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Wang C, Gu Y, Chu Q, Wang X, Ding Y, Qin X, Liu T, Wang S, Liu X, Wang B, Cao H. Gut microbiota and metabolites as predictors of biologics response in inflammatory bowel disease: A comprehensive systematic review. Microbiol Res 2024; 282:127660. [PMID: 38442454 DOI: 10.1016/j.micres.2024.127660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Nonresponse to biologic agents in patients with inflammatory bowel disease (IBD) poses a significant public health burden, and the prediction of response to biologics offers valuable insights for IBD management. Given the pivotal role of gut microbiota and their endogenous metabolites in IBD, we conducted a systematic review to investigate the potential of fecal microbiota and mucosal microbiota and endogenous metabolomic markers as predictors for biotherapy response in IBD patients. A total of 38 studies were included in the review. Following anti-TNF-α treatment, the bacterial community characteristics of IBD patients exhibited a tendency to resemble those observed in healthy controls, indicating an improved clinical response. The levels of endogenous metabolites butyrate and deoxycholic acid were significantly associated with clinical remission following anti-TNF-α therapy. IBD patients who responded well to vedolizumab treatment had higher levels of specific bacteria that produce butyrate, along with increased levels of metabolites such as butyrate, branched-chain amino acids and acetamide following vedolizumab treatment. Crohn's disease patients who responded positively to ustekinumab treatment showed higher levels of Faecalibacterium and lower levels of Escherichia/Shigella. In conclusion, fecal microbiota and mucosal microbiota as well as their endogenous metabolites could provide a predictive tool for assessing the response of IBD patients to various biological agents and serve as a valuable reference for precise drug selection in clinical IBD patients.
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Affiliation(s)
- Chen Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yu Gu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qiao Chu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xin Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yiyun Ding
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiali Qin
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Sinan Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiang Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
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2
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Zhang H, Lai J, Zhang L, Zhang W, Liu X, Gong Q, Tian H, Yang M, Yang T, Zhao R, Li D, Huang H, Zhao Y, Yan S, Yu M, Xiyang Y, Shi L, Yang L, Wang L, Chen W, Cao X. The co-regulation of the gut microbiome and host genes might play essential roles in metformin gastrointestinal intolerance. Toxicol Appl Pharmacol 2023; 481:116732. [PMID: 37871735 DOI: 10.1016/j.taap.2023.116732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/14/2023] [Accepted: 10/18/2023] [Indexed: 10/25/2023]
Abstract
Metformin is commonly used, but approximately 20% of patients experience gastrointestinal intolerance, leading to medication discontinuation for unclear reasons and a lack of effective management strategies. In this study, the 18 fecal and blood samples were analyzed using 16S rRNA and mRNA transcriptome, respectively. These samples included 3 fecal and 4 blood from metformin-tolerant T2D patients before and after metformin treatment (T and Ta), 3 fecal and 5 blood from metformin-intolerant T2D patients before and after treatment (TS and TSa), and 6 fecal samples from healthy controls. The results showed that certain anti-inflammatory gut bacteria and gene, such as Barnesiella (p = 0.046), Parabacteroides goldsteinii (p = 0.016), and the gene JUND (p = 0.0002), exhibited higher levels in metformin-intolerant patients, and which decreased after metformin treatment (p < 0.05). This potentially invalidates patients' anti-inflammatory effect and intestinal mucus barrier protection, which may lead to alterations in intestinal permeability, decreased gut barrier function, and gastrointestinal symptoms, including diarrhea, bloating, and nausea. After metformin treatment, primary bile acids (PBAs) production species: Weissella confusa, Weissella paramesenteroides, Lactobacillus brevis, and Lactobacillus plantarum increased (p < 0.05). The species converting PBAs to secondary bile acids (SBAs): Parabacteroides distasonis decreased (p < 0.05). This might result in accumulation of PBAs, which also may lead to anti-inflammatory gene JUND and SQSTM1 downregulated. In conclusion, this study suggests that metformin intolerance may be attributed to a decrease in anti-inflammatory-related flora and genes, and also alterations in PBAs accumulation-related flora. These findings open up possibilities for future research targeting gut flora and host genes to prevent metformin intolerance.
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Affiliation(s)
- Huixiang Zhang
- Institute of Neuroscience, Faculty of Basic Medical Science, Kunming Medical University, Kunming, Yunnan, China; Department of Laboratory Animal Science, Kunming Medical University, Kunming, Yunnan, China
| | - Jiao Lai
- Department of Endocrinology, Qujing NO.1 Hospital of Yunnan Province, Qujing, Yunnan, China
| | - Lihuan Zhang
- Department of Laboratory Animal Science, Kunming Medical University, Kunming, Yunnan, China
| | - Wei Zhang
- Department of Endocrinology, Qujing NO.1 Hospital of Yunnan Province, Qujing, Yunnan, China
| | - Xun Liu
- Institute of Neuroscience, Faculty of Basic Medical Science, Kunming Medical University, Kunming, Yunnan, China
| | - Qilin Gong
- Department of Endocrinology, Qujing NO.1 Hospital of Yunnan Province, Qujing, Yunnan, China
| | - Hongxi Tian
- Institute of Neuroscience, Faculty of Basic Medical Science, Kunming Medical University, Kunming, Yunnan, China
| | - Mingzhi Yang
- Institute of Neuroscience, Faculty of Basic Medical Science, Kunming Medical University, Kunming, Yunnan, China
| | - Tao Yang
- Institute of Neuroscience, Faculty of Basic Medical Science, Kunming Medical University, Kunming, Yunnan, China
| | - Rui Zhao
- Department of Endocrinology, Qujing NO.1 Hospital of Yunnan Province, Qujing, Yunnan, China
| | - Dongqing Li
- Department of Endocrinology, Qujing NO.1 Hospital of Yunnan Province, Qujing, Yunnan, China
| | - Hehua Huang
- Department of Endocrinology, Qujing NO.1 Hospital of Yunnan Province, Qujing, Yunnan, China
| | - Ya Zhao
- Department of Endocrinology, Qujing NO.1 Hospital of Yunnan Province, Qujing, Yunnan, China
| | - Shan Yan
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Bioengineering Centre, Kunming Medical University, Kunming, Yunnan, China
| | - Ming Yu
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Bioengineering Centre, Kunming Medical University, Kunming, Yunnan, China
| | - Yanbin Xiyang
- Institute of Neuroscience, Faculty of Basic Medical Science, Kunming Medical University, Kunming, Yunnan, China
| | - Lanlan Shi
- Department of Anatomy, Histology and Embryology, Basic Medical College, Kunming Medical University, Kunming, Yunnan, China
| | - Lirong Yang
- Institute of Neuroscience, Faculty of Basic Medical Science, Kunming Medical University, Kunming, Yunnan, China; No.1 School of Clinical Medicine, Kunming Medical University, Kunming, Yunnan, China
| | - Limei Wang
- Department of Laboratory Animal Science, Kunming Medical University, Kunming, Yunnan, China.
| | - Weiwen Chen
- Qujing Second People's Hospital of Yunnan Province, Qujing, Yunnan, China.
| | - Xue Cao
- Department of Laboratory Animal Science, Kunming Medical University, Kunming, Yunnan, China; State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, China.
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3
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Kemter AM, Patry RT, Arnold J, Hesser LA, Campbell E, Ionescu E, Mimee M, Wang S, Nagler CR. Commensal bacteria signal through TLR5 and AhR to improve barrier integrity and prevent allergic responses to food. Cell Rep 2023; 42:113153. [PMID: 37742185 PMCID: PMC10697505 DOI: 10.1016/j.celrep.2023.113153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/07/2023] [Accepted: 09/01/2023] [Indexed: 09/26/2023] Open
Abstract
The increasing prevalence of food allergies has been linked to reduced commensal microbial diversity. In this article, we describe two features of allergy-protective Clostridia that contribute to their beneficial effects. Some Clostridial taxa bear flagella (a ligand for TLR5) and produce indole (a ligand for the aryl hydrocarbon receptor [AhR]). Lysates and flagella from a Clostridia consortium induced interleukin-22 (IL-22) secretion from ileal explants. IL-22 production is abrogated in explants from mice in which TLR5 or MyD88 signaling is deficient either globally or conditionally in CD11c+ antigen-presenting cells. AhR signaling in RORγt+ cells is necessary for the induction of IL-22. Mice deficient in AhR in RORγt+ cells exhibit increased intestinal permeability and are more susceptible to an anaphylactic response to food. Our findings implicate TLR5 and AhR signaling in a molecular mechanism by which commensal Clostridia protect against allergic responses to food.
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Affiliation(s)
- Andrea M Kemter
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Robert T Patry
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Jack Arnold
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Lauren A Hesser
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Evelyn Campbell
- Committee on Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Edward Ionescu
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Mark Mimee
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA; Committee on Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Shan Wang
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Cathryn R Nagler
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA.
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4
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Hao Z, Meng C, Li L, Feng S, Zhu Y, Yang J, Han L, Sun L, Lv W, Figeys D, Liu H. Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the "Lunar Palace 365" experiment. MICROBIOME 2023; 11:88. [PMID: 37095530 PMCID: PMC10124008 DOI: 10.1186/s40168-023-01506-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 02/24/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Psychological health risk is one of the most severe and complex risks in manned deep-space exploration and long-term closed environments. Recently, with the in-depth research of the microbiota-gut-brain axis, gut microbiota has been considered a new approach to maintain and improve psychological health. However, the correlation between gut microbiota and psychological changes inside long-term closed environments is still poorly understood. Herein, we used the "Lunar Palace 365" mission, a 1-year-long isolation study in the Lunar Palace 1 (a closed manned Bioregenerative Life Support System facility with excellent performance), to investigate the correlation between gut microbiota and psychological changes, in order to find some new potential psychobiotics to maintain and improve the psychological health of crew members. RESULTS We report some altered gut microbiota that were associated with psychological changes in the long-term closed environment. Four potential psychobiotics (Bacteroides uniformis, Roseburia inulinivorans, Eubacterium rectale, and Faecalibacterium prausnitzii) were identified. On the basis of metagenomic, metaproteomic, and metabolomic analyses, the four potential psychobiotics improved mood mainly through three pathways related to nervous system functions: first, by fermenting dietary fibers, they may produce short-chain fatty acids, such as butyric and propionic acids; second, they may regulate amino acid metabolism pathways of aspartic acid, glutamic acid, tryptophan, etc. (e.g., converting glutamic acid to gamma-aminobutyric acid; converting tryptophan to serotonin, kynurenic acid, or tryptamine); and third, they may regulate other pathways, such as taurine and cortisol metabolism. Furthermore, the results of animal experiments confirmed the positive regulatory effect and mechanism of these potential psychobiotics on mood. CONCLUSIONS These observations reveal that gut microbiota contributed to a robust effect on the maintenance and improvement of mental health in a long-term closed environment. Our findings represent a key step towards a better understanding the role of the gut microbiome in mammalian mental health during space flight and provide a basis for future efforts to develop microbiota-based countermeasures that mitigate risks to crew mental health during future long-term human space expeditions on the moon or Mars. This study also provides an essential reference for future applications of psychobiotics to neuropsychiatric treatments. Video Abstract.
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Affiliation(s)
- Zikai Hao
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
- Key Laboratory of Molecular Medicine and Biotherapy, Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Chen Meng
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
- Beijing Institute of Otolaryngology, Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China
| | - Leyuan Li
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5, Canada
| | - Siyuan Feng
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Yinzhen Zhu
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Jianlou Yang
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Liangzhe Han
- State Key Laboratory of Software Development Environment, School of Computer Science and Engineering, Beihang University, Beijing, 100083, China
| | - Leilei Sun
- State Key Laboratory of Software Development Environment, School of Computer Science and Engineering, Beihang University, Beijing, 100083, China
| | - Weifeng Lv
- State Key Laboratory of Software Development Environment, School of Computer Science and Engineering, Beihang University, Beijing, 100083, China
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5, Canada
| | - Hong Liu
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
- State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100083, China.
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5
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Clasen SJ, Bell MEW, Borbón A, Lee DH, Henseler ZM, de la Cuesta-Zuluaga J, Parys K, Zou J, Wang Y, Altmannova V, Youngblut ND, Weir JR, Gewirtz AT, Belkhadir Y, Ley RE. Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5. Sci Immunol 2023; 8:eabq7001. [PMID: 36608151 DOI: 10.1126/sciimmunol.abq7001] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Flagellin, the protein subunit of the bacterial flagellum, stimulates the innate immune receptor Toll-like receptor 5 (TLR5) after pattern recognition or evades TLR5 through lack of recognition. This binary response fails to explain the weak agonism of flagellins from commensal bacteria, raising the question of how TLR5 response is tuned. Here, we screened abundant flagellins present in metagenomes from human gut for both TLR5 recognition and activation and uncovered a class of flagellin-TLR5 interaction termed silent recognition. Silent flagellins were weak TLR5 agonists despite pattern recognition. Receptor activity was tuned by a TLR5-flagellin interaction distal to the site of pattern recognition that was present in Salmonella flagellin but absent in silent flagellins. This interaction enabled flagellin binding to preformed TLR5 dimers and increased TLR5 signaling by several orders of magnitude. Silent recognition by TLR5 occurred in human organoids and mice, and silent flagellin proteins were present in human stool. These flagellins were produced primarily by the abundant gut bacteria Lachnospiraceae and were enriched in nonindustrialized populations. Our findings provide a mechanism for the innate immune system to tolerate commensal-derived flagellins while remaining vigilant to the presence of flagellins produced by pathogens.
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Affiliation(s)
- Sara J Clasen
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Michael E W Bell
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Andrea Borbón
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Du-Hwa Lee
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Zachariah M Henseler
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | | | - Katarzyna Parys
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Jun Zou
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Yanling Wang
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Veronika Altmannova
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, Tübingen 72076, Germany
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - John R Weir
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, Tübingen 72076, Germany
| | - Andrew T Gewirtz
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Youssef Belkhadir
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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6
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Exploring Bacterial Attributes That Underpin Symbiont Life in the Monogastric Gut. Appl Environ Microbiol 2022; 88:e0112822. [PMID: 36036591 PMCID: PMC9499014 DOI: 10.1128/aem.01128-22] [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] [Indexed: 11/20/2022] Open
Abstract
The large bowel of monogastric animals, such as that of humans, is home to a microbial community (microbiota) composed of a diversity of mostly bacterial species. Interrelationships between the microbiota as an entity and the host are complex and lifelong and are characteristic of a symbiosis. The relationships may be disrupted in association with disease, resulting in dysbiosis. Modifications to the microbiota to correct dysbiosis require knowledge of the fundamental mechanisms by which symbionts inhabit the gut. This review aims to summarize aspects of niche fitness of bacterial species that inhabit the monogastric gut, especially of humans, and to indicate the research path by which progress can be made in exploring bacterial attributes that underpin symbiont life in the gut.
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7
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Alexander KL, Zhao Q, Reif M, Rosenberg AF, Mannon PJ, Duck LW, Elson CO. Human Microbiota Flagellins Drive Adaptive Immune Responses in Crohn's Disease. Gastroenterology 2021; 161:522-535.e6. [PMID: 33844987 PMCID: PMC8489510 DOI: 10.1053/j.gastro.2021.03.064] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND AIMS Crohn's disease and ulcerative colitis are characterized by dysregulated adaptive immune responses to the microbiota in genetically susceptible individuals, but the specificity of these responses remains largely undefined. Therefore, we developed a microbiota antigen microarray to characterize microbial antibody reactivity, particularly to human-derived microbiota flagellins, in inflammatory bowel disease. METHODS Sera from healthy volunteers (n = 87) at the University of Alabama at Birmingham and from patients recruited from the Kirklin Clinic of University of Alabama at Birmingham Hospital, including patients with Crohn's disease (n = 152) and ulcerative colitis (n = 170), were individually probed against microbiota bacterial flagellins of both mouse and human origin and analyzed for IgG and IgA antibody responses. Circulating flagellin-reactive T effector (CD4+CD154+) and T regulatory (CD4+CD137+) cells were isolated and evaluated in selected patients. Resulting adaptive immune responses were compared with corresponding clinical data to determine relevancy to disease behavior. RESULTS We show that patients with IBD express selective patterns of antibody reactivity to microbiota flagellins. Patients with Crohn's disease, but not patients with ulcerative colitis, display augmented serum IgG to human ileal-localized Lachnospiraceae flagellins, with a subset of patients having high responses to more than 10 flagellins. Elevated responses to CBir1, a mouse Lachnospiraceae flagellin used clinically to diagnose CD, correlated with multi-Lachnospiraceae flagellin reactivity. In this subset of patients with CD, multi-flagellin reactivity was associated with elevated flagellin-specific CD154+CD45RA- T memory cells, a reduced ratio of flagellin-reactive CD4+ T regulatory to T effector cells, and a high frequency of disease complications. CONCLUSIONS Patients with Crohn's disease display strong adaptive immune response to human-derived Lachnospiraceae flagellins, which may be targeted for prognosis and future personalized therapies.
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Affiliation(s)
- Katie L. Alexander
- Department of Medicine, University of Alabama at
Birmingham, Birmingham, Alabama
| | - Qing Zhao
- Department of Medicine, University of Alabama at
Birmingham, Birmingham, Alabama
| | - Meagan Reif
- Department of Medicine, University of Alabama at
Birmingham, Birmingham, Alabama
| | - Alexander F. Rosenberg
- Department of Microbiology, University of Alabama at
Birmingham, Birmingham, Alabama,Informatics Institute, University of Alabama at Birmingham,
Birmingham, Alabama
| | - Peter J. Mannon
- Department of Medicine, University of Alabama at
Birmingham, Birmingham, Alabama,Birmingham Veterans Affairs Medical Center, Medical
Service, Birmingham, Alabama
| | - Lennard Wayne Duck
- Department of Medicine, University of Alabama at
Birmingham, Birmingham, Alabama
| | - Charles O. Elson
- Department of Medicine, University of Alabama at
Birmingham, Birmingham, Alabama,Department of Microbiology, University of Alabama at
Birmingham, Birmingham, Alabama
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8
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Bacterial Flagellar Filament: A Supramolecular Multifunctional Nanostructure. Int J Mol Sci 2021; 22:ijms22147521. [PMID: 34299141 PMCID: PMC8306008 DOI: 10.3390/ijms22147521] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/06/2021] [Accepted: 07/10/2021] [Indexed: 02/07/2023] Open
Abstract
The bacterial flagellum is a complex and dynamic nanomachine that propels bacteria through liquids. It consists of a basal body, a hook, and a long filament. The flagellar filament is composed of thousands of copies of the protein flagellin (FliC) arranged helically and ending with a filament cap composed of an oligomer of the protein FliD. The overall structure of the filament core is preserved across bacterial species, while the outer domains exhibit high variability, and in some cases are even completely absent. Flagellar assembly is a complex and energetically costly process triggered by environmental stimuli and, accordingly, highly regulated on transcriptional, translational and post-translational levels. Apart from its role in locomotion, the filament is critically important in several other aspects of bacterial survival, reproduction and pathogenicity, such as adhesion to surfaces, secretion of virulence factors and formation of biofilms. Additionally, due to its ability to provoke potent immune responses, flagellins have a role as adjuvants in vaccine development. In this review, we summarize the latest knowledge on the structure of flagellins, capping proteins and filaments, as well as their regulation and role during the colonization and infection of the host.
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9
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Yanez-Montalvo A, Gaona O, Águila B, Arias-Domínguez N, Falcón LI, Pérez-Flores J. Tapirus bairdii-Associated Fecal Microbiome from a Critical Conservation Area: Calakmul, México. Curr Microbiol 2021; 78:2648-2659. [PMID: 33990869 DOI: 10.1007/s00284-021-02531-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 05/03/2021] [Indexed: 11/28/2022]
Abstract
Baird's tapir (Tapirus bairdii) is the largest native terrestrial mammal in the Neotropics, which is endangered primarily as a consequence of habitat loss and overhunting. Baird's tapir is predominantly nocturnal and exists at low densities which complicates field studies. Baird's tapir is a large-bodied herbivore that plays a key role in maintaining healthy tropical forests through seed dispersal in its feces. Studies of gut microbiome are essential and valuable to assess the health status of the host and the interaction with the environment. In this study, we collected fresh fecal samples of T. bairdii to analyze its gut microbiome during the rainy and dry seasons in the Calakmul region, which is a critical rainforest conservation area in Mexico. The results of a high-throughput 16S rDNA gene sequencing approach suggest that the fecal microbiome of Baird's tapir has no significant differences in composition among seasons. The most common phyla were Firmicutes, Bacteroidetes, Proteobacteria, Kiritimatiellaeota, and Spirochaetes. This study suggests that the stability of the fecal microbiome is related to similar feeding strategies throughout the year, and emphasizes the value of tapir in seed dispersal (and associated microbes) to the well-conserved forests of the Greater Calakmul region as biodiversity hotspots for conservation.
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Affiliation(s)
- Alfredo Yanez-Montalvo
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, México.,El Colegio de La Frontera Sur, Unidad de Chetumal, Avenida Centenario Km 5.5, 77014, Chetumal, Quintana Roo, México
| | - Osiris Gaona
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, México
| | - Bernardo Águila
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, México
| | | | - Luisa I Falcón
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, México
| | - Jonathan Pérez-Flores
- El Colegio de La Frontera Sur, Unidad de Chetumal, Avenida Centenario Km 5.5, 77014, Chetumal, Quintana Roo, México. .,Universidad Tecnológica de Calakmul, Carretera Estatal Xpujil-Dzibalchen Km 2, 24640, Calakmul, Campeche, México.
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10
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Kolmeder CA, de Vos WM. Roadmap to functional characterization of the human intestinal microbiota in its interaction with the host. J Pharm Biomed Anal 2020; 194:113751. [PMID: 33328144 DOI: 10.1016/j.jpba.2020.113751] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/22/2022]
Abstract
It is known for more than 100 years that the intestinal microbes are important for the host's health and the last decade this is being intensely studied with a focus on the mechanistic aspects. Among the fundamental functions of the intestinal microbiome are the priming of the immune system, the production of essential vitamins and the energy harvest from foods. By now, several dozens of diseases, both intestinal and non-intestinal related, have been associated with the intestinal microbiome. Initially, this was based on the description of the composition between groups of different health status or treatment arms based on phylogenetic approaches based on the 16S rRNA gene sequences. This way of analysis has mostly moved to the analysis of all the genes or transcripts of the microbiome i.e. metagenomics and meta-transcriptomics. Differences are regularly found but these have to be taken with caution as we still do not know what the majority of genes of the intestinal microbiome are capable of doing. To circumvent this caveat researchers are studying the proteins and the metabolites of the microbiome and the host via metaproteomics and metabolomics approaches. However, also here the complexity is high and only a fraction of signals obtained with high throughput instruments can be identified and assigned to a known protein or molecule. Therefore, modern microbiome research needs advancement of existing and development of new analytical techniques. The usage of model systems like intestinal organoids where samples can be taken and processed rapidly as well as microfluidics systems may help. This review aims to elucidate what we know about the functionality of the human intestinal microbiome, what technologies are advancing this knowledge, and what innovations are still required to further evolve this actively developing field.
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Affiliation(s)
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Finland; Laboratory of Microbiology, Wageningen University, the Netherlands
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11
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Lagos L, Leanti La Rosa S, Ø. Arntzen M, Ånestad R, Terrapon N, Gaby JC, Westereng B. Isolation and Characterization of Extracellular Vesicles Secreted In Vitro by Porcine Microbiota. Microorganisms 2020; 8:microorganisms8070983. [PMID: 32630095 PMCID: PMC7409281 DOI: 10.3390/microorganisms8070983] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 12/23/2022] Open
Abstract
The secretion of extracellular vesicles, EVs, is a common process in both prokaryotic and eukaryotic cells for intercellular communication, survival, and pathogenesis. Previous studies have illustrated the presence of EVs in supernatants from pure cultures of bacteria, including Gram-positive and Gram-negative glycan-degrading gut commensals. However, the isolation and characterization of EVs secreted by a complex microbial community have not been clearly reported. In a recent paper, we showed that wood-derived, complex β-mannan, which shares a structural similarity with conventional dietary fibers, can be used to modulate the porcine gut microbiota composition and activity. In this paper, we investigated the production, size, composition, and proteome of EVs secreted by pig fecal microbiota after 24 h enrichment on complex β-mannan. Using transmission electron microscopy and nanoparticle tracking analysis, we identified EVs with an average size of 165 nm. We utilized mass spectrometry-based metaproteomic profiling of EV proteins against a database of 355 metagenome-assembled genomes (MAGs) from the porcine colon and thereby identified 303 proteins. For EVs isolated from the culture grown on β-mannan, most proteins mapped to two MAGs, MAG53 and MAG272, belonging to the orders Clostridiales and Bacilli, respectively. Furthermore, the MAG with the third-most-detected protein was MAG 343, belonging to the order Enterobacteriales. The most abundant proteins detected in the β-mannan EVs proteome were involved in translation, energy production, amino acid, and carbohydrate transport, as well as metabolism. Overall, this proof-of-concept study demonstrates the successful isolation of EVs released from a complex microbial community; furthermore, the protein content of the EVs reflects the response of specific microbes to the available carbohydrate source.
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Affiliation(s)
- Leidy Lagos
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Aas, Norway;
- Correspondence:
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1433 Aas, Norway; (S.L.L.R.); (M.Ø.A.); (J.C.G.); (B.W.)
| | - Magnus Ø. Arntzen
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1433 Aas, Norway; (S.L.L.R.); (M.Ø.A.); (J.C.G.); (B.W.)
| | - Ragnhild Ånestad
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Aas, Norway;
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS AMU, USC1408 INRAE, 13288 Marseille, France;
| | - John Christian Gaby
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1433 Aas, Norway; (S.L.L.R.); (M.Ø.A.); (J.C.G.); (B.W.)
| | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1433 Aas, Norway; (S.L.L.R.); (M.Ø.A.); (J.C.G.); (B.W.)
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12
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Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, Armanini F, Bain D, Duncan SH, Louis P, Zolfo M, Manghi P, Valles-Colomer M, Raffaetà R, Rota-Stabelli O, Collado MC, Zeller G, Falush D, Maixner F, Walker AW, Huttenhower C, Segata N. Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Genome Biol 2020; 21:138. [PMID: 32513234 PMCID: PMC7278147 DOI: 10.1186/s13059-020-02042-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/11/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out. RESULTS Here, we leverage metagenomic assembly followed by a reference-based binning strategy to screen over 6500 gut metagenomes spanning geography and lifestyle and reconstruct over 1300 E. rectale high-quality genomes from metagenomes. We extend previous results of biogeographic stratification, identifying a new subspecies predominantly found in African individuals and showing that closely related non-human primates do not harbor E. rectale. Comparison of pairwise genetic and geographic distances between subspecies suggests that isolation by distance and co-dispersal with human populations might have contributed to shaping the contemporary population structure of E. rectale. We confirm that a relatively recently diverged E. rectale subspecies specific to Europe consistently lacks motility operons and that it is immotile in vitro, probably due to ancestral genetic loss. The same subspecies exhibits expansion of its carbohydrate metabolism gene repertoire including the acquisition of a genomic island strongly enriched in glycosyltransferase genes involved in exopolysaccharide synthesis. CONCLUSIONS Our study provides new insights into the population structure and ecology of E. rectale and shows that shotgun metagenomes can enable population genomics studies of microbiota members at a resolution and scale previously attainable only by extensive isolate sequencing.
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Affiliation(s)
| | - Edoardo Pasolli
- Department of Agriculture, University of Naples, Naples, Italy
| | | | - Kun D Huang
- Department CIBIO, University of Trento, Trento, Italy
- Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
| | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Debbie Bain
- Rowett Institute, University of Aberdeen, Aberdeen, UK
| | | | - Petra Louis
- Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | | | | | | | - Frank Maixner
- Institute for Mummy studies, Eurac Research, Bolzano, Italy
| | - Alan W Walker
- Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute, Cambridge, MA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
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13
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Yan Y, Drew DA, Markowitz A, Lloyd-Price J, Abu-Ali G, Nguyen LH, Tran C, Chung DC, Gilpin KK, Meixell D, Parziale M, Schuck M, Patel Z, Richter JM, Kelsey PB, Garrett WS, Chan AT, Stadler ZK, Huttenhower C. Structure of the Mucosal and Stool Microbiome in Lynch Syndrome. Cell Host Microbe 2020; 27:585-600.e4. [PMID: 32240601 PMCID: PMC7453618 DOI: 10.1016/j.chom.2020.03.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/22/2019] [Accepted: 03/10/2020] [Indexed: 12/12/2022]
Abstract
The gut microbiota has been associated with colorectal cancer (CRC), but causal alterations preceding CRC have not been elucidated. To prospectively assess microbiome changes prior to colorectal neoplasia, we investigated samples from 100 Lynch syndrome patients using 16S rRNA gene sequencing of colon biopsies, coupled with metagenomic and metatranscriptomic sequencing of feces. Colectomy and CRC history represented the largest effects on microbiome profiles. A subset of Clostridiaceae were depleted in stool corresponding with baseline adenomas, while Desulfovibrio was enriched both in stool and in mucosal biopsies. A classifier leveraging stool metatranscriptomes resulted in modest power to predict interval development of preneoplastic colonic adenoma. Predictive transcripts corresponded with a shift in flagellin contributors and oxidative metabolic microenvironment, potentially factors in local CRC pathogenesis. This suggests that the effectiveness of prospective microbiome monitoring for adenomas may be limited but supports the potential causality of these consistent, early microbial changes in colonic neoplasia.
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Affiliation(s)
- Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David A Drew
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Arnold Markowitz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason Lloyd-Price
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Galeb Abu-Ali
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Long H Nguyen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Christina Tran
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel C Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Katherine K Gilpin
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dana Meixell
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Melanie Parziale
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Madeline Schuck
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Zalak Patel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James M Richter
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter B Kelsey
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wendy S Garrett
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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14
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Sheridan PO, Martin JC, Scott KP. Conjugation Protocol Optimised for Roseburia inulinivorans and Eubacterium rectale. Bio Protoc 2020; 10:e3575. [PMID: 33659545 DOI: 10.21769/bioprotoc.3575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/17/2020] [Accepted: 03/11/2020] [Indexed: 11/02/2022] Open
Abstract
Roseburia and Eubacterium species of the human gut microbiota play an important role in the maintaince of human health, partly by producing butyrate, the main energy source of our colonic epithelial cells. However, our knowledge of the biochemistry and physiology of these bacteria has been limited by a lack of genetic manipulation techniques. Conjugative transposons previously introduced into Roseburia species could not be easily modified, greatly limiting their applicability as genetic modification platforms. Modular plasmid shuttle vectors have previously been developed for Clostridium species, which share a taxonomic order with Roseburia and Eubacterium, raising the possibility that these vectors could be used in these organisms. Here, we describe an optimized conjugation protocol enabling the transfer of autonomously replicating plasmids from an E. coli donor strain into Roseburia inulinivorans and Eubacterium rectale. The modular nature of the plasmids and their ability to be maintained in the recipient bacterium by autonomous replication makes them ideal for investigating heterologous gene expression, and as a platform for other genetic tools including antisense RNA silencing or mobile group II interon gene disruption strategies.
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Affiliation(s)
- Paul O Sheridan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Jennifer C Martin
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Karen P Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
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15
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Blanco-Míguez A, Fdez-Riverola F, Sánchez B, Lourenço A. Resources and tools for the high-throughput, multi-omic study of intestinal microbiota. Brief Bioinform 2020; 20:1032-1056. [PMID: 29186315 DOI: 10.1093/bib/bbx156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/23/2017] [Indexed: 12/18/2022] Open
Abstract
The human gut microbiome impacts several aspects of human health and disease, including digestion, drug metabolism and the propensity to develop various inflammatory, autoimmune and metabolic diseases. Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts. These efforts demonstrate the power of standardized and reproducible computational workflows for integrating and analysing varied omics data and gaining deeper insights into microbe community structure and function as well as host-microbe interactions.
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Affiliation(s)
| | | | | | - Anália Lourenço
- Dpto. de Informática - Universidade de Vigo, ESEI - Escuela Superior de Ingeniería Informática, Edificio politécnico, Campus Universitario As Lagoas s/n, 32004 Ourense, Spain
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16
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Dekker Nitert M, Mousa A, Barrett HL, Naderpoor N, de Courten B. Altered Gut Microbiota Composition Is Associated With Back Pain in Overweight and Obese Individuals. Front Endocrinol (Lausanne) 2020; 11:605. [PMID: 32982987 PMCID: PMC7492308 DOI: 10.3389/fendo.2020.00605] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/27/2020] [Indexed: 01/10/2023] Open
Abstract
Background: Back pain is the leading cause of disability worldwide and is associated with obesity and chronic low-grade inflammation. Alterations in intestinal microbiota may contribute to the pathogenesis of back pain through metabolites affecting immune and inflammatory responses. Aims and Methods: We compared the gut microbiota composition in a cohort of 36 overweight or obese individuals with or without self-reported back pain in the preceding month. Participants were characterized for anthropometry; bone health; metabolic health; inflammation; dietary intake; and physical activity. Results: Demographic, clinical, biochemical characteristics, diet and physical activity were similar between participants with (n = 14) or without (n = 22) back pain. Individuals with back pain had a higher abundance of the genera Adlercreutzia (p = 0.0008; FDR = 0.027), Roseburia (p = 0.0098; FDR = 0.17), and Uncl. Christensenellaceae (p = 0.02; FDR = 0.27) than those without back pain. Adlercreutzia abundance remained higher in individuals with back pain in the past 2 weeks, 6 months, and 1 year. Adlercreutzia was positively correlated with BMI (rho = 0.35, p = 0.03), serum adipsin (rho = 0.33, p = 0.047), and serum leptin (rho = 0.38, p = 0.02). Conclusions: Our findings suggest that back pain is associated with altered gut microbiota composition, possibly through increased inflammation. Further studies delineating the underlying mechanisms may identify strategies for lowering Adlercreutzia abundance to treat back pain.
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Affiliation(s)
- Marloes Dekker Nitert
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- *Correspondence: Marloes Dekker Nitert
| | - Aya Mousa
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Clayton, VIC, Australia
| | - Helen L. Barrett
- Department of Endocrinology, Mater Hospital, Mater Misericordiae Ltd., South Brisbane, QLD, Australia
- Mater Research Institute, The University of Queensland, South Brisbane, QLD, Australia
| | - Negar Naderpoor
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Clayton, VIC, Australia
| | - Barbora de Courten
- Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
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17
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Sheridan PO, Martin JC, Minton NP, Flint HJ, O'Toole PW, Scott KP. Heterologous gene expression in the human gut bacteria Eubacterium rectale and Roseburia inulinivorans by means of conjugative plasmids. Anaerobe 2019; 59:131-140. [PMID: 31228669 DOI: 10.1016/j.anaerobe.2019.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/24/2019] [Accepted: 06/18/2019] [Indexed: 01/30/2023]
Abstract
Commensal butyrate-producing bacteria in the Firmicutes phylum are abundant in the human intestine and are important for maintaining health. However, understanding of the metabolism and host interaction of these bacteria is limited by the lack of genetic modification techniques. Here we establish a protocol enabling the transfer of autonomously-replicating shuttle vectors by conjugative plasmid transfer from an Escherichia coli donor into representatives of an important sub-group of strictly anaerobic human colonic Firmicutes. Five different plasmid shuttle vectors were tested, each carrying a different origin of replication from Gram-positive bacteria. Plasmid pMTL83151 (pCB102 replicon) were successfully transferred into two strains of Eubacterium rectale, while pMTL83151 and pMTL82151 (pBP1 replicon) were transferred into Roseburia inulinivorans A2-194. Plasmids that carried a Streptococcus bovis JB1 glycoside hydrolase family 16 β-(1,3-1,4)-glucanase gene were constructed and conjugated into Roseburia inulinivorans A2-194 and Eubacterium rectale T1-815, resulting in successful heterologous expression of this introduced enzymatic activity in these two strains of butyrate-producing Firmicutes.
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Affiliation(s)
- Paul O Sheridan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK; School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jennifer C Martin
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Nigel P Minton
- Centre for Biomolecular Sciences, University Park, Nottingham, NG7 2RD, UK
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Karen P Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
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18
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Zhang Y, Brady A, Jones C, Song Y, Darton TC, Jones C, Blohmke CJ, Pollard AJ, Magder LS, Fasano A, Sztein MB, Fraser CM. Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi. mBio 2018; 9:e00686-18. [PMID: 29739901 PMCID: PMC5941076 DOI: 10.1128/mbio.00686-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 01/09/2023] Open
Abstract
Insights into disease susceptibility as well as the efficacy of vaccines against typhoid and other enteric pathogens may be informed by better understanding the relationship between the effector immune response and the gut microbiota. In the present study, we characterized the composition (16S rRNA gene profiling) and function (RNA sequencing [RNA-seq]) of the gut microbiota following immunization and subsequent exposure to wild-type Salmonella enterica serovar Typhi in a human challenge model to further investigate the central hypothesis that clinical outcomes may be linked to the gut microbiota. Metatranscriptome analysis of longitudinal stool samples collected from study subjects revealed two stable patterns of gene expression for the human gut microbiota, dominated by transcripts from either Methanobrevibacter or a diverse representation of genera in the Firmicutes phylum. Immunization with one of two live oral attenuated vaccines against S. Typhi had minimal effects on the composition or function of the gut microbiota. It was observed that subjects harboring the methanogen-dominated transcriptome community at baseline displayed a lower risk of developing symptoms of typhoid following challenge with wild-type S. Typhi. Furthermore, genes encoding antioxidant proteins, metal homeostasis and transport proteins, and heat shock proteins were expressed at a higher level at baseline or after challenge with S. Typhi in subjects who did not develop symptoms of typhoid. These data suggest that functional differences relating to redox potential and ion homeostasis in the gut microbiota may impact clinical outcomes following exposure to wild-type S. Typhi.IMPORTANCES. Typhi is a significant cause of systemic febrile morbidity in settings with poor sanitation and limited access to clean water. It has been demonstrated that the human gut microbiota can influence mucosal immune responses, but there is little information available on the impact of the human gut microbiota on clinical outcomes following exposure to enteric pathogens. Here, we describe differences in the composition and function of the gut microbiota in healthy adult volunteers enrolled in a typhoid vaccine trial and report that these differences are associated with host susceptibility to or protection from typhoid after challenge with wild-type S Typhi. Our observations have important implications in interpreting the efficacy of oral attenuated vaccines against enteric pathogens in diverse populations.
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Affiliation(s)
- Yan Zhang
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Arthur Brady
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cheron Jones
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Thomas C Darton
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Claire Jones
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Christoph J Blohmke
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Laurence S Magder
- Department of Epidemiology and Preventive Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Alessio Fasano
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Harvard Medical School, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Marcelo B Sztein
- Department of Pediatrics, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Claire M Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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19
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Ananthakrishnan AN, Luo C, Yajnik V, Khalili H, Garber JJ, Stevens BW, Cleland T, Xavier RJ. Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases. Cell Host Microbe 2017; 21:603-610.e3. [PMID: 28494241 DOI: 10.1016/j.chom.2017.04.010] [Citation(s) in RCA: 264] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/14/2017] [Accepted: 04/24/2017] [Indexed: 02/07/2023]
Abstract
The gut microbiome plays a central role in inflammatory bowel diseases (IBDs) pathogenesis and propagation. To determine whether the gut microbiome may predict responses to IBD therapy, we conducted a prospective study with Crohn's disease (CD) or ulcerative colitis (UC) patients initiating anti-integrin therapy (vedolizumab). Disease activity and stool metagenomes at baseline, and weeks 14, 30, and 54 after therapy initiation were assessed. Community α-diversity was significantly higher, and Roseburia inulinivorans and a Burkholderiales species were more abundant at baseline among CD patients achieving week 14 remission. Several significant associations were identified with microbial function; 13 pathways including branched chain amino acid synthesis were significantly enriched in baseline samples from CD patients achieving remission. A neural network algorithm, vedoNet, incorporating microbiome and clinical data, provided highest classifying power for clinical remission. We hypothesize that the trajectory of early microbiome changes may be a marker of response to IBD treatment.
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Affiliation(s)
- Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Chengwei Luo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay Yajnik
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - John J Garber
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Thomas Cleland
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ramnik J Xavier
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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20
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Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P. Subspecies in the global human gut microbiome. Mol Syst Biol 2017; 13:960. [PMID: 29242367 PMCID: PMC5740502 DOI: 10.15252/msb.20177589] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 11/24/2017] [Accepted: 11/29/2017] [Indexed: 02/06/2023] Open
Abstract
Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies-specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro-inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.
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Affiliation(s)
- Paul I Costea
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luis Pedro Coelho
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Robin Munch
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jaime Huerta-Cepas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kristoffer Forslund
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Falk Hildebrand
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
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21
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Chung WSF, Meijerink M, Zeuner B, Holck J, Louis P, Meyer AS, Wells JM, Flint HJ, Duncan SH. Prebiotic potential of pectin and pectic oligosaccharides to promote anti-inflammatory commensal bacteria in the human colon. FEMS Microbiol Ecol 2017; 93:4331632. [DOI: 10.1093/femsec/fix127] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 09/29/2017] [Indexed: 01/16/2023] Open
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22
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Patterson AM, Mulder IE, Travis AJ, Lan A, Cerf-Bensussan N, Gaboriau-Routhiau V, Garden K, Logan E, Delday MI, Coutts AGP, Monnais E, Ferraria VC, Inoue R, Grant G, Aminov RI. Human Gut Symbiont Roseburia hominis Promotes and Regulates Innate Immunity. Front Immunol 2017; 8:1166. [PMID: 29018440 PMCID: PMC5622956 DOI: 10.3389/fimmu.2017.01166] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/04/2017] [Indexed: 12/19/2022] Open
Abstract
Objective Roseburia hominis is a flagellated gut anaerobic bacterium belonging to the Lachnospiraceae family within the Firmicutes phylum. A significant decrease of R. hominis colonization in the gut of ulcerative colitis patients has recently been demonstrated. In this work, we have investigated the mechanisms of R. hominis–host cross talk using both murine and in vitro models. Design The complete genome sequence of R. hominis A2-183 was determined. C3H/HeN germ-free mice were mono-colonized with R. hominis, and the host–microbe interaction was studied using histology, transcriptome analyses and FACS. Further investigations were performed in vitro and using the TLR5KO and DSS-colitis murine models. Results In the bacterium, R. hominis, host gut colonization upregulated genes involved in conjugation/mobilization, metabolism, motility, and chemotaxis. In the host cells, bacterial colonization upregulated genes related to antimicrobial peptides, gut barrier function, toll-like receptors (TLR) signaling, and T cell biology. CD4+CD25+FoxP3+ T cell numbers increased in the lamina propria of both mono-associated and conventional mice treated with R. hominis. Treatment with the R. hominis bacterium provided protection against DSS-induced colitis. The role of flagellin in host–bacterium interaction was also investigated. Conclusion Mono-association of mice with R. hominis bacteria results in specific bidirectional gene expression patterns. A set of genes thought to be important for host colonization are induced in R. hominis, while the host cells respond by strengthening gut barrier function and enhancing Treg population expansion, possibly via TLR5-flagellin signaling. Our data reveal the immunomodulatory properties of R. hominis that could be useful for the control and treatment of gut inflammation.
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Affiliation(s)
- Angela M Patterson
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Imke E Mulder
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Anthony J Travis
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Annaig Lan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Nadine Cerf-Bensussan
- INSERM, UMR1163, Lab Intestinal Immunity, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité and Institut Imagine, Paris, France
| | - Valerie Gaboriau-Routhiau
- INSERM, UMR1163, Lab Intestinal Immunity, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité and Institut Imagine, Paris, France.,Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Karen Garden
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Elizabeth Logan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Margaret I Delday
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Alistair G P Coutts
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Edouard Monnais
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Vanessa C Ferraria
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Ryo Inoue
- Kyoto Prefectural University, Kyoto, Japan
| | - George Grant
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.,School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Rustam I Aminov
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
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23
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Browne HP, Neville BA, Forster SC, Lawley TD. Transmission of the gut microbiota: spreading of health. Nat Rev Microbiol 2017; 15:531-543. [PMID: 28603278 PMCID: PMC5837012 DOI: 10.1038/nrmicro.2017.50] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Transmission of commensal intestinal bacteria between humans could promote health by establishing, maintaining and replenishing microbial diversity in the microbiota of an individual. Unlike pathogens, the routes of transmission for commensal bacteria remain unappreciated and poorly understood, despite the likely commonalities between both. Consequently, broad infection control measures that are designed to prevent pathogen transmission and infection, such as oversanitation and the overuse of antibiotics, may inadvertently affect human health by altering normal commensal transmission. In this Review, we discuss the mechanisms and factors that influence host-to-host transmission of the intestinal microbiota and examine how a better understanding of these processes will identify new approaches to nurture and restore transmission routes that are used by beneficial bacteria.
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Affiliation(s)
- Hilary P Browne
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - B Anne Neville
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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24
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Tamanai-Shacoori Z, Smida I, Bousarghin L, Loreal O, Meuric V, Fong SB, Bonnaure-Mallet M, Jolivet-Gougeon A. Roseburia spp.: a marker of health? Future Microbiol 2017; 12:157-170. [PMID: 28139139 DOI: 10.2217/fmb-2016-0130] [Citation(s) in RCA: 404] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The genus Roseburia consists of obligate Gram-positive anaerobic bacteria that are slightly curved, rod-shaped and motile by means of multiple subterminal flagella. It includes five species: Roseburia intestinalis, R. hominis, R. inulinivorans, R. faecis and R. cecicola. Gut Roseburia spp. metabolize dietary components that stimulate their proliferation and metabolic activities. They are part of commensal bacteria producing short-chain fatty acids, especially butyrate, affecting colonic motility, immunity maintenance and anti-inflammatory properties. Modification in Roseburia spp. representation may affect various metabolic pathways and is associated with several diseases (including irritable bowel syndrome, obesity, Type 2 diabetes, nervous system conditions and allergies). Roseburia spp. could also serve as biomarkers for symptomatic pathologies (e.g., gallstone formation) or as probiotics for restoration of beneficial flora.
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Affiliation(s)
- Zohreh Tamanai-Shacoori
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France
| | - Imen Smida
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France
| | - Latifa Bousarghin
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France
| | - Olivier Loreal
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France
| | - Vincent Meuric
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France.,CHU Rennes, 2 rue Henri Le Guilloux, 35000 Rennes, France.,Université de Rennes 1, 2 avenue du Professeur Léon Bernard, 35043 Rennes, France
| | - Shao Bing Fong
- Université de Rennes 1, 2 avenue du Professeur Léon Bernard, 35043 Rennes, France
| | - Martine Bonnaure-Mallet
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France.,CHU Rennes, 2 rue Henri Le Guilloux, 35000 Rennes, France.,Université de Rennes 1, 2 avenue du Professeur Léon Bernard, 35043 Rennes, France
| | - Anne Jolivet-Gougeon
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France.,CHU Rennes, 2 rue Henri Le Guilloux, 35000 Rennes, France.,Université de Rennes 1, 2 avenue du Professeur Léon Bernard, 35043 Rennes, France
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25
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Dehoux P, Marvaud JC, Abouelleil A, Earl AM, Lambert T, Dauga C. Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species-specific genomic properties and numerous putative antibiotic resistance determinants. BMC Genomics 2016; 17:819. [PMID: 27769168 PMCID: PMC5073890 DOI: 10.1186/s12864-016-3152-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 10/11/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Clostridium bolteae and Clostridium clostridioforme, previously included in the complex C. clostridioforme in the group Clostridium XIVa, remain difficult to distinguish by phenotypic methods. These bacteria, prevailing in the human intestinal microbiota, are opportunistic pathogens with various drug susceptibility patterns. In order to better characterize the two species and to obtain information on their antibiotic resistance genes, we analyzed the genomes of six strains of C. bolteae and six strains of C. clostridioforme, isolated from human infection. RESULTS The genome length of C. bolteae varied from 6159 to 6398 kb, and 5719 to 6059 CDSs were detected. The genomes of C. clostridioforme were smaller, between 5467 and 5927 kb, and contained 5231 to 5916 CDSs. The two species display different metabolic pathways. The genomes of C. bolteae contained lactose operons involving PTS system and complex regulation, which contribute to phenotypic differentiation from C. clostridioforme. The Acetyl-CoA pathway, similar to that of Faecalibacterium prausnitzii, a major butyrate producer in the human gut, was only found in C. clostridioforme. The two species have also developed diverse flagella mobility systems contributing to gut colonization. Their genomes harboured many CDSs involved in resistance to beta-lactams, glycopeptides, macrolides, chloramphenicol, lincosamides, rifampin, linezolid, bacitracin, aminoglycosides and tetracyclines. Overall antimicrobial resistance genes were similar within a species, but strain-specific resistance genes were found. We discovered a new group of genes coding for rifampin resistance in C. bolteae. C. bolteae 90B3 was resistant to phenicols and linezolide in producing a 23S rRNA methyltransferase. C. clostridioforme 90A8 contained the VanB-type Tn1549 operon conferring vancomycin resistance. We also detected numerous genes encoding proteins related to efflux pump systems. CONCLUSION Genomic comparison of C. bolteae and C. clostridiofrome revealed functional differences in butyrate pathways and in flagellar systems, which play a critical role within human microbiota. Most of the resistance genes detected in both species were previously characterized in other bacterial species. A few of them were related to antibiotics inactive against Clostridium spp. Some were part of mobile genetic elements suggesting that these commensals of the human microbiota act as reservoir of antimicrobial resistances.
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Affiliation(s)
- Pierre Dehoux
- Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Jean Christophe Marvaud
- Faculté de Pharmacie, EA4043 “Unité Bactéries Pathogènes et Santé” (UBaPS), Université Paris Sud, Châtenay-Malabry Cedex, 92296 France
| | - Amr Abouelleil
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Ashlee M. Earl
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thierry Lambert
- Faculté de Pharmacie, EA4043 “Unité Bactéries Pathogènes et Santé” (UBaPS), Université Paris Sud, Châtenay-Malabry Cedex, 92296 France
- Antibacterial Agents Unit, Department of Microbiology, Institut Pasteur, Paris, France
| | - Catherine Dauga
- Department of Genomes and Genetics, Institut Pasteur, Paris, France
- International Group of Data Analysis, Centre for Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France
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Sheridan PO, Duncan SH, Walker AW, Scott KP, Louis P, Flint HJ. Objections to the proposed reclassification of Eubacterium rectale as Agathobacter rectalis. Int J Syst Evol Microbiol 2016; 66:2106. [PMID: 26916277 DOI: 10.1099/ijsem.0.000969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Paul O Sheridan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Alan W Walker
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Karen P Scott
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Petra Louis
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
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27
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O Sheridan P, Martin JC, Lawley TD, Browne HP, Harris HMB, Bernalier-Donadille A, Duncan SH, O'Toole PW, P Scott K, J Flint H. Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes. Microb Genom 2016; 2:e000043. [PMID: 28348841 PMCID: PMC5320581 DOI: 10.1099/mgen.0.000043] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/11/2015] [Indexed: 12/25/2022] Open
Abstract
Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes, with very little known about the Firmicutes. This work investigates the carbohydrate-active enzymes (CAZymes) in a group of Firmicutes, Roseburia spp. and Eubacterium rectale, which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing E. rectale and four Roseburia spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and unique genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter-strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of different carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of Roseburia spp. and E. rectale, forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in Bacteroidetes, key differences were noted in these Firmicutes, including the absence of close homologues of Bacteroides polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the Roseburia/E. rectale group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.
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Affiliation(s)
- Paul O Sheridan
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Jennifer C Martin
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | | | | | - Hugh M B Harris
- 3 Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Annick Bernalier-Donadille
- 4 Unité de Microbiologie INRA, Centre de Recherche de Clermont-Ferrand/Theix, 63122 Saint Genès Champanelle, France
| | - Sylvia H Duncan
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Paul W O'Toole
- 3 Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Karen P Scott
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Harry J Flint
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
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Detection and genomic characterization of motility in Lactobacillus curvatus: confirmation of motility in a species outside the Lactobacillus salivarius clade. Appl Environ Microbiol 2016; 81:1297-1308. [PMID: 25501479 DOI: 10.1128/aem.03594-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Lactobacillus is the largest genus within the lactic acid bacteria (LAB), with almost 180 species currently identified. Motility has been reported for at least 13 Lactobacillus species, all belonging to the Lactobacillus salivarius clade. Motility in lactobacilli is poorly characterized. It probably confers competitive advantages, such as superior nutrient acquisition and niche colonization, but it could also play an important role in innate immune system activation through flagellin–Toll-like receptor 5 (TLR5) interaction. We now report strong evidence of motility in a species outside the L. salivarius clade, Lactobacillus curvatus (strain NRIC0822). The motility of L. curvatus NRIC 0822 was revealed by phase-contrast microscopy and soft-agar motility assays. Strain NRIC 0822 was motile at temperatures between 15 °C and 37 °C, with a range of different carbohydrates, and under varying atmospheric conditions. We sequenced the L. curvatus NRIC 0822 genome, which revealed that the motility genes are organized in a single operon and that the products are very similar (>98.5% amino acid similarity over >11,000 amino acids) to those encoded by the motility operon of Lactobacillus acidipiscis KCTC 13900 (shown for the first time to be motile also). Moreover, the presence of a large number of mobile genetic elements within and flanking the motility operon of L. curvatus suggests recent horizontal transfer between members of two distinct Lactobacillus clades: L. acidipiscis in the L. salivarius clade and L. curvatus inthe L. sakei clade. This study provides novel phenotypic, genetic, and phylogenetic insights into flagellum-mediated motility in lactobacilli.
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29
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Functional dynamics of the gut microbiome in elderly people during probiotic consumption. mBio 2015; 6:mBio.00231-15. [PMID: 25873374 PMCID: PMC4453556 DOI: 10.1128/mbio.00231-15] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A mechanistic understanding of the purported health benefits conferred by consumption of probiotic bacteria has been limited by our knowledge of the resident gut microbiota and its interaction with the host. Here, we detail the impact of a single-organism probiotic, Lactobacillus rhamnosus GG ATCC 53103 (LGG), on the structure and functional dynamics (gene expression) of the gut microbiota in a study of 12 healthy individuals, 65 to 80 years old. The analysis revealed that while the overall community composition was stable as assessed by 16S rRNA profiling, the transcriptional response of the gut microbiota was modulated by probiotic treatment. Comparison of transcriptional profiles based on taxonomic composition yielded three distinct transcriptome groups that displayed considerable differences in functional dynamics. The transcriptional profile of LGG in vivo was remarkably concordant across study subjects despite the considerable interindividual nature of the gut microbiota. However, we identified genes involved in flagellar motility, chemotaxis, and adhesion from Bifidobacterium and the dominant butyrate producers Roseburia and Eubacterium whose expression was increased during probiotic consumption, suggesting that LGG may promote interactions between key constituents of the microbiota and the host epithelium. These results provide evidence for the discrete functional effects imparted by a specific single-organism probiotic and challenge the prevailing notion that probiotics substantially modify the resident microbiota within nondiseased individuals in an appreciable fashion. Probiotic bacteria have been used for over a century to promote digestive health. Many individuals report that probiotics alleviate a number of digestive issues, yet little evidence links how probiotic microbes influence human health. Here, we show how the resident microbes that inhabit the healthy human gut respond to a probiotic. The well-studied probiotic Lactobacillus rhamnosus GG ATCC 53103 (LGG) was administered in a clinical trial, and a suite of measurements of the resident microbes were taken to evaluate potential changes over the course of probiotic consumption. We found that LGG transiently enriches for functions to potentially promote anti-inflammatory pathways in the resident microbes.
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30
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Pekkala S, Munukka E, Kong L, Pöllänen E, Autio R, Roos C, Wiklund P, Fischer-Posovszky P, Wabitsch M, Alen M, Huovinen P, Cheng S. Toll-like receptor 5 in obesity: the role of gut microbiota and adipose tissue inflammation. Obesity (Silver Spring) 2015; 23:581-90. [PMID: 25611816 DOI: 10.1002/oby.20993] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/03/2014] [Indexed: 12/24/2022]
Abstract
OBJECTIVE This study aimed at establishing bacterial flagellin-recognizing toll-like receptor 5 (TLR5) as a novel link between gut microbiota composition, adipose tissue inflammation, and obesity. METHODS An adipose tissue microarray database was used to compare women having the highest (n = 4, H-TLR) and lowest (n = 4, L-TLR) expression levels of TLR5-signaling pathway genes. Gut microbiota composition was profiled using flow cytometry and FISH. Standard laboratory techniques were used to determine anthropometric and clinical variables. In vivo results were verified using cultured human adipocytes. RESULTS The H-TLR group had higher flagellated Clostridium cluster XIV abundance and Firmicutes-to-Bacteroides ratio. H-TLR subjects had obese phenotype characterized by greater waist circumference, fat %, and blood pressure (P < 0.05 for all). They also had higher leptin and lower adiponectin levels (P < 0.05 for both). Six hundred and sixty-eight metabolism- and inflammation-related adipose tissue genes were differentially expressed between the groups. In vitro studies confirmed that flagellin activated TLR5 inflammatory pathways, decreased insulin signaling, and increased glycerol secretion. CONCLUSIONS The in vivo findings suggest that flagellated Clostridium cluster XIV bacteria contribute to the development of obesity through distorted adipose tissue metabolism and inflammation. The in vitro studies in adipocytes show that the underlying mechanisms of the human findings may be due to flagellin-activated TLR5 signaling.
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Affiliation(s)
- Satu Pekkala
- Department of Health Sciences, University of Jyväskylä, Jyväskylä, Finland; Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
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Greenblum S, Carr R, Borenstein E. Extensive strain-level copy-number variation across human gut microbiome species. Cell 2015; 160:583-594. [PMID: 25640238 DOI: 10.1016/j.cell.2014.12.038] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/30/2014] [Accepted: 12/24/2014] [Indexed: 12/22/2022]
Abstract
Within each bacterial species, different strains may vary in the set of genes they encode or in the copy number of these genes. Yet, taxonomic characterization of the human microbiota is often limited to the species level or to previously sequenced strains, and accordingly, the prevalence of intra-species variation, its functional role, and its relation to host health remain unclear. Here, we present a comprehensive large-scale analysis of intra-species copy-number variation in the gut microbiome, introducing a rigorous computational pipeline for detecting such variation directly from shotgun metagenomic data. We uncover a large set of variable genes in numerous species and demonstrate that this variation has significant functional and clinically relevant implications. We additionally infer intra-species compositional profiles, identifying population structure shifts and the presence of yet uncharacterized variants. Our results highlight the complex relationship between microbiome composition and functional capacity, linking metagenome-level compositional shifts to strain-level variation.
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Affiliation(s)
- Sharon Greenblum
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Rogan Carr
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA; Santa Fe Institute, Santa Fe, NM 87501, USA.
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Lv XM, Shao MF, Li CL, Li J, Gao XL, Sun FY. A comparative study of the bacterial community in denitrifying and traditional enhanced biological phosphorus removal processes. Microbes Environ 2014; 29:261-8. [PMID: 24964811 PMCID: PMC4159037 DOI: 10.1264/jsme2.me13132] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Denitrifying phosphorus removal is an attractive wastewater treatment process due to its reduced carbon source demand and sludge minimization potential. Two lab-scale sequencing batch reactors (SBRs) were operated in alternating anaerobic-anoxic (A-A) or anaerobic-oxic (A-O) conditions to achieve denitrifying enhanced biological phosphate removal (EBPR) and traditional EBPR. No significant differences were observed in phosphorus removal efficiencies between A-A SBR and A-O SBR, with phosphorus removal rates being 87.9% and 89.0% respectively. The community structures in denitrifying and traditional EBPR processes were evaluated by high-throughput sequencing of the PCR-amplified partial 16S rRNA genes from each sludge. The results obtained showed that the bacterial community was more diverse in A-O sludge than in A-A sludge. Taxonomy and β-diversity analyses indicated that a significant shift occurred in the dominant microbial community in A-A sludge compared with the seed sludge during the whole acclimation phase, while a slight fluctuation was observed in the abundance of the major taxonomies in A-O sludge. One Dechloromonas-related OTU outside the 4 known Candidatus “Accumulibacter” clades was detected as the main OTU in A-A sludge at the stationary operation, while Candidatus “Accumulibacter” dominated in A-O sludge.
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Affiliation(s)
- Xiao-Mei Lv
- Harbin Institute of Technology Shenzhen Graduate School
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33
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Boyd JH, Russell JA, Fjell CD. The meta-genome of sepsis: host genetics, pathogens and the acute immune response. J Innate Immun 2014; 6:272-83. [PMID: 24525633 DOI: 10.1159/000358835] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 01/20/2014] [Indexed: 12/22/2022] Open
Abstract
Severe infection and the patient response constitute sepsis. Here, we review the meta-genome (patient genetics, pathogen communities and host response) and its impact upon the outcome of severe sepsis. Patient genetics, both predisposition for infection and the subsequent response to infection are reviewed. The pathogen is discussed with particular emphasis upon the modern era of microbiome analysis and nucleic acid diagnostics. Finally, we discuss the host clinical and immune responses and present new data to suggest that the immune response is the key to understanding sepsis and improving a death rate of nearly 30%.
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Affiliation(s)
- John H Boyd
- Division of Critical Care Medicine, St. Paul's Hospital, Vancouver, B.C., Canada
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