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Rolhion N, Chassaing B, Nahori MA, de Bodt J, Moura A, Lecuit M, Dussurget O, Bérard M, Marzorati M, Fehlner-Peach H, Littman DR, Gewirtz AT, Van de Wiele T, Cossart P. A Listeria monocytogenes Bacteriocin Can Target the Commensal Prevotella copri and Modulate Intestinal Infection. Cell Host Microbe 2020; 26:691-701.e5. [PMID: 31726031 PMCID: PMC6854461 DOI: 10.1016/j.chom.2019.10.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/05/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022]
Abstract
Understanding the role of the microbiota components in either preventing or favoring enteric infections is critical. Here, we report the discovery of a Listeria bacteriocin, Lmo2776, which limits Listeria intestinal colonization. Oral infection of conventional mice with a Δlmo2776 mutant leads to a thinner intestinal mucus layer and higher Listeria loads both in the intestinal content and deeper tissues compared to WT Listeria. This latter difference is microbiota dependent, as it is not observed in germ-free mice. Strikingly, it is phenocopied by pre-colonization of germ-free mice before Listeria infection with Prevotella copri, an abundant gut-commensal bacteria, but not with the other commensals tested. We further show that Lmo2776 targets P. copri and reduces its abundance. Together, these data unveil a role for P.copri in exacerbating intestinal infection, highlighting that pathogens such as Listeria may selectively deplete microbiota bacterial species to avoid excessive inflammation. L. monocytogenes secretes a bacteriocin (Lmo2776) homologous to the lactococcin 972 Lmo2776 controls Listeria intestinal colonization in a microbiota-dependent manner Lmo2776 targets the abundant gut commensal Prevotella copri Presence of P. copri exacerbates infection
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Affiliation(s)
- Nathalie Rolhion
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Inserm, U604, 75015 Paris, France; INRA, Unité sous-contrat 2020, 75015 Paris, France
| | - Benoit Chassaing
- Neurosciences Institute, Georgia State University (GSU), Atlanta, GA 30303, USA; Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, GSU, Atlanta, GA 30303, USA
| | - Marie-Anne Nahori
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Inserm, U604, 75015 Paris, France; INRA, Unité sous-contrat 2020, 75015 Paris, France
| | - Jana de Bodt
- Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Alexandra Moura
- Institut Pasteur, Unité Biologie des Infections, 75015 Paris, France; Inserm, U1117, 75015 Paris, France
| | - Marc Lecuit
- Institut Pasteur, Unité Biologie des Infections, 75015 Paris, France; Inserm, U1117, 75015 Paris, France; Paris Descartes University, Sorbonne Paris Cité, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Institut Imagine, 75743 Paris, France
| | - Olivier Dussurget
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Inserm, U604, 75015 Paris, France; INRA, Unité sous-contrat 2020, 75015 Paris, France; Université de Paris, 75013 Paris, France
| | - Marion Bérard
- Animalerie Centrale, Department of Technology and Scientific Programmes, Institut Pasteur, 75015 Paris, France
| | - Massimo Marzorati
- Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Hannah Fehlner-Peach
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Dan R Littman
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York, NY 10016, USA
| | - Andrew T Gewirtz
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, GSU, Atlanta, GA 30303, USA
| | - Tom Van de Wiele
- Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015 Paris, France; Inserm, U604, 75015 Paris, France; INRA, Unité sous-contrat 2020, 75015 Paris, France.
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Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, De Filippis F, Magnabosco C, Bonneau R, Lusingu J, Amuasi J, Reinhard K, Rattei T, Boulund F, Engstrand L, Zink A, Collado MC, Littman DR, Eibach D, Ercolini D, Rota-Stabelli O, Huttenhower C, Maixner F, Segata N. The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Cell Host Microbe 2019; 26:666-679.e7. [PMID: 31607556 PMCID: PMC6854460 DOI: 10.1016/j.chom.2019.08.018] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/05/2019] [Accepted: 08/28/2019] [Indexed: 12/29/2022]
Abstract
Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.
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Affiliation(s)
- Adrian Tett
- CIBIO Department, University of Trento, 38123 Trento, Italy.
| | - Kun D Huang
- CIBIO Department, University of Trento, 38123 Trento, Italy; Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 1 38010 S, San Michele all'Adige, Italy
| | | | - Hannah Fehlner-Peach
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | | | | | | | - Paolo Manghi
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Kevin Bonham
- The Broad Institute of MIT and Harvard, Cambridge, MA 02115, USA; Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy
| | - Moreno Zolfo
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy
| | - Cara Magnabosco
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA; Departments of Biology and Computer Science, New York University, New York, NY 10003, USA
| | - John Lusingu
- National Institute for Medical Research, Tanga Centre, Tanzania
| | - John Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Ghana
| | - Karl Reinhard
- Hardin Hall, School of Natural Resources, University of Nebraska, Lincoln, NE 68583-0987, USA
| | - Thomas Rattei
- CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Fredrik Boulund
- Centre for Translational Microbiome Research, Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden
| | - Lars Engstrand
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), 46980 Paterna, Valencia, Spain
| | - Dan R Littman
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, 20359 Hamburg, Germany
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 1 38010 S, San Michele all'Adige, Italy
| | - Curtis Huttenhower
- The Broad Institute of MIT and Harvard, Cambridge, MA 02115, USA; Biostatistics Department, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, 38123 Trento, Italy.
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Kim M, Galan C, Hill AA, Wu WJ, Fehlner-Peach H, Song HW, Schady D, Bettini ML, Simpson KW, Longman RS, Littman DR, Diehl GE. Critical Role for the Microbiota in CX 3CR1 + Intestinal Mononuclear Phagocyte Regulation of Intestinal T Cell Responses. Immunity 2018; 49:151-163.e5. [PMID: 29980437 PMCID: PMC6051886 DOI: 10.1016/j.immuni.2018.05.009] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 02/20/2018] [Accepted: 05/22/2018] [Indexed: 12/11/2022]
Abstract
The intestinal barrier is vulnerable to damage by microbiota-induced inflammation that is normally restrained through mechanisms promoting homeostasis. Such disruptions contribute to autoimmune and inflammatory diseases including inflammatory bowel disease. We identified a regulatory loop whereby, in the presence of the normal microbiota, intestinal antigen-presenting cells (APCs) expressing the chemokine receptor CX3CR1 reduced expansion of intestinal microbe-specific T helper 1 (Th1) cells and promoted generation of regulatory T cells responsive to food antigens and the microbiota itself. We identified that disruption of the microbiota resulted in CX3CR1+ APC-dependent inflammatory Th1 cell responses with increased pathology after pathogen infection. Colonization with microbes that can adhere to the epithelium was able to compensate for intestinal microbiota loss, indicating that although microbial interactions with the epithelium can be pathogenic, they can also activate homeostatic regulatory mechanisms. Our results identify a cellular mechanism by which the microbiota limits intestinal inflammation and promotes tissue homeostasis.
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Affiliation(s)
- Myunghoo Kim
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carolina Galan
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Andrea A Hill
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wan-Jung Wu
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hannah Fehlner-Peach
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Hyo Won Song
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Deborah Schady
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew L Bettini
- Department of Pediatrics, Section of Diabetes and Endocrinology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA; Biology of Inflammation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kenneth W Simpson
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Randy S Longman
- Jill Roberts Center for IBD Research and Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Dan R Littman
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York, NY 10016, USA
| | - Gretchen E Diehl
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Biology of Inflammation Center, Baylor College of Medicine, Houston, TX 77030, USA.
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4
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Meisel M, Mayassi T, Fehlner-Peach H, Koval JC, O'Brien SL, Hinterleitner R, Lesko K, Kim S, Bouziat R, Chen L, Weber CR, Mazmanian SK, Jabri B, Antonopoulos DA. Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis. ISME J 2016; 11:15-30. [PMID: 27648810 DOI: 10.1038/ismej.2016.114] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 06/17/2016] [Accepted: 06/27/2016] [Indexed: 02/07/2023]
Abstract
Dysbiosis resulting in gut-microbiome alterations with reduced butyrate production are thought to disrupt intestinal immune homeostasis and promote complex immune disorders. However, whether and how dysbiosis develops before the onset of overt pathology remains poorly defined. Interleukin-15 (IL-15) is upregulated in distressed tissue and its overexpression is thought to predispose susceptible individuals to and have a role in the pathogenesis of celiac disease and inflammatory bowel disease (IBD). Although the immunological roles of IL-15 have been largely studied, its potential impact on the microbiota remains unexplored. Analysis of 16S ribosomal RNA-based inventories of bacterial communities in mice overexpressing IL-15 in the intestinal epithelium (villin-IL-15 transgenic (v-IL-15tg) mice) shows distinct changes in the composition of the intestinal bacteria. Although some alterations are specific to individual intestinal compartments, others are found across the ileum, cecum and feces. In particular, IL-15 overexpression restructures the composition of the microbiota with a decrease in butyrate-producing bacteria that is associated with a reduction in luminal butyrate levels across all intestinal compartments. Fecal microbiota transplant experiments of wild-type and v-IL-15tg microbiota into germ-free mice further indicate that diminishing butyrate concentration observed in the intestinal lumen of v-IL-15tg mice is the result of intrinsic alterations in the microbiota induced by IL-15. This reconfiguration of the microbiota is associated with increased susceptibility to dextran sodium sulfate-induced colitis. Altogether, this study reveals that IL-15 impacts butyrate-producing bacteria and lowers butyrate levels in the absence of overt pathology, which represent events that precede and promote intestinal inflammatory diseases.
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Affiliation(s)
- Marlies Meisel
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Toufic Mayassi
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | | | - Jason C Koval
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Sarah L O'Brien
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | | | - Kathryn Lesko
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Sangman Kim
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Romain Bouziat
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Li Chen
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | | | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Bana Jabri
- Department of Medicine, The University of Chicago, Chicago, IL, USA.,Department of Pathology, Department of Pediatrics, The University of Chicago, Chicago, IL, USA
| | - Dionysios A Antonopoulos
- Department of Medicine, The University of Chicago, Chicago, IL, USA.,Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
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Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A, Antonopoulos DA, Jabri B, Chang EB. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Nature 2012; 487:104-8. [PMID: 22722865 PMCID: PMC3393783 DOI: 10.1038/nature11225] [Citation(s) in RCA: 1265] [Impact Index Per Article: 105.4] [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: 10/19/2011] [Accepted: 05/10/2012] [Indexed: 02/06/2023]
Abstract
The composite human microbiome of Western populations has probably changed over the past century, brought on by new environmental triggers that often have a negative impact on human health. Here we show that consumption of a diet high in saturated (milk-derived) fat, but not polyunsaturated (safflower oil) fat, changes the conditions for microbial assemblage and promotes the expansion of a low-abundance, sulphite-reducing pathobiont, Bilophila wadsworthia. This was associated with a pro-inflammatory T helper type 1 (T(H)1) immune response and increased incidence of colitis in genetically susceptible Il10(−/−), but not wild-type mice. These effects are mediated by milk-derived-fat-promoted taurine conjugation of hepatic bile acids, which increases the availability of organic sulphur used by sulphite-reducing microorganisms like B. wadsworthia. When mice were fed a low-fat diet supplemented with taurocholic acid, but not with glycocholic acid, for example, a bloom of B. wadsworthia and development of colitis were observed in Il10(−/−) mice. Together these data show that dietary fats, by promoting changes in host bile acid composition, can markedly alter conditions for gut microbial assemblage, resulting in dysbiosis that can perturb immune homeostasis. The data provide a plausible mechanistic basis by which Western-type diets high in certain saturated fats might increase the prevalence of complex immune-mediated diseases like inflammatory bowel disease in genetically susceptible hosts.
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Affiliation(s)
- Suzanne Devkota
- Department of Medicine, Section of Gastroenterology, The University of Chicago, Knapp Center for Biomedical Discovery, 900 East 57th Street, Chicago, Illinois 60637, USA
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DePaolo RW, Abadie V, Tang F, Fehlner-Peach H, Hall JA, Wang W, Marietta EV, Kasarda DD, Waldmann TA, Murray JA, Semrad C, Kupfer SS, Belkaid Y, Guandalini S, Jabri B. Co-adjuvant effects of retinoic acid and IL-15 induce inflammatory immunity to dietary antigens. Nature 2011; 471:220-4. [PMID: 21307853 DOI: 10.1038/nature09849] [Citation(s) in RCA: 303] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 01/19/2011] [Indexed: 12/18/2022]
Abstract
Under physiological conditions the gut-associated lymphoid tissues not only prevent the induction of a local inflammatory immune response, but also induce systemic tolerance to fed antigens. A notable exception is coeliac disease, where genetically susceptible individuals expressing human leukocyte antigen (HLA) HLA-DQ2 or HLA-DQ8 molecules develop inflammatory T-cell and antibody responses against dietary gluten, a protein present in wheat. The mechanisms underlying this dysregulated mucosal immune response to a soluble antigen have not been identified. Retinoic acid, a metabolite of vitamin A, has been shown to have a critical role in the induction of intestinal regulatory responses. Here we find in mice that in conjunction with IL-15, a cytokine greatly upregulated in the gut of coeliac disease patients, retinoic acid rapidly activates dendritic cells to induce JNK (also known as MAPK8) phosphorylation and release the proinflammatory cytokines IL-12p70 and IL-23. As a result, in a stressed intestinal environment, retinoic acid acted as an adjuvant that promoted rather than prevented inflammatory cellular and humoral responses to fed antigen. Altogether, these findings reveal an unexpected role for retinoic acid and IL-15 in the abrogation of tolerance to dietary antigens.
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Affiliation(s)
- R W DePaolo
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
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