1
|
Pereira GV, Boudaud M, Wolter M, Alexander C, De Sciscio A, Grant ET, Trindade BC, Pudlo NA, Singh S, Campbell A, Shan M, Zhang L, Yang Q, Willieme S, Kim K, Denike-Duval T, Fuentes J, Bleich A, Schmidt TM, Kennedy L, Lyssiotis CA, Chen GY, Eaton KA, Desai MS, Martens EC. Opposing diet, microbiome, and metabolite mechanisms regulate inflammatory bowel disease in a genetically susceptible host. Cell Host Microbe 2024; 32:527-542.e9. [PMID: 38513656 PMCID: PMC11064055 DOI: 10.1016/j.chom.2024.03.001] [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: 06/30/2023] [Revised: 12/18/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
Inflammatory bowel diseases (IBDs) are chronic conditions characterized by periods of spontaneous intestinal inflammation and are increasing in industrialized populations. Combined with host genetics, diet and gut bacteria are thought to contribute prominently to IBDs, but mechanisms are still emerging. In mice lacking the IBD-associated cytokine, interleukin-10, we show that a fiber-deprived gut microbiota promotes the deterioration of colonic mucus, leading to lethal colitis. Inflammation starts with the expansion of natural killer cells and altered immunoglobulin-A coating of some bacteria. Lethal colitis is then driven by Th1 immune responses to increased activities of mucin-degrading bacteria that cause inflammation first in regions with thinner mucus. A fiber-free exclusive enteral nutrition diet also induces mucus erosion but inhibits inflammation by simultaneously increasing an anti-inflammatory bacterial metabolite, isobutyrate. Our findings underscore the importance of focusing on microbial functions-not taxa-contributing to IBDs and that some diet-mediated functions can oppose those that promote disease.
Collapse
Affiliation(s)
| | - Marie Boudaud
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Celeste Alexander
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alessandro De Sciscio
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Erica T Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | | | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shaleni Singh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mengrou Shan
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Li Zhang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Qinnan Yang
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stéphanie Willieme
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Kwi Kim
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Trisha Denike-Duval
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jaime Fuentes
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - André Bleich
- Institute for Laboratory Animal Science, Hanover Medical School, Hanover, Germany
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lucy Kennedy
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Costas A Lyssiotis
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Grace Y Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kathryn A Eaton
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
| |
Collapse
|
2
|
Parrish A, Boudaud M, Grant ET, Willieme S, Neumann M, Wolter M, Craig SZ, De Sciscio A, Cosma A, Hunewald O, Ollert M, Desai MS. Akkermansia muciniphila exacerbates food allergy in fibre-deprived mice. Nat Microbiol 2023; 8:1863-1879. [PMID: 37696941 PMCID: PMC10522492 DOI: 10.1038/s41564-023-01464-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [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: 06/10/2022] [Accepted: 08/05/2023] [Indexed: 09/13/2023]
Abstract
Alterations in the gut microbiome, including diet-driven changes, are linked to the rising prevalence of food allergy. However, little is known about how specific gut bacteria trigger the breakdown of oral tolerance. Here we show that depriving specific-pathogen-free mice of dietary fibre leads to a gut microbiota signature with increases in the mucin-degrading bacterium Akkermansia muciniphila. This signature is associated with intestinal barrier dysfunction, increased expression of type 1 and 2 cytokines and IgE-coated commensals in the colon, which result in an exacerbated allergic reaction to food allergens, ovalbumin and peanut. To demonstrate the causal role of A. muciniphila, we employed a tractable synthetic human gut microbiota in gnotobiotic mice. The presence of A. muciniphila within the microbiota, combined with fibre deprivation, resulted in stronger anti-commensal IgE coating and innate type-2 immune responses, which worsened symptoms of food allergy. Our study provides important insights into how gut microbes can regulate immune pathways of food allergy in a diet-dependent manner.
Collapse
Affiliation(s)
- Amy Parrish
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Marie Boudaud
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Erica T Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Stéphanie Willieme
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Mareike Neumann
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sophie Z Craig
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alessandro De Sciscio
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Antonio Cosma
- National Cytometry Platform, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Oliver Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark.
| |
Collapse
|
3
|
Pereira GV, Boudaud M, Wolter M, Alexander C, De Sciscio A, Grant ET, Trindade BC, Pudlo NA, Singh S, Campbell A, Shan M, Zhang L, Willieme S, Kim K, Denike-Duval T, Bleich A, Schmidt TM, Kennedy L, Lyssiotis CA, Chen GY, Eaton KA, Desai MS, Martens EC. Unravelling specific diet and gut microbial contributions to inflammatory bowel disease. Res Sq 2023:rs.3.rs-2518251. [PMID: 36993463 PMCID: PMC10055531 DOI: 10.21203/rs.3.rs-2518251/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Inflammatory bowel disease (IBD) is a chronic condition characterized by periods of spontaneous intestinal inflammation and is increasing in industrialized populations. Combined with host genetic predisposition, diet and gut bacteria are thought to be prominent features contributing to IBD, but little is known about the precise mechanisms involved. Here, we show that low dietary fiber promotes bacterial erosion of protective colonic mucus, leading to lethal colitis in mice lacking the IBD-associated cytokine, interleukin-10. Diet-induced inflammation is driven by mucin-degrading bacteria-mediated Th1 immune responses and is preceded by expansion of natural killer T cells and reduced immunoglobulin A coating of some bacteria. Surprisingly, an exclusive enteral nutrition diet, also lacking dietary fiber, reduced disease by increasing bacterial production of isobutyrate, which is dependent on the presence of a specific bacterial species, Eubacterium rectale. Our results illuminate a mechanistic framework using gnotobiotic mice to unravel the complex web of diet, host and microbial factors that influence IBD.
Collapse
Affiliation(s)
| | - Marie Boudaud
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Celeste Alexander
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alessandro De Sciscio
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Erica. T. Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | | | - Nicholas A. Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Shaleni Singh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mengrou Shan
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Li Zhang
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stéphanie Willieme
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Kwi Kim
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Trisha Denike-Duval
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - André Bleich
- Institute for Laboratory Animal Science, Hanover Medical School, Hanover, Germany
| | - Thomas M. Schmidt
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lucy Kennedy
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Costas A. Lyssiotis
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Dept. of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Grace Y. Chen
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Kathryn A. Eaton
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mahesh S. Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, 5000 Odense, Denmark
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| |
Collapse
|
4
|
Steimle A, De Sciscio A, Neumann M, Grant ET, Pereira GV, Ohno H, Martens EC, Desai MS. Constructing a gnotobiotic mouse model with a synthetic human gut microbiome to study host-microbe cross talk. STAR Protoc 2021; 2:100607. [PMID: 34179836 PMCID: PMC8209845 DOI: 10.1016/j.xpro.2021.100607] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Reproducible in vivo models are necessary to address functional aspects of the gut microbiome in various diseases. Here, we present a gnotobiotic mouse model that allows for the investigation of specific microbial functions within the microbiome. We describe how to culture 14 different well-characterized human gut species and how to verify their proper colonization in germ-free mice. This protocol can be modified to add or remove certain species of interest to investigate microbial mechanistic details in various disease models. For complete details on the use and execution of this protocol, please refer to Desai et al. (2016).
Collapse
Affiliation(s)
- Alex Steimle
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
| | - Alessandro De Sciscio
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
| | - Mareike Neumann
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg.,Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette 4365, Luxembourg
| | - Erica T Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg.,Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette 4365, Luxembourg
| | | | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,Immunobiology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan.,Laboratory for Immune Regulation, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-8670, Japan
| | - Eric C Martens
- University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg.,Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, 5000 Odense, Denmark
| |
Collapse
|