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Zhao H, Zhang W, Cheng D, You L, Huang Y, Lu Y. Investigating dysbiosis and microbial treatment strategies in inflammatory bowel disease based on two modified Koch's postulates. Front Med (Lausanne) 2022; 9:1023896. [PMID: 36438062 PMCID: PMC9684636 DOI: 10.3389/fmed.2022.1023896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/28/2022] [Indexed: 12/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic non-specific inflammatory disease that occurs in the intestinal tract. It is mainly divided into two subtypes, i.e., the Crohn's disease (CD) and ulcerative colitis (UC). At present, its pathogenesis has not been fully elucidated, but it has been generally believed that the environment, immune disorders, genetic susceptibility, and intestinal microbes are the main factors for the disease pathogenesis. With the development of the sequencing technology, microbial factors have received more and more attention. The gut microbiota is in a state of precise balance with the host, in which the host immune system is tolerant to immunogenic antigens produced by gut commensal microbes. In IBD patients, changes in the balance between pathogenic microorganisms and commensal microbes lead to changes in the composition and diversity of gut microbes, and the balance between microorganisms and the host would be disrupted. This new state is defined as dysbiosis. It has been confirmed, in both clinical and experimental settings, that dysbiosis plays an important role in the occurrence and development of IBD, but the causal relationship between dysbiosis and inflammation has not been elucidated. On the other hand, as a classic research method for pathogen identification, the Koch's postulates sets the standard for verifying the role of pathogens in disease. With the further acknowledgment of the disease pathogenesis, it is realized that the traditional Koch's postulates is not applicable to the etiology research (determination) of infectious diseases. Thus, many researchers have carried out more comprehensive and complex elaboration of Koch's postulates to help people better understand and explain disease pathogenesis through the improved Koch's postulates. Therefore, focusing on the new perspective of the improved Koch's postulates is of great significance for deeply understanding the relationship between dysbiosis and IBD. This article has reviewed the studies on dysbiosis in IBD, the use of microbial agents in the treatment of IBD, and their relationship to the modified Koch's postulates.
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Affiliation(s)
- HanZheng Zhao
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - WenHui Zhang
- Department of Pain Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Die Cheng
- Cancer Research Laboratory, Chengde Medical College, Chengde, China
| | - LiuPing You
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - YueNan Huang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - YanJie Lu
- Cancer Research Laboratory, Chengde Medical College, Chengde, China
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Aguanno D, Metwaly A, Coleman OI, Haller D. Modeling microbiota-associated human diseases: from minimal models to complex systems. MICROBIOME RESEARCH REPORTS 2022; 1:17. [PMID: 38046357 PMCID: PMC10688821 DOI: 10.20517/mrr.2022.01] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/08/2022] [Accepted: 04/24/2022] [Indexed: 12/05/2023]
Abstract
Alterations in the intestinal microbiota are associated with various human diseases of the digestive system, including obesity and its associated metabolic diseases, inflammatory bowel diseases (IBD), and colorectal cancer (CRC). All three diseases are characterized by modifications of the richness, composition, and metabolic functions of the human intestinal microbiota. Despite being multi-factorial diseases, studies in germ-free animal models have unarguably identified the intestinal microbiota as a causal driver of disease pathogenesis. However, for an increased mechanistic understanding of microbial signatures in human diseases, models require detailed refinement to closely mimic the human microbiota and reflect the complexity and range of dysbiosis observed in patients. The transplantation of human fecal microbiota into animal models represents a powerful tool for studying the causal and functional role of the dysbiotic human microbiome in a pathological context. While human microbiota-associated models were initially employed to study obesity, an increasing number of studies have applied this approach in the context of IBD and CRC over the past decade. In this review, we discuss different approaches that allow the functional validation of the bacterial contribution to human diseases, with emphasis on obesity and its associated metabolic diseases, IBD, and CRC. We discuss the utility of simple models, such as in vitro fermentation systems of the human microbiota and ex vivo intestinal organoids, as well as more complex whole organism models. Our focus here lies on human microbiota-associated mouse models in the context of all three diseases, as well as highlighting the advantages and limitations of this approach.
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Affiliation(s)
- Doriane Aguanno
- Chair of Nutrition and Immunology, Technical University of Munich, Freising 85354, Germany
| | - Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising 85354, Germany
| | - Olivia I. Coleman
- Chair of Nutrition and Immunology, Technical University of Munich, Freising 85354, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising 85354, Germany
- ZIEL Institute for Food & Health, Technical University of Munich, Freising 85354, Germany
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Parthasarathy S, Wang X, Carr KR, Varahan S, Hancock EB, Hancock LE. SigV Mediates Lysozyme Resistance in Enterococcus faecalis via RsiV and PgdA. J Bacteriol 2021; 203:e0025821. [PMID: 34370556 PMCID: PMC8459761 DOI: 10.1128/jb.00258-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Enterococcus faecalis is a gut commensal but transitions to a pathogenic state as a consequence of intestinal dysbiosis and/or the presence of indwelling medical devices, causing a wide range of infections. One of the unique features of E. faecalis is its ability to display high level resistance to lysozyme, an important host defense of the innate immune response. Lysozyme resistance in E. faecalis is known to be mediated by the extracytoplasmic function (ECF) sigma factor SigV. PgdA and RsiV expression is directly regulated by SigV, but pgdA and rsiV mutants display nominal changes in lysozyme resistance, suggesting that additional gene products in the SigV regulon contribute to lysozyme resistance. Using transcriptome sequencing (RNA-seq) analysis, we compared the transcriptional profile of the parental strain to that of an isogenic sigV mutant and show that apart from sigV, only rsiV and pgdA expression was induced upon lysozyme exposure. The combined deletion mutant of both rsiV and pgdA rendered E. faecalis sensitive to lysozyme at a level comparable to that of the sigV mutant, highlighting the limited SigV regulon. Several additional genes were also induced upon lysozyme exposure, but in a SigV-independent fashion. Overexpression of pgdA from a SigV-independent promoter restored lysozyme resistance in a sigV deletion mutant and also induced cell chaining. Overexpression of rsiV from a SigV-independent promoter only partially restored lysozyme resistance in a sigV mutant. Overall, we provide evidence for a simple adaptation to lysozyme stress, in which SigV controls the expression of rsiV and pgdA, and that both gene products contribute to lysozyme resistance. IMPORTANCE Enterococcus faecalis causes health care-associated infections and displays resistance to a variety of antibiotics and molecules of the innate immune system. SigV has been shown to play an important role in enterococcal lysozyme resistance. Even though several proteins have been implicated in enterococcal lysozyme resistance, a complete SigV-dependent regulon has not been functionally characterized as being responsible for the dramatic increase in lysozyme susceptibility displayed by a sigV mutant. Using RNA-seq, we have identified the SigV regulon to be comprised of two gene loci, sigV-rsiV and pgdA. Deletion of both rsiV and pgdA renders E. faecalis susceptible to lysozyme on par with a sigV mutant. We also demonstrate that overproduction of rsiV and pgdA contributes to lysozyme resistance in susceptible strains.
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Affiliation(s)
- Srivatsan Parthasarathy
- Department of Molecular Biosciences, University of Kansasgrid.266515.3, Lawrence, Kansas, USA
| | - Xiaofei Wang
- Department of Molecular Biosciences, University of Kansasgrid.266515.3, Lawrence, Kansas, USA
| | - Kristen R. Carr
- Department of Molecular Biosciences, University of Kansasgrid.266515.3, Lawrence, Kansas, USA
| | - Sriram Varahan
- Department of Molecular Biosciences, University of Kansasgrid.266515.3, Lawrence, Kansas, USA
| | - Elyssa B. Hancock
- Department of Molecular Biosciences, University of Kansasgrid.266515.3, Lawrence, Kansas, USA
| | - Lynn E. Hancock
- Department of Molecular Biosciences, University of Kansasgrid.266515.3, Lawrence, Kansas, USA
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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] [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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Genua F, Raghunathan V, Jenab M, Gallagher WM, Hughes DJ. The Role of Gut Barrier Dysfunction and Microbiome Dysbiosis in Colorectal Cancer Development. Front Oncol 2021; 11:626349. [PMID: 33937029 PMCID: PMC8082020 DOI: 10.3389/fonc.2021.626349] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/12/2021] [Indexed: 02/06/2023] Open
Abstract
Accumulating evidence indicates that breakdown of the+ protective mucosal barrier of the gut plays a role in colorectal cancer (CRC) development. Inflammation and oxidative stress in the colonic epithelium are thought to be involved in colorectal carcinogenesis and the breakdown of the integrity of the colonic barrier may increase the exposure of colonocytes to toxins from the colonic milieu, enhancing inflammatory processes and release of Reactive Oxygen Species (ROS). The aetiological importance of the gut microbiome and its composition - influenced by consumption of processed meats, red meats and alcoholic drinks, smoking, physical inactivity, obesity - in CRC development is also increasingly being recognized. The gut microbiome has diverse roles, such as in nutrient metabolism and immune modulation. However, microbial encroachment towards the colonic epithelium may promote inflammation and oxidative stress and even translocation of species across the colonic lumen. Recent research suggests that factors that modify the above mechanisms, e.g., obesity and Western diet, also alter gut microbiota, degrade the integrity of the gut protective barrier, and expose colonocytes to toxins. However, it remains unclear how obesity, lifestyle and metabolic factors contribute to gut-barrier integrity, leading to metabolic disturbance, colonocyte damage, and potentially to CRC development. This review will discuss the interactive roles of gut-barrier dysfunction, microbiome dysbiosis, and exposure to endogenous toxins as another mechanism in CRC development, and how biomarkers of colonic mucosal barrier function may provide avenues for disease, prevention and detection.
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Affiliation(s)
- Flavia Genua
- Cancer Biology and Therapeutics Laboratory, Conway Institute, School of Biomedical and Biomolecular Sciences, University College Dublin, Dublin, Ireland
| | - Vedhika Raghunathan
- College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI, United States
| | - Mazda Jenab
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - William M. Gallagher
- Cancer Biology and Therapeutics Laboratory, Conway Institute, School of Biomedical and Biomolecular Sciences, University College Dublin, Dublin, Ireland
| | - David J. Hughes
- Cancer Biology and Therapeutics Laboratory, Conway Institute, School of Biomedical and Biomolecular Sciences, University College Dublin, Dublin, Ireland
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Becattini S, Sorbara MT, Kim SG, Littmann EL, Dong Q, Walsh G, Wright R, Amoretti L, Fontana E, Hohl TM, Pamer EG. Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation. Cell Host Microbe 2021; 29:378-393.e5. [PMID: 33539766 PMCID: PMC7954923 DOI: 10.1016/j.chom.2021.01.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/08/2020] [Accepted: 01/07/2021] [Indexed: 12/17/2022]
Abstract
The gut microbiota produces metabolites that regulate host immunity, thereby impacting disease resistance and susceptibility. The extent to which commensal bacteria reciprocally respond to immune activation, however, remains largely unexplored. Herein, we colonized mice with four anaerobic symbionts and show that acute immune responses result in dramatic transcriptional reprogramming of these commensals with minimal changes in their relative abundance. Transcriptomic changes include induction of stress-response mediators and downregulation of carbohydrate-degrading factors such as polysaccharide utilization loci (PULs). Flagellin and anti-CD3 antibody, two distinct immune stimuli, induced similar transcriptional profiles, suggesting that commensal bacteria detect common effectors or activate shared pathways when facing different host responses. Immune activation altered the intestinal metabolome within 6 hours, decreasing luminal short-chain fatty acid and increasing aromatic metabolite concentrations. Thus, intestinal bacteria, prior to detectable shifts in community composition, respond to acute host immune activation by rapidly changing gene transcription and immunomodulatory metabolite production.
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Affiliation(s)
- Simone Becattini
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology and Immunology, School of Medicine, University of Geneva, 1206 Geneva, Switzerland.
| | - Matthew T Sorbara
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Sohn G Kim
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Eric L Littmann
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Qiwen Dong
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Gavin Walsh
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Roberta Wright
- Center for Microbes Inflammation and Cancer, Molecular Microbiology Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Luigi Amoretti
- Center for Microbes Inflammation and Cancer, Molecular Microbiology Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Emily Fontana
- Center for Microbes Inflammation and Cancer, Molecular Microbiology Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Tobias M Hohl
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Infectious Diseases Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA.
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Molecular characterization of the virulence genes gelE and cylA in the Enterococcus species isolated from clinical samples. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Complete Structure of the Enterococcal Polysaccharide Antigen (EPA) of Vancomycin-Resistant Enterococcus faecalis V583 Reveals that EPA Decorations Are Teichoic Acids Covalently Linked to a Rhamnopolysaccharide Backbone. mBio 2020; 11:mBio.00277-20. [PMID: 32345640 PMCID: PMC7188991 DOI: 10.1128/mbio.00277-20] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Enterococci are opportunistic pathogens responsible for hospital- and community-acquired infections. All enterococci produce a surface polysaccharide called EPA (enterococcal polysaccharide antigen) required for biofilm formation, antibiotic resistance, and pathogenesis. Despite the critical role of EPA in cell growth and division and as a major virulence factor, no information is available on its structure. Here, we report the complete structure of the EPA polymer produced by the model strain E. faecalis V583. We describe the structure of the EPA backbone, made of a rhamnan hexasaccharide substituted by Glc and GlcNAc residues, and show that teichoic acids are covalently bound to this rhamnan chain, forming the so-called “EPA decorations” essential for host colonization and pathogenesis. This report represents a key step in efforts to identify the structural properties of EPA that are essential for its biological activity and to identify novel targets to develop preventive and therapeutic approaches against enterococci. All enterococci produce a complex polysaccharide called the enterococcal polysaccharide antigen (EPA). This polymer is required for normal cell growth and division and for resistance to cephalosporins and plays a critical role in host-pathogen interaction. The EPA contributes to host colonization and is essential for virulence, conferring resistance to phagocytosis during the infection. Recent studies revealed that the “decorations” of the EPA polymer, encoded by genetic loci that are variable between isolates, underpin the biological activity of this surface polysaccharide. In this work, we investigated the structure of the EPA polymer produced by the high-risk enterococcal clonal complex Enterococcus faecalis V583. We analyzed purified EPA from the wild-type strain and a mutant lacking decorations and elucidated the structure of the EPA backbone and decorations. We showed that the rhamnan backbone of EPA is composed of a hexasaccharide repeat unit of C2- and C3-linked rhamnan chains, partially substituted in the C3 position by α-glucose (α-Glc) and in the C2 position by β-N-acetylglucosamine (β-GlcNAc). The so-called “EPA decorations” consist of phosphopolysaccharide chains corresponding to teichoic acids covalently bound to the rhamnan backbone. The elucidation of the complete EPA structure allowed us to propose a biosynthetic pathway, a first essential step toward the design of antimicrobials targeting the synthesis of this virulence factor.
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Yue B, Luo X, Yu Z, Mani S, Wang Z, Dou W. Inflammatory Bowel Disease: A Potential Result from the Collusion between Gut Microbiota and Mucosal Immune System. Microorganisms 2019; 7:microorganisms7100440. [PMID: 31614539 PMCID: PMC6843348 DOI: 10.3390/microorganisms7100440] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/02/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022] Open
Abstract
Host health depends on the intestinal homeostasis between the innate/adaptive immune system and the microbiome. Numerous studies suggest that gut microbiota are constantly monitored by the host mucosal immune system, and any slight disturbance in the microbial communities may contribute to intestinal immune disruption and increased susceptibility to inflammatory bowel disease (IBD), a chronic relapsing inflammatory condition of the gastrointestinal tract. Therefore, maintaining intestinal immune homeostasis between microbiota composition and the mucosal immune system is an effective approach to prevent and control IBD. The overall theme of this review is to summarize the research concerning the pathogenesis of IBD, with particular focus on the factors of gut microbiota-mucosal immune interactions in IBD. This is a comprehensive and in-depth report of the crosstalk between gut microbiota and the mucosal immune system in IBD pathogenesis, which may provide insight into the further evaluation of the therapeutic strategies for IBD.
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Affiliation(s)
- Bei Yue
- Shanghai Key Laboratory of Formulated Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai 201203, China.
| | - Xiaoping Luo
- Shanghai Key Laboratory of Formulated Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai 201203, China.
| | - Zhilun Yu
- Shanghai Key Laboratory of Formulated Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai 201203, China.
| | - Sridhar Mani
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, The Bronx, NY 10461, USA.
| | - Zhengtao Wang
- Shanghai Key Laboratory of Formulated Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai 201203, China.
| | - Wei Dou
- Shanghai Key Laboratory of Formulated Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai 201203, China.
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Fitness Restoration of a Genetically Tractable Enterococcus faecalis V583 Derivative To Study Decoration-Related Phenotypes of the Enterococcal Polysaccharide Antigen. mSphere 2019; 4:4/4/e00310-19. [PMID: 31292230 PMCID: PMC6620374 DOI: 10.1128/msphere.00310-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
E. faecalis strain VE14089 was derived from V583 cured of its plasmids. Although VE14089 had no major DNA rearrangements, it presented significant growth and host adaptation differences from the reference strain V583 of our collection. To construct a strain with better fitness, we sequenced the genome of VE14089, identified single nucleotide polymorphisms (SNPs), and repaired the genes that could account for these changes. Using this reference-derivative strain, we provide a novel genetic system to understand the role of the variable region of epa in the enterococcal lifestyle. Commensal and generally harmless in healthy individuals, Enterococcus faecalis causes opportunistic infections in immunocompromised patients. Plasmid-cured E. faecalis strain VE14089, derived from sequenced reference strain V583, is widely used for functional studies due to its improved genetic amenability. Although strain VE14089 has no major DNA rearrangements, with the exception of an ∼20-kb integrated region of pTEF1 plasmid, the strain presented significant growth differences from the V583 reference strain of our collection (renamed VE14002). In the present study, genome sequencing of strain VE14089 identified additional point mutations. Excision of the integrated pTEF1 plasmid region and sequential restoration of wild-type alleles showing nonsilent mutations were performed to obtain the VE18379 reference-derivative strain. Recovery of the growth ability of the restored VE18379 strain at a level similar to that seen with the reference strain points to GreA and Spx as bacterial fitness determinants. Virulence potential in Galleria mellonella and intestinal colonization in mouse demonstrated host adaptation of the VE18379 strain equivalent to VE14002 host adaptation. We further demonstrated that deletion of the 16.8-kb variable region of the epa locus recapitulates the key role of Epa decoration in host adaptation, providing a genetic system to study the role of specific epa-variable regions in host adaptation independently of other genetic variations. IMPORTANCEE. faecalis strain VE14089 was derived from V583 cured of its plasmids. Although VE14089 had no major DNA rearrangements, it presented significant growth and host adaptation differences from the reference strain V583 of our collection. To construct a strain with better fitness, we sequenced the genome of VE14089, identified single nucleotide polymorphisms (SNPs), and repaired the genes that could account for these changes. Using this reference-derivative strain, we provide a novel genetic system to understand the role of the variable region of epa in the enterococcal lifestyle.
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Fiore E, Van Tyne D, Gilmore MS. Pathogenicity of Enterococci. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0053-2018. [PMID: 31298205 PMCID: PMC6629438 DOI: 10.1128/microbiolspec.gpp3-0053-2018] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Indexed: 12/19/2022] Open
Abstract
Enterococci are unusually well adapted for survival and persistence in a variety of adverse environments, including on inanimate surfaces in the hospital environment and at sites of infection. This intrinsic ruggedness undoubtedly played a role in providing opportunities for enterococci to interact with other overtly drug-resistant microbes and acquire additional resistances on mobile elements. The rapid rise of antimicrobial resistance among hospital-adapted enterococci has rendered hospital-acquired infections a leading therapeutic challenge. With about a quarter of a genome of additional DNA conveyed by mobile elements, there are undoubtedly many more properties that have been acquired that help enterococci persist and spread in the hospital setting and cause diseases that have yet to be defined. Much remains to be learned about these ancient and rugged microbes, particularly in the area of pathogenic mechanisms involved with human diseases.
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Affiliation(s)
- Elizabeth Fiore
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
| | - Daria Van Tyne
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
| | - Michael S Gilmore
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
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Enterococcus faecalis Gluconate Phosphotransferase System Accelerates Experimental Colitis and Bacterial Killing by Macrophages. Infect Immun 2019; 87:IAI.00080-19. [PMID: 31036600 DOI: 10.1128/iai.00080-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/21/2019] [Indexed: 02/07/2023] Open
Abstract
Enterococcus faecalis strains are resident intestinal bacteria associated with invasive infections, inflammatory bowel diseases, and colon cancer. Although factors promoting E. faecalis colonization of intestines are not fully known, one implicated pathway is a phosphotransferase system (PTS) in E. faecalis strain OG1RF that phosphorylates gluconate and contains the genes OG1RF_12399 to OG1RF_12402 (OG1RF_12399-12402). We hypothesize that this PTS permits growth in gluconate, facilitates E. faecalis intestinal colonization, and exacerbates colitis. We generated E. faecalis strains containing deletions/point mutations in this PTS and measured bacterial growth and PTS gene expression in minimal medium supplemented with selected carbohydrates. We show that E. faecalis upregulates OG1RF_12399 transcription specifically in the presence of gluconate and that E. faecalis strains lacking, or harboring a single point mutation in, OG1RF_12399-12402 are unable to grow in minimal medium containing gluconate. We colonized germfree wild-type and colitis-prone interleukin-10-deficient mice with defined bacterial consortia containing the E. faecalis strains and measured inflammation and bacterial abundance in the colon. We infected macrophage and intestinal epithelial cell lines with the E. faecalis strains and measured intracellular bacterial survival and proinflammatory cytokine secretion. The presence of OG1RF_12399-12402 is not required for E. faecalis colonization of the mouse intestine but is associated with an accelerated onset of experimental colitis in interleukin-10-deficient mice, altered bacterial composition in the colon, enhanced E. faecalis survival within macrophages, and increased proinflammatory cytokine secretion by colon tissue and macrophages. Further studies of bacterial carbohydrate metabolism in general, and E. faecalis PTS-gluconate in particular, during inflammation may identify new mechanisms of disease pathogenesis.
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13
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Lengfelder I, Sava IG, Hansen JJ, Kleigrewe K, Herzog J, Neuhaus K, Hofmann T, Sartor RB, Haller D. Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis. Front Immunol 2019; 10:1420. [PMID: 31281321 PMCID: PMC6596359 DOI: 10.3389/fimmu.2019.01420] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/05/2019] [Indexed: 12/17/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are associated with compositional and functional changes of the intestinal microbiota, but specific contributions of individual bacteria to chronic intestinal inflammation remain unclear. Enterococcus faecalis is a resident member of the human intestinal core microbiota that has been linked to the pathogenesis of IBD and induces chronic colitis in susceptible monoassociated IL-10-deficient (IL-10−/−) mice. In this study, we characterized the colitogenic activity of E. faecalis as part of a simplified human microbial consortium based on seven enteric bacterial strains (SIHUMI). RNA sequencing analysis of E. faecalis isolated from monoassociated wild type and IL-10−/− mice identified 408 genes including 14 genes of the ethanolamine utilization (eut) locus that were significantly up-regulated in response to inflammation. Despite considerable up-regulation of eut genes, deletion of ethanolamine utilization (ΔeutVW) had no impact on E. faecalis colitogenic activity in monoassociated IL-10−/− mice. However, replacement of the E. faecalis wild type bacteria by a ΔeutVW mutant in SIHUMI-colonized IL-10−/− mice resulted in exacerbated colitis, suggesting protective functions of E. faecalis ethanolamine utilization in complex bacterial communities. To better understand E. faecalis gene response in the presence of other microbes, we purified wild type E. faecalis cells from the colon content of SIHUMI-colonized wild type and IL-10−/− mice using immuno-magnetic separation and performed RNA sequencing. Transcriptional profiling revealed that the bacterial environment reprograms E. faecalis gene expression in response to inflammation, with the majority of differentially expressed genes not being shared between monocolonized and SIHUMI conditions. While in E. faecalis monoassociation a general bacterial stress response could be observed, expression of E. faecalis genes in SIHUMI-colonized mice was characterized by up-regulation of genes involved in growth and replication. Interestingly, in mice colonized with SIHUMI lacking E. faecalis enhanced inflammation was observed in comparison to SIHUMI-colonized mice, supporting the hypothesis that E. faecalis ethanolamine metabolism protects against colitis in complex consortia. In conclusion, this study demonstrates that complex bacterial consortia interactions reprogram the gene expression profile and colitogenic activity of the opportunistic pathogen E. faecalis toward a protective function.
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Affiliation(s)
- Isabella Lengfelder
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Irina G Sava
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Jonathan J Hansen
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, Technische Universität München, Freising, Germany
| | - Jeremy Herzog
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
| | - Klaus Neuhaus
- ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany.,ZIEL Core Facility Microbiome, Technische Universität München, Freising, Germany
| | - Thomas Hofmann
- Bavarian Center for Biomolecular Mass Spectrometry, Technische Universität München, Freising, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - R Balfour Sartor
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
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14
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Smith RE, Salamaga B, Szkuta P, Hajdamowicz N, Prajsnar TK, Bulmer GS, Fontaine T, Kołodziejczyk J, Herry JM, Hounslow AM, Williamson MP, Serror P, Mesnage S. Decoration of the enterococcal polysaccharide antigen EPA is essential for virulence, cell surface charge and interaction with effectors of the innate immune system. PLoS Pathog 2019; 15:e1007730. [PMID: 31048927 PMCID: PMC6497286 DOI: 10.1371/journal.ppat.1007730] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/26/2019] [Indexed: 12/13/2022] Open
Abstract
Enterococcus faecalis is an opportunistic pathogen with an intrinsically high resistance to lysozyme, a key effector of the innate immune system. This high level of resistance requires a complex network of transcriptional regulators and several genes (oatA, pgdA, dltA and sigV) acting synergistically to inhibit both the enzymatic and cationic antimicrobial peptide activities of lysozyme. We sought to identify novel genes modulating E. faecalis resistance to lysozyme. Random transposon mutagenesis carried out in the quadruple oatA/pgdA/dltA/sigV mutant led to the identification of several independent insertions clustered on the chromosome. These mutations were located in a locus referred to as the enterococcal polysaccharide antigen (EPA) variable region located downstream of the highly conserved epaA-epaR genes proposed to encode a core synthetic machinery. The epa variable region was previously proposed to be responsible for EPA decorations, but the role of this locus remains largely unknown. Here, we show that EPA decoration contributes to resistance towards charged antimicrobials and underpins virulence in the zebrafish model of infection by conferring resistance to phagocytosis. Collectively, our results indicate that the production of the EPA rhamnopolysaccharide backbone is not sufficient to promote E. faecalis infections and reveal an essential role of the modification of this surface polymer for enterococcal pathogenesis. Enterococcus faecalis is a commensal bacterium colonizing the gastro-intestinal tract of humans. This organism can cause life-threatening opportunistic infections and represents a reservoir for the transmission of antibiotic resistance genes such as resistance to vancomycin. E. faecalis strains responsible for nosocomial infections are also found in healthy individuals and the virulence factors identified so far are not strictly associated with clinical isolates. The molecular basis underpinning E. faecalis infections therefore remains unclear. In this work, we identify several mutations clustered on the chromosome, which play a role in the resistance of E. faecalis to effectors of the innate immune system such as lysozyme and bile salts. We show that the corresponding genes contribute to the decoration of a conserved polysaccharide called the enterococcal polysaccharide antigen and that this decoration is essential for E. faecalis virulence. This mechanism critical for pathogenesis represents an attractive therapeutic target to control enterococcal infections.
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Affiliation(s)
- Robert E. Smith
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - Bartłomiej Salamaga
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - Piotr Szkuta
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - Natalia Hajdamowicz
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - Tomasz K. Prajsnar
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - Gregory S. Bulmer
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | | | - Justyna Kołodziejczyk
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - Jean-Marie Herry
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Andrea M. Hounslow
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - Mike P. Williamson
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - Pascale Serror
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
- * E-mail: (PS); (SM)
| | - Stéphane Mesnage
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
- * E-mail: (PS); (SM)
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15
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Loss of a Major Enterococcal Polysaccharide Antigen (Epa) by Enterococcus faecalis Is Associated with Increased Resistance to Ceftriaxone and Carbapenems. Antimicrob Agents Chemother 2019; 63:AAC.00481-19. [PMID: 30858216 DOI: 10.1128/aac.00481-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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16
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Bertolini M, Ranjan A, Thompson A, Diaz PI, Sobue T, Maas K, Dongari-Bagtzoglou A. Candida albicans induces mucosal bacterial dysbiosis that promotes invasive infection. PLoS Pathog 2019; 15:e1007717. [PMID: 31009520 PMCID: PMC6497318 DOI: 10.1371/journal.ppat.1007717] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/02/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022] Open
Abstract
Infectious complications are a common cause of morbidity and mortality in cancer patients undergoing chemotherapy due to increased risk of oral and gastrointestinal candidiasis, candidemia and septicemia. Interactions between C. albicans and endogenous mucosal bacteria are important in understanding the mechanisms of invasive infection. We published a mouse intravenous chemotherapy model that recapitulates oral and intestinal mucositis, and myelosuppression in patients receiving 5-fluorouracil. We used this model to study the influence of C. albicans on the mucosal bacterial microbiome and compared global community changes in the oral and intestinal mucosa of the same mice. We validated 16S rRNA gene sequencing data by qPCR, in situ hybridization and culture approaches. Mice receiving both 5Fu and C. albicans had an endogenous bacterial overgrowth on the oral but not the small intestinal mucosa. C. albicans infection was associated with loss of mucosal bacterial diversity in both sites with indigenous Stenotrophomonas, Alphaproteobacteria and Enterococcus species dominating the small intestinal, and Enterococcus species dominating the oral mucosa. Both immunosuppression and Candida infection contributed to changes in the oral microbiota. Enterococci isolated from mice with oropharyngeal candidiasis were implicated in degrading the epithelial junction protein E-cadherin and increasing the permeability of the oral epithelial barrier in vitro. Importantly, depletion of these organisms with antibiotics in vivo attenuated oral mucosal E-cadherin degradation and C. albicans invasion without affecting fungal burdens, indicating that bacterial community changes represent overt dysbiosis. Our studies demonstrate a complex interaction between C. albicans, the resident mucosal bacterial microbiota and the host environment in pathogenesis. We shed significant new light on the role of C. albicans in shaping resident bacterial communities and driving mucosal dysbiosis.
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Affiliation(s)
- Martinna Bertolini
- Department of Oral Health Sciences, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Amit Ranjan
- Department of Oral Health Sciences, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Angela Thompson
- Department of Oral Health Sciences, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Patricia I. Diaz
- Department of Oral Health Sciences, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Takanori Sobue
- Department of Oral Health Sciences, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Kendra Maas
- Microbial Analysis, Resources, and Services Core, University of Connecticut, Storrs, Connecticut, United States of America
| | - Anna Dongari-Bagtzoglou
- Department of Oral Health Sciences, University of Connecticut Health Center, Farmington, Connecticut, United States of America
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17
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King SJ, McCole DF. Epithelial-microbial diplomacy: escalating border tensions drive inflammation in inflammatory bowel disease. Intest Res 2019; 17:177-191. [PMID: 30836737 PMCID: PMC6505084 DOI: 10.5217/ir.2018.00170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 02/01/2019] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic conditions of the gastrointestinal tract-the main site of host-microbial interaction in the body. Development of IBD is not due to a single event but rather is a multifactorial process where a patient’s genetic background, behavioral habits, and environmental exposures contribute to disease pathogenesis. IBD patients exhibit alterations to gut bacterial populations “dysbiosis” due to the inflammatory microenvironment, however whether this alteration of the gut microbiota precedes inflammation has not been confirmed. Emerging evidence has highlighted the important role of gut microbes in developing measured immune responses and modulating other host responses such as metabolism. Much of the work on the gut microbiota has been correlative and there is an increasing need to understand the intimate relationship between host and microbe. In this review, we highlight how commensal and pathogenic bacteria interact with host intestinal epithelial cells and explore how altered microenvironments impact these connections.
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Affiliation(s)
- Stephanie J King
- Division of Biomedical Sciences, University of California, Riverside, CA, USA
| | - Declan F McCole
- Division of Biomedical Sciences, University of California, Riverside, CA, USA
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18
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Yu LCH. Microbiota dysbiosis and barrier dysfunction in inflammatory bowel disease and colorectal cancers: exploring a common ground hypothesis. J Biomed Sci 2018; 25:79. [PMID: 30413188 PMCID: PMC6234774 DOI: 10.1186/s12929-018-0483-8] [Citation(s) in RCA: 237] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/29/2018] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a multifactorial disease which arises as a result of the interaction of genetic, environmental, barrier and microbial factors leading to chronic inflammation in the intestine. Patients with IBD had a higher risk of developing colorectal carcinoma (CRC), of which the subset was classified as colitis-associated cancers. Genetic polymorphism of innate immune receptors had long been considered a major risk factor for IBD, and the mutations were also recently observed in CRC. Altered microbial composition (termed microbiota dybiosis) and dysfunctional gut barrier manifested by epithelial hyperpermeability and high amount of mucosa-associated bacteria were observed in IBD and CRC patients. The findings suggested that aberrant immune responses to penetrating commensal microbes may play key roles in fueling disease progression. Accumulative evidence demonstrated that mucosa-associated bacteria harbored colitogenic and protumoral properties in experimental models, supporting an active role of bacteria as pathobionts (commensal-derived opportunistic pathogens). Nevertheless, the host factors involved in bacterial dysbiosis and conversion mechanisms from lumen-dwelling commensals to mucosal pathobionts remain unclear. Based on the observation of gut leakiness in patients and the evidence of epithelial hyperpermeability prior to the onset of mucosal histopathology in colitic animals, it was postulated that the epithelial barrier dysfunction associated with mucosal enrichment of specific bacterial strains may predispose the shift to disease-associated microbiota. The speculation of leaky gut as an initiating factor for microbiota dysbiosis that eventually led to pathological consequences was proposed as the "common ground hypothesis", which will be highlighted in this review. Overall, the understanding of the core interplay between gut microbiota and epithelial barriers at early subclinical phases will shed light to novel therapeutic strategies to manage chronic inflammatory disorders and colitis-associated cancers.
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Affiliation(s)
- Linda Chia-Hui Yu
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Suite 1020, #1 Jen-Ai Rd. Sec. 1, Taipei, 100, Taiwan, Republic of China.
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19
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Vogelzang A, Guerrini MM, Minato N, Fagarasan S. Microbiota - an amplifier of autoimmunity. Curr Opin Immunol 2018; 55:15-21. [PMID: 30248521 DOI: 10.1016/j.coi.2018.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/07/2018] [Indexed: 02/08/2023]
Abstract
Many studies describe dysbiosis as a change in the microbiota that accompanies autoimmune illnesses, but little is known about whether these changes are a cause or consequence of an altered immune state. The immune system actively shapes the composition of the microbiota, with divergent outcomes in healthy or autoimmune-prone individuals. The gut microbiota in turn acts as an acquired endocrine organ, influencing the physiology of the host via release of nutrients and chemical messengers. Dysbiosis arising from abnormal immune function can initiate or amplify autoimmunity through multiple mechanisms. We examine how the bidirectional relationship between resident microbes and the immune system contributes to autoimmune diseases.
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Affiliation(s)
- Alexis Vogelzang
- Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Tsurumi Ward, Suehirocho, 1 Chome-7-22, Yokohama, Kanagawa Prefecture, 230-0045, Japan
| | - Matteo M Guerrini
- Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Tsurumi Ward, Suehirocho, 1 Chome-7-22, Yokohama, Kanagawa Prefecture, 230-0045, Japan
| | - Nagahiro Minato
- Medical Innovation Center, Kyoto University Graduate School of Medicine, Sakyo Ward, Yoshida-Konoe, Kyoto, Kyoto Prefecture, 606-8501, Japan
| | - Sidonia Fagarasan
- Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Tsurumi Ward, Suehirocho, 1 Chome-7-22, Yokohama, Kanagawa Prefecture, 230-0045, Japan.
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20
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Testa A, Rispo A, Imperatore N, Nardone OM, Trinchese G, Cavaliere G, Castiglione F, Mollica MP. Gut microbiota and Crohn’s disease. MEDITERRANEAN JOURNAL OF NUTRITION AND METABOLISM 2018. [DOI: 10.3233/mnm-17182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
INTRODUCTION: Crohn’s disease (CD) is characterized by a chronic inflammation of the gastrointestinal tract causing abdominal pain, diarrhea, weight loss and systemic symptoms. Although the etiology of this disease is unknown, current knowledge suggests a multifactorial genesis involving genetic, environmental and immunological factors. EVIDENCE ACQUISITION: We focused our attention on critical analysis of the recent literature on the role of gut microbiota in inflammatory bowel disease (IBD), by evaluating the differences of composition, functions and role of intestinal flora. In particular, we focused on evidences about the interaction between gut microbiota and pathogenesis of IBD. In this setting, we conducted a PUBMED search for guidelines, systematic reviews (SR) and primary studies. EVIDENCE SYNTHESIS: Some data suggest that, in a significant percentage of patients, the microbiota plays an important role in the genesis and maintenance of CD. Probiotic supplementation and antibiotic treatment appear to be a valid therapeutic approach, although the clinical data remain controversial. CONCLUSIONS: Despite the exciting and growing research on the role of gut microbiota in IBD, our knowledge remains fairly limited. Further studies are needed to measure the diversity, function and resistance to antibiotics of the intestinal microbiota in CD.
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Affiliation(s)
- Anna Testa
- Department of Clinical Medicine and Surgery, Gastroenterology, School of Medicine “Federico II” of Naples, Naples, Italy
| | - Antonio Rispo
- Department of Clinical Medicine and Surgery, Gastroenterology, School of Medicine “Federico II” of Naples, Naples, Italy
| | - Nicola Imperatore
- Department of Clinical Medicine and Surgery, Gastroenterology, School of Medicine “Federico II” of Naples, Naples, Italy
| | - Olga Maria Nardone
- Department of Clinical Medicine and Surgery, Gastroenterology, School of Medicine “Federico II” of Naples, Naples, Italy
| | - Giovanna Trinchese
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Gina Cavaliere
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Fabiana Castiglione
- Department of Clinical Medicine and Surgery, Gastroenterology, School of Medicine “Federico II” of Naples, Naples, Italy
| | - Maria Pina Mollica
- Department of Biology, University of Naples “Federico II”, Naples, Italy
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21
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Coleman OI, Haller D. Bacterial Signaling at the Intestinal Epithelial Interface in Inflammation and Cancer. Front Immunol 2018; 8:1927. [PMID: 29354132 PMCID: PMC5760496 DOI: 10.3389/fimmu.2017.01927] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/15/2017] [Indexed: 12/11/2022] Open
Abstract
The gastrointestinal (GI) tract provides a compartmentalized interface with an enormous repertoire of immune and metabolic activities, where the multicellular structure of the mucosa has acquired mechanisms to sense luminal factors, such as nutrients, microbes, and a variety of host-derived and microbial metabolites. The GI tract is colonized by a complex ecosystem of microorganisms, which have developed a highly coevolved relationship with the host’s cellular and immune system. Intestinal epithelial pattern recognition receptors (PRRs) substantially contribute to tissue homeostasis and immune surveillance. The role of bacteria-derived signals in intestinal epithelial homeostasis and repair has been addressed in mouse models deficient in PRRs and signaling adaptors. While critical for host physiology and the fortification of barrier function, the intestinal microbiota poses a considerable health challenge. Accumulating evidence indicates that dysbiosis is associated with the pathogenesis of numerous GI tract diseases, including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). Aberrant signal integration at the epithelial cell level contributes to such diseases. An increased understanding of bacterial-specific structure recognition and signaling mechanisms at the intestinal epithelial interface is of great importance in the translation to future treatment strategies. In this review, we summarize the growing understanding of the regulation and function of the intestinal epithelial barrier, and discuss microbial signaling in the dynamic host–microbe mutualism in both health and disease.
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Affiliation(s)
| | - Dirk Haller
- Technical University of Munich, Munich, Germany.,ZIEL-Institute for Food & Health, Technical University of Munich, Munich, Germany
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22
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Goh HMS, Yong MHA, Chong KKL, Kline KA. Model systems for the study of Enterococcal colonization and infection. Virulence 2017; 8:1525-1562. [PMID: 28102784 PMCID: PMC5810481 DOI: 10.1080/21505594.2017.1279766] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/30/2016] [Accepted: 01/04/2017] [Indexed: 02/07/2023] Open
Abstract
Enterococcus faecalis and Enterococcus faecium are common inhabitants of the human gastrointestinal tract, as well as frequent opportunistic pathogens. Enterococci cause a range of infections including, most frequently, infections of the urinary tract, catheterized urinary tract, bloodstream, wounds and surgical sites, and heart valves in endocarditis. Enterococcal infections are often biofilm-associated, polymicrobial in nature, and resistant to antibiotics of last resort. Understanding Enterococcal mechanisms of colonization and pathogenesis are important for identifying new ways to manage and intervene with these infections. We review vertebrate and invertebrate model systems applied to study the most common E. faecalis and E. faecium infections, with emphasis on recent findings examining Enterococcal-host interactions using these models. We discuss strengths and shortcomings of each model, propose future animal models not yet applied to study mono- and polymicrobial infections involving E. faecalis and E. faecium, and comment on the significance of anti-virulence strategies derived from a fundamental understanding of host-pathogen interactions in model systems.
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Affiliation(s)
- H. M. Sharon Goh
- Singapore Centre for Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore
| | - M. H. Adeline Yong
- Singapore Centre for Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Kelvin Kian Long Chong
- Singapore Centre for Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School, Nanyang Technological University, Singapore
| | - Kimberly A. Kline
- Singapore Centre for Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore
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23
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Media from macrophages co-incubated with Enterococcus faecalis induces epithelial cell monolayer reassembly and altered cell morphology. PLoS One 2017; 12:e0182825. [PMID: 28793333 PMCID: PMC5549984 DOI: 10.1371/journal.pone.0182825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022] Open
Abstract
Signal exchange between intestinal epithelial cells, microbes and local immune cells is an important mechanism of intestinal homeostasis. Given that intestinal macrophages are in close proximity to both the intestinal epithelium and the microbiota, their pathologic interactions may result in epithelial damage. The present study demonstrates that co-incubation of murine macrophages with E. faecalis strains producing gelatinase (GelE) and serine protease (SprE) leads to resultant condition media (CM) capable of inducing reassembly of primary colonic epithelial cell monolayers. Following the conditioned media (CM) exposure, some epithelial cells are shed whereas adherent cells are observed to undergo dissolution of cell-cell junctions and morphologic transformation with actin cytoskeleton reorganization resulting in flattened and elongated shapes. These cells exhibit marked filamentous filopodia and lamellipodia formation. Cellular reorganization is not observed when epithelial monolayers are exposed to: CM from macrophages co-incubated with E. faecalis GelE/SprE-deficient mutants, CM from macrophages alone, or E. faecalis (GelE/SprE) alone. Flow cytometry analysis reveals increased expression of CD24 and CD44 in cells treated with macrophage/E. faecalis CM. This finding in combination with the appearance colony formation in matrigel demonstrate that the cells treated with macrophage/E. faecalis CM contain a higher proportion progenitor cells compared to untreated control. Taken together, these findings provide evidence for a triangulated molecular dialogue between E. faecalis, macrophages and colonic epithelial cells, which may have important implications for conditions in the gut that involve inflammation, injury or tumorigenesis.
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24
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Restructuring of Enterococcus faecalis biofilm architecture in response to antibiotic-induced stress. NPJ Biofilms Microbiomes 2017; 3:15. [PMID: 28685097 PMCID: PMC5493694 DOI: 10.1038/s41522-017-0023-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 05/31/2017] [Accepted: 06/09/2017] [Indexed: 12/19/2022] Open
Abstract
Bacterial biofilms are intrinsically resistant to antimicrobial treatment, which contributes to microbial persistence in clinical infections. Enterococcus faecalis is an opportunistic pathogen that readily forms biofilms and is the most prevalent enterococcal species identified in healthcare-associated infections. Since intrinsic resistance to multiple antibiotics is common for enterococci, and antibiotic resistance is elevated in biofilm populations, it is imperative to understand the mechanisms involved. Previously, we identified two glycosyltransferase genes whose disruption resulted in impaired nascent biofilm formation in the presence of antibiotic concentrations subinhibitory for parent growth and biofilm formation. The glycosyltransferases are involved in synthesis of the cell-wall-associated rhamnopolysaccharide Epa. Here we examined the effect of epa mutations on the temporal development of E. faecalis biofilms, and on the effects of antibiotics on pre-formed biofilms using scanning electron microscopy. We show that ΔepaOX mutant cells arrange into complex multidimensional biofilms independent of antibiotic exposure, while parent cells form biofilms that are monolayers in the absence of antibiotics. Remarkably, upon exposure to antibiotics parent biofilm cells restructure into complex three-dimensional biofilms resembling those of the ΔepaOX mutant without antibiotics. All biofilms exhibiting complex cellular architectures were less structurally stable than monolayer biofilms, with the biofilm cells exhibiting increased detachment. Our results indicate that E. faecalis biofilms restructure in response to cellular stress whether induced by antibiotics in the case of parent cells, or by deficiencies in Epa composition for the ΔepaOX strain. The data demonstrate a link between cellular architecture and antibiotic resistance of E. faecalis biofilms. Studying how the architecture of bacterial biofilms can change on exposure to antibiotics could help tackle persistent clinical infections. Enterococcus faecalis is one of the most prevalent bacteria involved in healthcare situations. Its resistance to antibiotics is elevated by the formation of biofilms. Gary Dunny and colleagues at the University of Minnesota, USA studied genetic factors related to the response of E. faecalis biofilms to antibiotics. They identified mutations that caused the bacterial cells to produce structurally altered biofilms and found that similar structural alterations were induced in biofilms made by normal cells in the presence of antibiotics. The altered architecture can make the biofilms less stable and therefore more easily disrupted by treatments. Learning more about the mechanisms underlying these structural changes in biofilms might lead to new options in treating antibiotic resistant infections.
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Sartor RB, Wu GD. Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches. Gastroenterology 2017; 152:327-339.e4. [PMID: 27769810 PMCID: PMC5511756 DOI: 10.1053/j.gastro.2016.10.012] [Citation(s) in RCA: 520] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 02/08/2023]
Abstract
Intestinal microbiota are involved in the pathogenesis of Crohn's disease, ulcerative colitis, and pouchitis. We review the mechanisms by which these gut bacteria, fungi, and viruses mediate mucosal homeostasis via their composite genes (metagenome) and metabolic products (metabolome). We explain how alterations to their profiles and functions under conditions of dysbiosis contribute to inflammation and effector immune responses that mediate inflammatory bowel diseases (IBD) in humans and enterocolitis in mice. It could be possible to engineer the intestinal environment by modifying the microbiota community structure or function to treat patients with IBD-either with individual agents, via dietary management, or as adjuncts to immunosuppressive drugs. We summarize the latest information on therapeutic use of fecal microbial transplantation and propose improved strategies to selectively normalize the dysbiotic microbiome in personalized approaches to treatment.
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Affiliation(s)
- R Balfour Sartor
- Departments of Medicine, Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
| | - Gary D Wu
- Division of Gastroenterology, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, Pennsylvania.
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Abstract
Gut homeostasis involves interrelated biological networks that include the immune system, specialized cells of the epithelium, such as Paneth and goblet cells, as well as triggers derived from the microbiota. Disruption of these homeostatic interactions may lead to the pathogenesis of inflammatory bowel diseases (IBD). To develop more targeted and individual treatments in Crohn's disease and ulcerative colitis, it becomes more and more important to link key mechanisms of the disease pathogenesis to distinct IBD subsets. For the first time, our laboratory demonstrated a causal role of the microbiota for the development of Crohn's disease (CD)-like ileitis, supporting the hypothesis that a non-infectious, dysbiotic microbial ecosystem harbors aggressive traits relevant for the induction of chronic inflammation in the disease-susceptible host (i.e. TNFΔARE mouse model). Despite a growing body of evidence claiming a primary role for Paneth cells in the pathogenesis of ileal CD, we showed in the TNFΔARE mouse model that Paneth cell failure or exhaustion is a secondary event to inflammation. Therefore, additional mechanisms may act synergistically to initialize the development of CD-like pathology. Hereby, we propose a novel hypothesis suggesting that individual development of dysbiotic communities is based on stochastic injury and focal inflammation of the epithelial lining that propagate radially, finally leading to an aggressive microbial milieu.
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Affiliation(s)
- Ludovica F. Buttó
- Technische Universität München, Chair of Nutrition and Immunology, Freising, Germany
| | - Dirk Haller
- Technische Universität München, Chair of Nutrition and Immunology, Freising, Germany
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The mouse gut microbiome revisited: From complex diversity to model ecosystems. Int J Med Microbiol 2016; 306:316-327. [DOI: 10.1016/j.ijmm.2016.03.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 02/06/2023] Open
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Crosstalk between microbiota, pathogens and the innate immune responses. Int J Med Microbiol 2016; 306:257-265. [PMID: 26996809 DOI: 10.1016/j.ijmm.2016.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 02/07/2023] Open
Abstract
Research in the last decade has convincingly demonstrated that the microbiota is crucial in order to prime and orchestrate innate and adaptive immune responses of their host and influence barrier function as well as multiple developmental and metabolic parameters of the host. Reciprocally, host reactions and immune responses instruct the composition of the microbiota. This review summarizes recent evidence from experimental and human studies which supports these arms of mutual relationship and crosstalk between host and resident microbiota, with a focus on innate immune responses in the gut, the role of cell death pathways and antimicrobial peptides. We also provide some recent examples on how dysbiosis and pathogens can act in concert to promote intestinal infection, inflammatory pathologies and cancer. The future perspectives of these combined research efforts include the discovery of protective species within the microbiota and specific traits and factors of microbes that weaken or enforce host intestinal homeostasis.
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Dysbiosis in intestinal inflammation: Cause or consequence. Int J Med Microbiol 2016; 306:302-309. [PMID: 27012594 DOI: 10.1016/j.ijmm.2016.02.010] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 02/07/2023] Open
Abstract
The intestinal microbiota encompasses hundreds of bacterial species that constitute a relatively stable ecosystem. Alteration in the microbiota composition may arise from infections, immune defects, metabolic alterations, diet or antibiotic treatment. Dysbiosis is considered as an alteration in microbiota community structure and/or function, capable of causing/driving a detrimental distortion of microbe-host homeostasis. A variety of pathologies are associated with changes in the community structure and function of the gut microbiota, suggesting a link between dysbiosis and disease etiology. With an emphasis in this review on inflammatory bowel diseases (IBD), the non-trivial question is whether dysbiosis is the cause or consequence of inflammation. It is important to understand whether changes in microbial ecosystems are causally linked to the pathology and to what extend disease risk is predicable based on characteristic changes in community structure and/or function. Local changes in tissue integrity associated with focal areas of inflammation may result in the selection of a dysbiotic bacterial community associated with the propagation of a disease phenotype. This review outlines the role of dysbiosis in intestinal inflammation with particular focus on IBD-relevant gnotobiotic mouse models, the factors implicated in the development of dysbiosis and the means available to investigate dysbiosis in the context of human diseases.
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Øyri SF, Műzes G, Sipos F. Dysbiotic gut microbiome: A key element of Crohn's disease. Comp Immunol Microbiol Infect Dis 2015; 43:36-49. [PMID: 26616659 DOI: 10.1016/j.cimid.2015.10.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/06/2015] [Accepted: 10/22/2015] [Indexed: 02/06/2023]
Abstract
Since the first publication on "regional ileitis", the relevance of this chronic inflammatory disease condition termed finally as Crohn's disease is continuously increasing. Although we are beginning to comprehend certain aspects of its pathogenesis, many facets remain unexplored. Host's gut microbiota is involved in a wide range of physiological and pathological processes including immune system development, and pathogen regulation. Further, the microbiome is thought to play a key role in Crohn's disease. The presence of Crohn's-associated variants of NOD2 and ATG16L genes appears to be associated not only with alterations of mucosal barrier functions, and bacterial killing, but the gut microbiota, as well, reflecting a potential relationship between the host's genotype and intestinal dysbiosis, involved in disease etiology. This review aims to characterize some exciting new aspect of Crohn's disease pathology, focusing mainly on the role of intestinal microbes, and their interplay with the immune system of the host.
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Affiliation(s)
- Styrk Furnes Øyri
- Faculty of Medicine, Semmelweis University, Szentkirályi Street 46, 1088 Budapest, Hungary.
| | - Györgyi Műzes
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi Street 46, 1088 Budapest, Hungary.
| | - Ferenc Sipos
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi Street 46, 1088 Budapest, Hungary.
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Buttó LF, Schaubeck M, Haller D. Mechanisms of Microbe-Host Interaction in Crohn's Disease: Dysbiosis vs. Pathobiont Selection. Front Immunol 2015; 6:555. [PMID: 26635787 PMCID: PMC4652232 DOI: 10.3389/fimmu.2015.00555] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/16/2015] [Indexed: 12/11/2022] Open
Abstract
Crohn’s disease (CD) is a systemic chronic inflammatory condition mainly characterized by discontinuous transmural pathology of the gastrointestinal tract and frequent extraintestinal manifestations with intermittent episodes of remission and relapse. Genome-wide association studies identified a number of risk loci that, catalyzed by environmental triggers, result in the loss of tolerance toward commensal bacteria based on dysregulated innate effector functions and antimicrobial defense, leading to exacerbated adaptive immune responses responsible for chronic immune-mediated tissue damage. In this review, we discuss the inter-related role of changes in the intestinal microbiota, epithelial barrier integrity, and immune cell functions on the pathogenesis of CD, describing the current approaches available to investigate the molecular mechanisms underlying the disease. Substantial effort has been dedicated to define disease-associated changes in the intestinal microbiota (dysbiosis) and to link pathobionts to the etiology of inflammatory bowel diseases. A cogent definition of dysbiosis is lacking, as well as an agreement of whether pathobionts or complex shifts in the microbiota trigger inflammation in the host. Among the rarely available animal models, SAMP/Yit and TNFdeltaARE mice are the best known displaying a transmural CD-like phenotype. New hypothesis-driven mouse models, e.g., epithelial-specific Caspase8−/−, ATG16L1−/−, and XBP1−/− mice, validate pathway-focused function of specific CD-associated risk genes highlighting the role of Paneth cells in antimicrobial defense. To study the causal role of bacteria in initiating inflammation in the host, the use of germ-free mouse models is indispensable. Unraveling the interactions of genes, immune cells and microbes constitute a criterion for the development of safe, reliable, and effective treatment options for CD.
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Affiliation(s)
- Ludovica F Buttó
- Chair of Nutrition and Immunology, Technische Universität München , Freising-Weihenstephan , Germany
| | - Monika Schaubeck
- Chair of Nutrition and Immunology, Technische Universität München , Freising-Weihenstephan , Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technische Universität München , Freising-Weihenstephan , Germany
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