-019-12540-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 09/19/2018] [Accepted: 09/17/2019] [Indexed: 12/19/2022] Open
Abstract
Neonatal inflammatory diseases are associated with severe morbidity, but the inflammatory factors underlying them and their potential effector mechanisms are poorly defined. Here we show that necrotizing enterocolitis in neonate mice is accompanied by elevation of IL-23 and IL-22 and decreased production of pancreatic enzymes. These phenotypes are mirrored in neonate mice overexpressing IL-23 in CX3CR1+ myeloid cells or in keratinocytes. The mice fail to grow and die prematurely, displaying systemic inflammation, nutrient malabsorption and decreased expression of intestinal and pancreatic genes mediating digestion and absorption of carbohydrates, proteins, and lipids. Germ-free environment improves, and genetic ablation of IL-22 restores normal growth in mice overexpressing IL-23. Mechanistically, IL-22 acts directly at the level of pancreatic acinar cells to decrease expression of the pancreas associated transcription factor 1a (PTF1a). These results show that augmented production of IL-23 and IL-22 in early life has a negative impact on pancreatic enzyme secretion and food absorption.
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Affiliation(s)
- Lili Chen
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Valentina Strohmeier
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Zhengxiang He
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Madhura Deshpande
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jovani Catalan-Dibene
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Scott K Durum
- Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Thomas M Moran
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Therapeutic Antibody Development, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Thomas Kraus
- Center for Therapeutic Antibody Development, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Huabao Xiong
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chhinder P Sodhi
- Division of General Pediatric Surgery, Johns Hopkins University and Bloomberg Children's Center, Johns Hopkins Hospital, Baltimore, MD, 21287, USA
| | - David J Hackam
- Division of General Pediatric Surgery, Johns Hopkins University and Bloomberg Children's Center, Johns Hopkins Hospital, Baltimore, MD, 21287, USA
| | - Sergio A Lira
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Glaucia C Furtado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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25
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Pizarro TT, Stappenbeck TS, Rieder F, Rosen MJ, Colombel JF, Donowitz M, Towne J, Mazmanian SK, Faith JJ, Hodin RA, Garrett WS, Fichera A, Poritz LS, Cortes CJ, Shtraizent N, Honig G, Snapper SB, Hurtado-Lorenzo A, Salzman NH, Chang EB. Challenges in IBD Research: Preclinical Human IBD Mechanisms. Inflamm Bowel Dis 2019; 25:S5-S12. [PMID: 31095706 DOI: 10.1093/ibd/izz075] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [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: 03/29/2019] [Indexed: 12/21/2022]
Abstract
Preclinical human IBD mechanisms is part of five focus areas of the Challenges in IBD research document, which also include environmental triggers, novel technologies, precision medicine and pragmatic clinical research. The Challenges in IBD research document provides a comprehensive overview of current gaps in inflammatory bowel diseases (IBD) research and delivers actionable approaches to address them. It is the result of a multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient centric research prioritization. In particular, the preclinical human IBD mechanisms manuscript is focused on highlighting the main research gaps in the pathophysiological understanding of human IBD. These research gap areas include: 1) triggers of immune responses; 2) intestinal epithelial homeostasis and wound repair; 3) age-specific pathophysiology; 4) disease complications; 5) heterogeneous response to treatments; and 6) determination of disease location. As an approach to address these research gaps, the prioritization of reverse translation studies is proposed in which clinical observations are the foundation for experimental IBD research in the lab, and for the identification of new therapeutic targets and biomarkers. The use of human samples in validating basic research findings and development of precision medicine solutions is also proposed. This prioritization aims to put emphasis on relevant biochemical pathways and humanized in vitro and in vivo models that extrapolate meaningfully to human IBD, to eventually yield first-in-class and effective therapies.
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Affiliation(s)
- Theresa T Pizarro
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | | | | | - Michael J Rosen
- Cincinnati Children's Hospital and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Mark Donowitz
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | - Richard A Hodin
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wendy S Garrett
- School of Public Health, Harvard University, Boston, MA, USA
| | | | - Lisa S Poritz
- Pennsylvania State University College of Medicine, Hershey, PA, USA
| | | | | | | | - Scott B Snapper
- Harvard Medical School and Boston Children's Hospital, Boston, MA, USA
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26
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Hirten RP, Grinspan A, Fu SC, Luo Y, Suarez-Farinas M, Rowland J, Contijoch EJ, Mogno I, Yang N, Luong T, Labrias PR, Peter I, Cho JH, Sands BE, Colombel JF, Faith JJ, Clemente JC. Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium Difficile in Patients With and Without Inflammatory Bowel Disease. Inflamm Bowel Dis 2019; 25:969-979. [PMID: 30852592 PMCID: PMC6499938 DOI: 10.1093/ibd/izy398] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 08/27/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Recurrent and severe Clostridium difficile infections (CDI) are treated with fecal microbiota transplant (FMT). Uncertainty exists regarding FMT effectiveness for CDI with underlying inflammatory bowel disease (IBD) and regarding its effects on disease activity and effectiveness in transferring the donor microbiota to patients with and without IBD. METHODS Subjects with and without IBD who underwent FMT for recurrent or severe CDI between 2013 and 2016 at The Mount Sinai Hospital were followed for up to 6 months. The primary outcome was CDI recurrence 6 months after FMT. Secondary outcomes were (1) CDI recurrence 2 months after FMT; (2) frequency of IBD flare after FMT; (3) microbiota engraftment after FMT; (and 4) predictors of CDI recurrence. RESULTS One hundred thirty-four patients, 46 with IBD, were treated with FMT. Follow-up was available in 83 and 118 patients at 6 and 2 months, respectively. There was no difference in recurrence in patients with and without IBD at 6 months (38.7% vs 36.5%; P > 0.99) and 2 months (22.5% vs 17.9%; P = 0.63). Proton pump inhibitor use, severe CDI, and comorbid conditions were predictors of recurrence. Pre-FMT microbiota was not predictive of CDI recurrence. Subjects with active disease requiring medication escalation had reduced engraftment, with no difference in engraftment based on CDI recurrence or IBD endoscopic severity at FMT. CONCLUSIONS Inflammatory bowel disease did not affect CDI recurrence rates 6 months after FMT. Pre-FMT microbiota was not predictive of recurrence, and microbial engraftment was impacted in those requiring IBD treatment escalation, though not by CDI recurrence or IBD disease severity.
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Affiliation(s)
- Robert P Hirten
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ari Grinspan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shih-Chen Fu
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Yuying Luo
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mayte Suarez-Farinas
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Rowland
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eduardo J Contijoch
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Ilaria Mogno
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Nancy Yang
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tramy Luong
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Philippe R Labrias
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Inga Peter
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Judy H Cho
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Bruce E Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah J Faith
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Jose C Clemente
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York NY, USA
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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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28
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Paramsothy S, Nielsen S, Kamm MA, Deshpande NP, Faith JJ, Clemente JC, Paramsothy R, Walsh AJ, van den Bogaerde J, Samuel D, Leong RWL, Connor S, Ng W, Lin E, Borody TJ, Wilkins MR, Colombel JF, Mitchell HM, Kaakoush NO. Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis. Gastroenterology 2019; 156:1440-1454.e2. [PMID: 30529583 DOI: 10.1053/j.gastro.2018.12.001] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [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: 08/27/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis (UC). In a randomized controlled trial of FMT in patients with active UC, we aimed to identify bacterial taxonomic and functional factors associated with response to therapy. METHODS We performed a double-blind trial of 81 patients with active UC randomly assigned to groups that received an initial colonoscopic infusion and then intensive multidonor FMT or placebo enemas, 5 d/wk for 8 weeks. Patients in the FMT group received blended homogenized stool from 3-7 unrelated donors. Patients in the placebo group were eligible to receive open-label FMT after the double-blind study period. We collected 314 fecal samples from the patients at screening, every 4 weeks during treatment, and 8 weeks after the blinded or open-label FMT therapy. We also collected 160 large-bowel biopsy samples from the patients at study entry, at completion of 8 weeks of blinded therapy, and at the end of open-label FMT, if applicable. We analyzed 105 fecal samples from the 14 individual donors (n = 55), who in turn contributed to 21 multidonor batches (n = 50). Bacteria in colonic and fecal samples were analyzed by both 16S ribosomal RNA gene and transcript amplicon sequencing; 285 fecal samples were analyzed by shotgun metagenomics, and 60 fecal samples were analyzed for metabolome features. RESULTS FMT increased microbial diversity and altered composition, based on analyses of colon and fecal samples collected before vs after FMT. Diversity was greater in fecal and colon samples collected before and after FMT treatment from patients who achieved remission compared with patients who did not. Patients in remission after FMT had enrichment of Eubacterium hallii and Roseburia inulivorans compared with patients who did not achieve remission after FMT and had increased levels of short-chain fatty acid biosynthesis and secondary bile acids. Patients who did not achieve remission had enrichment of Fusobacterium gonidiaformans, Sutterella wadsworthensis, and Escherichia species and increased levels of heme and lipopolysaccharide biosynthesis. Bacteroides in donor stool were associated with remission in patients receiving FMT, and Streptococcus species in donor stool was associated with no response to FMT. CONCLUSIONS In an analysis of fecal and colonic mucosa samples from patients receiving FMT for active UC and stool samples from donors, we associated specific bacteria and metabolic pathways with induction of remission. These findings may be of value in the design of microbe-based therapies for UC. ClinicalTrials.gov, Number NCT01896635.
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Affiliation(s)
- Sudarshan Paramsothy
- University of New South Wales, Sydney, Australia; Icahn School of Medicine at Mount Sinai, New York, New York; St Vincent's Hospital, Sydney, Australia; Nambour General Hospital, Nambour, Australia; Bankstown-Lidcombe Hospital, Sydney, Australia
| | | | - Michael A Kamm
- St Vincent's Hospital and University of Melbourne, Melbourne, Australia
| | | | | | | | | | | | | | | | | | | | - Watson Ng
- Liverpool Hospital, Sydney, Australia
| | - Enmoore Lin
- Centre for Digestive Diseases, Sydney, Australia
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29
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Contijoch EJ, Britton GJ, Yang C, Mogno I, Li Z, Ng R, Llewellyn SR, Hira S, Johnson C, Rabinowitz KM, Barkan R, Dotan I, Hirten RP, Fu SC, Luo Y, Yang N, Luong T, Labrias PR, Lira S, Peter I, Grinspan A, Clemente JC, Kosoy R, Kim-Schulze S, Qin X, Castillo A, Hurley A, Atreja A, Rogers J, Fasihuddin F, Saliaj M, Nolan A, Reyes-Mercedes P, Rodriguez C, Aly S, Santa-Cruz K, Peters L, Suárez-Fariñas M, Huang R, Hao K, Zhu J, Zhang B, Losic B, Irizar H, Song WM, Di Narzo A, Wang W, Cohen BL, DiMaio C, Greenwald D, Itzkowitz S, Lucas A, Marion J, Maser E, Ungaro R, Naymagon S, Novak J, Shah B, Ullman T, Rubin P, George J, Legnani P, Telesco SE, Friedman JR, Brodmerkel C, Plevy S, Cho JH, Colombel JF, Schadt EE, Argmann C, Dubinsky M, Kasarskis A, Sands B, Faith JJ. Gut microbiota density influences host physiology and is shaped by host and microbial factors. eLife 2019; 8:e40553. [PMID: 30666957 PMCID: PMC6342524 DOI: 10.7554/elife.40553] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [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: 07/28/2018] [Accepted: 01/04/2019] [Indexed: 12/14/2022] Open
Abstract
To identify factors that regulate gut microbiota density and the impact of varied microbiota density on health, we assayed this fundamental ecosystem property in fecal samples across mammals, human disease, and therapeutic interventions. Physiologic features of the host (carrying capacity) and the fitness of the gut microbiota shape microbiota density. Therapeutic manipulation of microbiota density in mice altered host metabolic and immune homeostasis. In humans, gut microbiota density was reduced in Crohn's disease, ulcerative colitis, and ileal pouch-anal anastomosis. The gut microbiota in recurrent Clostridium difficile infection had lower density and reduced fitness that were restored by fecal microbiota transplantation. Understanding the interplay between microbiota and disease in terms of microbiota density, host carrying capacity, and microbiota fitness provide new insights into microbiome structure and microbiome targeted therapeutics. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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30
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Britton GJ, Contijoch EJ, Mogno I, Vennaro OH, Llewellyn SR, Ng R, Li Z, Mortha A, Merad M, Das A, Gevers D, McGovern DPB, Singh N, Braun J, Jacobs JP, Clemente JC, Grinspan A, Sands BE, Colombel JF, Dubinsky MC, Faith JJ. Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt + Regulatory T Cells and Exacerbate Colitis in Mice. Immunity 2019; 50:212-224.e4. [PMID: 30650377 PMCID: PMC6512335 DOI: 10.1016/j.immuni.2018.12.015] [Citation(s) in RCA: 296] [Impact Index Per Article: 59.2] [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: 05/03/2018] [Revised: 10/03/2018] [Accepted: 12/13/2018] [Indexed: 12/13/2022]
Abstract
Microbiota are thought to influence the development and progression of inflammatory bowel disease (IBD), but determining generalizable effects of microbiota on IBD etiology requires larger-scale functional analyses. We colonized germ-free mice with intestinal microbiotas from 30 healthy and IBD donors and determined the homeostatic intestinal T cell response to each microbiota. Compared to microbiotas from healthy donors, transfer of IBD microbiotas into germ-free mice increased numbers of intestinal Th17 cells and Th2 cells and decreased numbers of RORγt+ Treg cells. Colonization with IBD microbiotas exacerbated disease in a model where colitis is induced upon transfer of naive T cells into Rag1-/- mice. The proportions of Th17 and RORγt+ Treg cells induced by each microbiota were predictive of human disease status and accounted for disease severity in the Rag1-/- colitis model. Thus, an impact on intestinal Th17 and RORγt+ Treg cell compartments emerges as a unifying feature of IBD microbiotas, suggesting a general mechanism for microbial contribution to IBD pathogenesis.
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Affiliation(s)
- Graham J Britton
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eduardo J Contijoch
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ilaria Mogno
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia H Vennaro
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sean R Llewellyn
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruby Ng
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhihua Li
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arthur Mortha
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anuk Das
- Janssen Human Microbiome Institute, Janssen Research and Development, LLC, Spring House, PA, USA
| | - Dirk Gevers
- Janssen Human Microbiome Institute, Janssen Research and Development, LLC, Spring House, PA, USA
| | - Dermot P B McGovern
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Namita Singh
- Pediatric Gastroenterology and Inflammatory Bowel Disease, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jonathan Braun
- UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jonathan P Jacobs
- Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jose C Clemente
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ari Grinspan
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce E Sands
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla C Dubinsky
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Pediatric Gastroenterology and Hepatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah J Faith
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Chen L, He Z, Iuga AC, Martins Filho SN, Faith JJ, Clemente JC, Deshpande M, Jayaprakash A, Colombel JF, Lafaille JJ, Sachidanandam R, Furtado GC, Lira SA. Diet Modifies Colonic Microbiota and CD4 + T-Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-Cell Expression of Interleukin 23. Gastroenterology 2018; 155:1177-1191.e16. [PMID: 29909020 PMCID: PMC6174107 DOI: 10.1053/j.gastro.2018.06.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 02/12/2018] [Revised: 05/24/2018] [Accepted: 06/11/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Several studies have shown that signaling via the interleukin 23 (IL23) receptor is required for development of colitis. We studied the roles of IL23, dietary factors, alterations to the microbiota, and T cells in the development and progression of colitis in mice. METHODS All mice were maintained on laboratory diet 5053, unless otherwise noted. We generated mice that express IL23 in CX3CR1-positive myeloid cells (R23FR mice) upon cyclic administration of tamoxifen dissolved in diet 2019. Diets 2019 and 5053 have minor differences in the overall composition of protein, fat, fiber, minerals, and vitamins. CX3CR1CreER mice (FR mice) were used as controls. Some mice were given antibiotics, and others were raised in a germ-free environment. Intestinal tissues were collected and analyzed by histology and flow cytometry. Feces were collected and analyzed by 16S rDNA sequencing. Feces from C57/Bl6, R23FR, or FR mice were fed to FR and R23FR germ-free mice in microbiota transplant experiments. We also performed studies with R23FR/Rag-/-, R23FR/Mu-/-, and R23FR/Tcrd-/- mice. R23FR mice were given injections of antibodies against CD4 or CD8 to deplete T cells. Mesenteric lymph nodes and large intestine CD4+ cells from R23FR or FR mice in remission from colitis were transferred into Rag-/- mice. CD4+ cells were isolated from donor R23FR mice and recipient Rag-/- mice, and T-cell receptor sequences were determined. RESULTS Expression of IL23 led to development of a relapsing-remitting colitis that was dependent on the microbiota and CD4+ T cells. The relapses were caused by switching from the conventional diet used in our facility (diet 5053) to the diet 2019 and were not dependent on tamoxifen after the first cycle. The switch in the diet modified the microbiota but did not alter levels of IL23 in intestinal tissues compared with mice that remained on the conventional diet. Mesenteric lymph nodes and large intestine CD4+ cells from R23FR mice in remission, but not from FR mice, induced colitis after transfer into Rag-/- mice, but only when these mice were placed on the diet 2019. The CD4+ T-cell receptor repertoire of Rag-/- mice with colitis (fed the 2019 diet) was less diverse than that from donor mice and Rag-/- mice without colitis (fed the 5053 diet) because of expansion of dominant T-cell clones. CONCLUSIONS We developed mice that express IL23 in CX3CR1-positive myeloid cells (R23FR mice) and found that they are more susceptible to diet-induced colitis than mice that do not express IL23. The R23FR mice have a population of CD4+ T cells that becomes activated in response to dietary changes and alterations to the intestinal microbiota. The results indicate that alterations in the diet, intestinal microbiota, and IL23 signaling can contribute to pathogenesis of inflammatory bowel disease.
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Affiliation(s)
- Lili Chen
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhengxiang He
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alina Cornelia Iuga
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Sebastião N. Martins Filho
- Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil,Department of Pathology and Laboratory Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Jeremiah J. Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jose C. Clemente
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Madhura Deshpande
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan J. Lafaille
- Department of Pathology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Ravi Sachidanandam
- Girihlet Inc. Oakland, CA 94609, USA,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Glaucia C. Furtado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio A. Lira
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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32
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Llewellyn SR, Britton GJ, Contijoch EJ, Vennaro OH, Mortha A, Colombel JF, Grinspan A, Clemente JC, Merad M, Faith JJ. Interactions Between Diet and the Intestinal Microbiota Alter Intestinal Permeability and Colitis Severity in Mice. Gastroenterology 2018; 154:1037-1046.e2. [PMID: 29174952 PMCID: PMC5847454 DOI: 10.1053/j.gastro.2017.11.030] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [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: 03/20/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS It is not clear how the complex interactions between diet and the intestinal microbiota affect development of mucosal inflammation or inflammatory bowel disease. We investigated interactions between dietary ingredients, nutrients, and the microbiota in specific pathogen-free (SPF) and germ-free (GF) mice given more than 40 unique diets; we quantified individual and synergistic effects of dietary macronutrients and the microbiota on intestinal health and development of colitis. METHODS C56BL/6J SPF and GF mice were placed on custom diets containing different concentrations and sources of protein, fat, digestible carbohydrates, and indigestible carbohydrates (fiber). After 1 week, SPF and GF mice were given dextran sulfate sodium (DSS) to induce colitis. Disease severity was determined based on the percent weight change from baseline, and modeled as a function of the concentration of each macronutrient in the diet. In unchallenged mice, we measured intestinal permeability by feeding mice labeled dextran and measuring levels in blood. Feces were collected and microbiota were analyzed by 16S rDNA sequencing. We collected colons from mice and performed transcriptome analyses. RESULTS Fecal microbiota varied with diet; the concentration of protein and fiber had the strongest effect on colitis development. Among 9 fiber sources tested, psyllium, pectin, and cellulose fiber reduced the severity of colitis in SPF mice, whereas methylcellulose increased severity. Increasing dietary protein increased the density of the fecal microbiota and the severity of colitis in SPF mice, but not in GF mice or mice given antibiotics. Psyllium fiber reduced the severity of colitis through microbiota-dependent and microbiota-independent mechanisms. Combinatorial perturbations to dietary casein protein and psyllium fiber in parallel accounted for most variation in gut microbial density and intestinal permeability in unchallenged mice, as well as the severity of DSS-induced colitis; changes in 1 ingredient could be offset by changes in another. CONCLUSIONS In an analysis of the effects of different dietary components and the gut microbiota on mice with and without DSS-induced colitis, we found complex mixtures of nutrients affect intestinal permeability, gut microbial density, and development of intestinal inflammation.
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Affiliation(s)
- Sean R. Llewellyn
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Graham J. Britton
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Eduardo J. Contijoch
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Olivia H. Vennaro
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Arthur Mortha
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ari Grinspan
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jose C. Clemente
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Miriam Merad
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Department of Oncological Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jeremiah J. Faith
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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33
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Abstract
Despite the wealth of metagenomic sequencing data, the functions of most bacterial genes from the mammalian microbiota have remained poorly understood. In their recent study (Yaung et al 2015), Wang, Gerber, and colleagues present a platform which allows functional mining of bacterial genomes for genes that contribute to fitness in vivo and holds great potential for forward engineering microbes with enhanced colonization abilities in the microbiota.
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Affiliation(s)
- Jeremiah J Faith
- Immunology Institute and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount SinaiNew York, NY, USA
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34
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Faith JJ. A key to gut health in a few microns of mucus. Sci Transl Med 2015. [DOI: 10.1126/scitranslmed.aad4449] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Quantitative imaging facilitates assessment of gut mucus and reveals a protective influence of certain dietary carbohydrates on mucus layer thickness.
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Affiliation(s)
- Jeremiah J. Faith
- Immunology Institute and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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35
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Zhang D, Chen G, Manwani D, Mortha A, Xu C, Faith JJ, Burk RD, Kunisaki Y, Jang JE, Scheiermann C, Merad M, Frenette PS. Neutrophil ageing is regulated by the microbiome. Nature 2015; 525:528-32. [PMID: 26374999 PMCID: PMC4712631 DOI: 10.1038/nature15367] [Citation(s) in RCA: 542] [Impact Index Per Article: 60.2] [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: 05/06/2015] [Accepted: 07/29/2015] [Indexed: 12/11/2022]
Abstract
Blood polymorphonuclear neutrophils provide immune protection against pathogens, but may also promote tissue injury in inflammatory diseases. Although neutrophils are generally considered to be a relatively homogeneous population, evidence for heterogeneity is emerging. Under steady-state conditions, neutrophil heterogeneity may arise from ageing and replenishment by newly released neutrophils from the bone marrow. Aged neutrophils upregulate CXCR4, a receptor allowing their clearance in the bone marrow, with feedback inhibition of neutrophil production via the IL-17/G-CSF axis, and rhythmic modulation of the haematopoietic stem-cell niche. The aged subset also expresses low levels of L-selectin. Previous studies have suggested that in vitro-aged neutrophils exhibit impaired migration and reduced pro-inflammatory properties. Here, using in vivo ageing analyses in mice, we show that neutrophil pro-inflammatory activity correlates positively with their ageing whilst in circulation. Aged neutrophils represent an overly active subset exhibiting enhanced αMβ2 integrin activation and neutrophil extracellular trap formation under inflammatory conditions. Neutrophil ageing is driven by the microbiota via Toll-like receptor and myeloid differentiation factor 88-mediated signalling pathways. Depletion of the microbiota significantly reduces the number of circulating aged neutrophils and dramatically improves the pathogenesis and inflammation-related organ damage in models of sickle-cell disease or endotoxin-induced septic shock. These results identify a role for the microbiota in regulating a disease-promoting neutrophil subset.
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Affiliation(s)
- Dachuan Zhang
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Grace Chen
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Deepa Manwani
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Arthur Mortha
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, New York 10029, USA.,The Immunology Institute, Mount Sinai School of Medicine, New York, New York 10029, USA
| | - Chunliang Xu
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Jeremiah J Faith
- The Immunology Institute, Mount Sinai School of Medicine, New York, New York 10029, USA.,The Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, New York 10029, USA
| | - Robert D Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Yuya Kunisaki
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Jung-Eun Jang
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Christoph Scheiermann
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Miriam Merad
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, New York 10029, USA.,The Immunology Institute, Mount Sinai School of Medicine, New York, New York 10029, USA
| | - Paul S Frenette
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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36
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Faith JJ, Ahern PP, Ridaura VK, Cheng J, Gordon JI. Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice. Sci Transl Med 2014; 6:220ra11. [PMID: 24452263 DOI: 10.1126/scitranslmed.3008051] [Citation(s) in RCA: 259] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Identifying a scalable, unbiased method for discovering which members of the human gut microbiota influence specific physiologic, metabolic, and immunologic phenotypes remains a challenge. We describe a method in which a clonally arrayed collection of cultured, sequenced bacteria was generated from one of several human fecal microbiota samples found to transmit a particular phenotype to recipient germ-free mice. Ninety-four bacterial consortia of diverse size, randomly drawn from the culture collection, were introduced into germ-free animals. We identified an unanticipated range of bacterial strains that promoted accumulation of colonic regulatory T cells (T(regs)) and expansion of Nrp1(lo/-) peripheral T(regs), as well as strains that modulated mouse adiposity and cecal metabolite concentrations, using feature selection algorithms and follow-up monocolonizations. This combinatorial approach enables a systems-level understanding of microbial contributions to human biology.
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Affiliation(s)
- Jeremiah J Faith
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
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37
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Ahern PP, Faith JJ, Gordon JI. Mining the human gut microbiota for effector strains that shape the immune system. Immunity 2014; 40:815-23. [PMID: 24950201 DOI: 10.1016/j.immuni.2014.05.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/24/2014] [Indexed: 02/07/2023]
Abstract
The gut microbiota codevelops with the immune system beginning at birth. Mining the microbiota for bacterial strains responsible for shaping the structure and dynamic operations of the innate and adaptive arms of the immune system represents a formidable combinatorial problem but one that needs to be overcome to advance mechanistic understanding of microbial community and immune system coregulation and to develop new diagnostic and therapeutic approaches that promote health. Here, we discuss a scalable, less biased approach for identifying effector strains in complex microbial communities that impact immune function. The approach begins by identifying uncultured human fecal microbiota samples that transmit immune phenotypes to germ-free mice. Clonally arrayed sequenced collections of bacterial strains are constructed from representative donor microbiota. If the collection transmits phenotypes, effector strains are identified by testing randomly generated subsets with overlapping membership in individually housed germ-free animals. Detailed mechanistic studies of effector strain-host interactions can then be performed.
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Affiliation(s)
- Philip P Ahern
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jeremiah J Faith
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA; Immunology Institute and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
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38
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Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 2013; 341:1241214. [PMID: 24009397 DOI: 10.1126/science.1241214] [Citation(s) in RCA: 2473] [Impact Index Per Article: 224.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The role of specific gut microbes in shaping body composition remains unclear. We transplanted fecal microbiota from adult female twin pairs discordant for obesity into germ-free mice fed low-fat mouse chow, as well as diets representing different levels of saturated fat and fruit and vegetable consumption typical of the U.S. diet. Increased total body and fat mass, as well as obesity-associated metabolic phenotypes, were transmissible with uncultured fecal communities and with their corresponding fecal bacterial culture collections. Cohousing mice harboring an obese twin's microbiota (Ob) with mice containing the lean co-twin's microbiota (Ln) prevented the development of increased body mass and obesity-associated metabolic phenotypes in Ob cage mates. Rescue correlated with invasion of specific members of Bacteroidetes from the Ln microbiota into Ob microbiota and was diet-dependent. These findings reveal transmissible, rapid, and modifiable effects of diet-by-microbiota interactions.
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Affiliation(s)
- Vanessa K Ridaura
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
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39
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Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, Gordon JI. The long-term stability of the human gut microbiota. Science 2013; 341:1237439. [PMID: 23828941 DOI: 10.1126/science.1237439] [Citation(s) in RCA: 1306] [Impact Index Per Article: 118.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A low-error 16S ribosomal RNA amplicon sequencing method, in combination with whole-genome sequencing of >500 cultured isolates, was used to characterize bacterial strain composition in the fecal microbiota of 37 U.S. adults sampled for up to 5 years. Microbiota stability followed a power-law function, which when extrapolated suggests that most strains in an individual are residents for decades. Shared strains were recovered from family members but not from unrelated individuals. Sampling of individuals who consumed a monotonous liquid diet for up to 32 weeks indicated that changes in strain composition were better predicted by changes in weight than by differences in sampling interval. This combination of stability and responsiveness to physiologic change confirms the potential of the gut microbiota as a diagnostic tool and therapeutic target.
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Affiliation(s)
- Jeremiah J Faith
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
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40
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Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 2012. [PMID: 23202435 PMCID: PMC3531572 DOI: 10.1038/nmeth.2276] [Citation(s) in RCA: 2332] [Impact Index Per Article: 194.3] [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: 12/16/2022]
Abstract
High-throughput sequencing has revolutionized microbial ecology, but read quality remains a significant barrier to accurate taxonomy assignment and alpha diversity assessment for microbial communities. We demonstrate that high-quality read length and abundance are the primary factors differentiating correct from erroneous reads produced by Illumina GAIIx, HiSeq, and MiSeq instruments. We present guidelines for user-defined quality-filtering strategies, enabling efficient extraction of high-quality data from, and facilitating interpretation of Illumina sequencing results.
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Affiliation(s)
- Nicholas A Bokulich
- Department of Viticulture and Enology, University of California, Davis, Davis, California, USA
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41
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Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res 2012; 22:1974-84. [PMID: 22665442 PMCID: PMC3460192 DOI: 10.1101/gr.138198.112] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [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: 12/21/2022]
Abstract
We lack a deep understanding of genetic and metabolic attributes specializing in microbial consortia for initial and subsequent waves of colonization of our body habitats. Here we show that phylogenetically interspersed bacteria in Clostridium cluster XIVa, an abundant group of bacteria in the adult human gut also known as the Clostridium coccoides or Eubacterium rectale group, contains species that have evolved distribution patterns consistent with either early successional or stable gut communities. The species that specialize to the infant gut are more likely to associate with systemic infections and can reach high abundances in individuals with Inflammatory Bowel Disease (IBD), indicating that a subset of the microbiota that have adapted to pioneer/opportunistic lifestyles may do well in both early development and with disease. We identified genes likely selected during adaptation to pioneer/opportunistic lifestyles as those for which early succession association and not phylogenetic relationships explain genomic abundance. These genes reveal potential mechanisms by which opportunistic gut bacteria tolerate osmotic and oxidative stress and potentially important aspects of their metabolism. These genes may not only be biomarkers of properties associated with adaptation to early succession and disturbance, but also leads for developing therapies aimed at promoting reestablishment of stable gut communities following physiologic or pathologic disturbances.
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Affiliation(s)
- Catherine Lozupone
- Department of Chemistry & Biochemistry and Biofrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
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42
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McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL, Henrissat B, Oozeer R, Cools-Portier S, Gobert G, Chervaux C, Knights D, Lozupone CA, Knight R, Duncan AE, Bain JR, Muehlbauer MJ, Newgard CB, Heath AC, Gordon JI. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med 2012; 3:106ra106. [PMID: 22030749 DOI: 10.1126/scitranslmed.3002701] [Citation(s) in RCA: 373] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding how the human gut microbiota and host are affected by probiotic bacterial strains requires carefully controlled studies in humans and in mouse models of the gut ecosystem where potentially confounding variables that are difficult to control in humans can be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of adult female monozygotic twin pairs through repeated sampling 4 weeks before, 7 weeks during, and 4 weeks after consumption of a commercially available fermented milk product (FMP) containing a consortium of Bifidobacterium animalis subsp. lactis, two strains of Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis subsp. cremoris, and Streptococcus thermophilus. In addition, gnotobiotic mice harboring a 15-species model human gut microbiota whose genomes contain 58,399 known or predicted protein-coding genes were studied before and after gavage with all five sequenced FMP strains. No significant changes in bacterial species composition or in the proportional representation of genes encoding known enzymes were observed in the feces of humans consuming the FMP. Only minimal changes in microbiota configuration were noted in mice after single or repeated gavage with the FMP consortium. However, RNA-Seq analysis of fecal samples and follow-up mass spectrometry of urinary metabolites disclosed that introducing the FMP strains into mice results in significant changes in expression of microbiome-encoded enzymes involved in numerous metabolic pathways, most prominently those related to carbohydrate metabolism. B. animalis subsp. lactis, the dominant persistent member of the FMP consortium in gnotobiotic mice, up-regulates a locus in vivo that is involved in the catabolism of xylooligosaccharides, a class of glycans widely distributed in fruits, vegetables, and other foods, underscoring the importance of these sugars to this bacterial species. The human fecal metatranscriptome exhibited significant changes, confined to the period of FMP consumption, that mirror changes in gnotobiotic mice, including those related to plant polysaccharide metabolism. These experiments illustrate a translational research pipeline for characterizing the effects of FMPs on the human gut microbiome.
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Affiliation(s)
- Nathan P McNulty
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
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43
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Abstract
The interrelationships between our diets and the structure and operations of our gut microbial communities are poorly understood. A model community of 10 sequenced human gut bacteria was introduced into gnotobiotic mice, and changes in species abundance and microbial gene expression were measured in response to randomized perturbations of four defined ingredients in the host diet. From the responses, we developed a statistical model that predicted over 60% of the variation in species abundance evoked by diet perturbations, and we were able to identify which factors in the diet best explained changes seen for each community member. The approach is generally applicable, as shown by a follow-up study involving diets containing various mixtures of pureed human baby foods.
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Affiliation(s)
- Jeremiah J Faith
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
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44
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Faith JJ, Rey FE, O'Donnell D, Karlsson M, McNulty NP, Kallstrom G, Goodman AL, Gordon JI. Creating and characterizing communities of human gut microbes in gnotobiotic mice. ISME J 2010; 4:1094-8. [PMID: 20664551 DOI: 10.1038/ismej.2010.110] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jeremiah J Faith
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
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45
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Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 2010; 1:6ra14. [PMID: 20368178 DOI: 10.1126/scitranslmed.3000322] [Citation(s) in RCA: 2039] [Impact Index Per Article: 145.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Diet and nutritional status are among the most important modifiable determinants of human health. The nutritional value of food is influenced in part by a person's gut microbial community (microbiota) and its component genes (microbiome). Unraveling the interrelations among diet, the structure and operations of the gut microbiota, and nutrient and energy harvest is confounded by variations in human environmental exposures, microbial ecology, and genotype. To help overcome these problems, we created a well-defined, representative animal model of the human gut ecosystem by transplanting fresh or frozen adult human fecal microbial communities into germ-free C57BL/6J mice. Culture-independent metagenomic analysis of the temporal, spatial, and intergenerational patterns of bacterial colonization showed that these humanized mice were stably and heritably colonized and reproduced much of the bacterial diversity of the donor's microbiota. Switching from a low-fat, plant polysaccharide-rich diet to a high-fat, high-sugar "Western" diet shifted the structure of the microbiota within a single day, changed the representation of metabolic pathways in the microbiome, and altered microbiome gene expression. Reciprocal transplants involving various combinations of donor and recipient diets revealed that colonization history influences the initial structure of the microbial community but that these effects can be rapidly altered by diet. Humanized mice fed the Western diet have increased adiposity; this trait is transmissible via microbiota transplantation. Humanized gnotobiotic mice will be useful for conducting proof-of-principle "clinical trials" that test the effects of environmental and genetic factors on the gut microbiota and host physiology. Nearly full-length 16S rRNA gene sequences are deposited in GenBank under the accession numbers GQ491120 to GQ493997.
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Affiliation(s)
- Peter J Turnbaugh
- Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108, USA
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Rey FE, Faith JJ, Bain J, Muehlbauer MJ, Stevens RD, Newgard CB, Gordon JI. Dissecting the in vivo metabolic potential of two human gut acetogens. J Biol Chem 2010; 285:22082-90. [PMID: 20444704 PMCID: PMC2903421 DOI: 10.1074/jbc.m110.117713] [Citation(s) in RCA: 265] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Fermenting microbial communities generate hydrogen; its removal through the production of acetate, methane, or hydrogen sulfide modulates the efficiency of energy extraction from available nutrients in many ecosystems. We noted that pathway components for acetogenesis are more abundantly and consistently represented in the gut microbiomes of monozygotic twins and their mothers than components for methanogenesis or sulfate reduction and subsequently analyzed the metabolic potential of two sequenced human gut acetogens, Blautia hydrogenotrophica and Marvinbryantia formatexigens in vitro and in the intestines of gnotobiotic mice harboring a prominent saccharolytic bacterium. To do so, we developed a generally applicable method for multiplex sequencing of expressed microbial mRNAs (microbial RNA-Seq) and, together with mass spectrometry of metabolites, showed that these organisms have distinct patterns of substrate utilization. B. hydrogenotrophica targets aliphatic and aromatic amino acids. It increases the efficiency of fermentation by consuming reducing equivalents, thereby maintaining a high NAD+/NADH ratio and boosting acetate production. In contrast, M. formatexigens consumes oligosaccharides, does not impact the redox state of the gut, and boosts the yield of succinate. These findings have strategic implications for those who wish to manipulate the hydrogen economy of gut microbial communities in ways that modulate energy harvest.
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Affiliation(s)
- Federico E Rey
- Center for Genome Sciences, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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47
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Giannakis M, Bäckhed HK, Chen SL, Faith JJ, Wu M, Guruge JL, Engstrand L, Gordon JI. Response of gastric epithelial progenitors to Helicobacter pylori Isolates obtained from Swedish patients with chronic atrophic gastritis. J Biol Chem 2009; 284:30383-94. [PMID: 19723631 PMCID: PMC2781593 DOI: 10.1074/jbc.m109.052738] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [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] [Indexed: 01/01/2023] Open
Abstract
Helicobacter pylori infection is associated with gastric adenocarcinoma in some humans, especially those that develop an antecedent condition, chronic atrophic gastritis (ChAG). Gastric epithelial progenitors (GEPs) in transgenic gnotobiotic mice with a ChAG-like phenotype harbor intracellular collections of H. pylori. To characterize H. pylori adaptations to ChAG, we sequenced the genomes of 24 isolates obtained from 6 individuals, each sampled over a 4-year interval, as they did or did not progress from normal gastric histology to ChAG and/or adenocarcinoma. H. pylori populations within study participants were largely clonal and remarkably stable regardless of disease state. GeneChip studies of the responses of a cultured mouse gastric stem cell-like line (mGEPs) to infection with sequenced strains yielded a 695-member dataset of transcripts that are (i) differentially expressed after infection with ChAG-associated isolates, but not with a “normal” or a heat-killed ChAG isolate, and (ii) enriched in genes and gene functions associated with tumorigenesis in general and gastric carcinogenesis in specific cases. Transcriptional profiling of a ChAG strain during mGEP infection disclosed a set of responses, including up-regulation of hopZ, an adhesin belonging to a family of outer membrane proteins. Expression profiles of wild-type and ΔhopZ strains revealed a number of pH-regulated genes modulated by HopZ, including hopP, which binds sialylated glycans produced by GEPs in vivo. Genetic inactivation of hopZ produced a fitness defect in the stomachs of gnotobiotic transgenic mice but not in wild-type littermates. This study illustrates an approach for identifying GEP responses specific to ChAG-associated H. Pylori strains and bacterial genes important for survival in a model of the ChAG gastric ecosystem.
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Affiliation(s)
- Marios Giannakis
- Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
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Faith JJ, Driscoll ME, Fusaro VA, Cosgrove EJ, Hayete B, Juhn FS, Schneider SJ, Gardner TS. Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res 2007; 36:D866-70. [PMID: 17932051 PMCID: PMC2238822 DOI: 10.1093/nar/gkm815] [Citation(s) in RCA: 197] [Impact Index Per Article: 11.6] [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: 11/13/2022] Open
Abstract
Many Microbe Microarrays Database (M3D) is designed to facilitate the analysis and visualization of expression data in compendia compiled from multiple laboratories. M3D contains over a thousand Affymetrix microarrays for Escherichia coli, Saccharomyces cerevisiae and Shewanella oneidensis. The expression data is uniformly normalized to make the data generated by different laboratories and researchers more comparable. To facilitate computational analyses, M3D provides raw data (CEL file) and normalized data downloads of each compendium. In addition, web-based construction, visualization and download of custom datasets are provided to facilitate efficient interrogation of the compendium for more focused analyses. The experimental condition metadata in M3D is human curated with each chemical and growth attribute stored as a structured and computable set of experimental features with consistent naming conventions and units. All versions of the normalized compendia constructed for each species are maintained and accessible in perpetuity to facilitate the future interpretation and comparison of results published on M3D data. M3D is accessible at http://m3d.bu.edu/.
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Affiliation(s)
- Jeremiah J Faith
- Program in Bioinformatics, Boston University, 24 Cummington St. and Department of Biomedical Engineering, Boston University, 44 Cummington St., Boston, Massachusetts, 02215, USA
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Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 2007; 5:e8. [PMID: 17214507 PMCID: PMC1764438 DOI: 10.1371/journal.pbio.0050008] [Citation(s) in RCA: 962] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Accepted: 11/07/2006] [Indexed: 11/19/2022] Open
Abstract
Machine learning approaches offer the potential to systematically identify transcriptional regulatory interactions from a compendium of microarray expression profiles. However, experimental validation of the performance of these methods at the genome scale has remained elusive. Here we assess the global performance of four existing classes of inference algorithms using 445 Escherichia coli Affymetrix arrays and 3,216 known E. coli regulatory interactions from RegulonDB. We also developed and applied the context likelihood of relatedness (CLR) algorithm, a novel extension of the relevance networks class of algorithms. CLR demonstrates an average precision gain of 36% relative to the next-best performing algorithm. At a 60% true positive rate, CLR identifies 1,079 regulatory interactions, of which 338 were in the previously known network and 741 were novel predictions. We tested the predicted interactions for three transcription factors with chromatin immunoprecipitation, confirming 21 novel interactions and verifying our RegulonDB-based performance estimates. CLR also identified a regulatory link providing central metabolic control of iron transport, which we confirmed with real-time quantitative PCR. The compendium of expression data compiled in this study, coupled with RegulonDB, provides a valuable model system for further improvement of network inference algorithms using experimental data.
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Affiliation(s)
- Jeremiah J Faith
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Boris Hayete
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Joshua T Thaden
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Ilaria Mogno
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Department of Computer and Systems Science A. Ruberti, University of Rome, La Sapienza, Rome, Italy
| | - Jamey Wierzbowski
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Cellicon Biotechnologies, Boston, Massachusetts, United States of America
| | - Guillaume Cottarel
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Cellicon Biotechnologies, Boston, Massachusetts, United States of America
| | - Simon Kasif
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - James J Collins
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Timothy S Gardner
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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Faith JJ, Olson AJ, Gardner TS, Sachidanandam R. Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context. BMC Bioinformatics 2007; 8:344. [PMID: 17877794 PMCID: PMC2238324 DOI: 10.1186/1471-2105-8-344] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Accepted: 09/18/2007] [Indexed: 11/10/2022] Open
Abstract
Background Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. Results lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. Conclusion lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired.
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