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Moreau GB, Naz F, Petri WA. Fecal microbiota transplantation stimulates type 2 and tolerogenic immune responses in a mouse model. Anaerobe 2024; 86:102841. [PMID: 38521227 DOI: 10.1016/j.anaerobe.2024.102841] [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: 12/21/2023] [Revised: 03/03/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
OBJECTIVES Clostridioides difficile infection (CDI) is the leading hospital-acquired infection in North America. While previous work on fecal microbiota transplantation (FMT), a highly effective treatment for CDI, has focused on colonization resistance mounted against C. difficile by FMT-delivered commensals, the effects of FMT on host gene expression are relatively unexplored. This study aims to identify transcriptional changes associated with FMT, particularly changes associated with protective immune responses. METHODS Gene expression was assessed on day 2 and day 7 after FMT in mice after antibiotic-induced dysbiosis. Flow cytometry was also performed on colon and mesenteric lymph nodes at day 7 to investigate changes in immune cell populations. RESULTS FMT administration after antibiotic-induced dysbiosis successfully restored microbial alpha diversity to levels of donor mice by day 7 post-FMT. Bulk RNA sequencing of cecal tissue at day 2 identified immune genes, including both pro-inflammatory and Type 2 immune pathways as upregulated after FMT. RNA sequencing was repeated on day 7 post-FMT, and expression of these immune genes was decreased along with upregulation of genes associated with restoration of intestinal homeostasis. Immunoprofiling on day 7 identified increased colonic CD45+ immune cells that exhibited dampened Type 1 and heightened regulatory and Type 2 responses. These include an increased abundance of eosinophils, alternatively activated macrophages, Th2, and T regulatory cell populations. CONCLUSION These results highlight the impact of FMT on host gene expression, providing evidence that FMT restores intestinal homeostasis after antibiotic treatment and facilitates tolerogenic and Type 2 immune responses.
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Affiliation(s)
- G Brett Moreau
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Farha Naz
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - William A Petri
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA.
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2
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Cuthbertson L, Löber U, Ish-Horowicz JS, McBrien CN, Churchward C, Parker JC, Olanipekun MT, Burke C, McGowan A, Davies GA, Lewis KE, Hopkin JM, Chung KF, O'Carroll O, Faul J, Creaser-Thomas J, Andrews M, Ghosal R, Piatek S, Willis-Owen SAG, Bartolomaeus TUP, Birkner T, Dwyer S, Kumar N, Turek EM, William Musk A, Hui J, Hunter M, James A, Dumas ME, Filippi S, Cox MJ, Lawley TD, Forslund SK, Moffatt MF, Cookson WOC. Genomic attributes of airway commensal bacteria and mucosa. Commun Biol 2024; 7:171. [PMID: 38347162 PMCID: PMC10861553 DOI: 10.1038/s42003-024-05840-3] [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: 01/30/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
Microbial communities at the airway mucosal barrier are conserved and highly ordered, in likelihood reflecting co-evolution with human host factors. Freed of selection to digest nutrients, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the initial results of systematic culture and whole-genome sequencing of the thoracic airway bacteria, identifying 52 novel species amongst 126 organisms that constitute 75% of commensals typically present in heathy individuals. Clinically relevant genes encode antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. Using whole-genome content we identify dysbiotic features that may influence asthma and chronic obstructive pulmonary disease. We match isolate gene content to transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways to sustain host interactions with microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosa in lung diseases of global significance.
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Affiliation(s)
- Leah Cuthbertson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Ulrike Löber
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site, 10785, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Jonathan S Ish-Horowicz
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Mathematics, Imperial College London, London, UK
| | - Claire N McBrien
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Colin Churchward
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jeremy C Parker
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Conor Burke
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - Aisling McGowan
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - Gwyneth A Davies
- Population Data Science and Health Data Research UK BREATHE Hub, Swansea University Medical School, Swansea University, Swansea, UK
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Keir E Lewis
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
- Respiratory Medicine, Hywel Dda University Health Board, Llanelli, UK
| | - Julian M Hopkin
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Orla O'Carroll
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - John Faul
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - Joy Creaser-Thomas
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Mark Andrews
- Respiratory Medicine, Hywel Dda University Health Board, Llanelli, UK
| | - Robin Ghosal
- Respiratory Medicine, Hywel Dda University Health Board, Llanelli, UK
| | - Stefan Piatek
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Theda U P Bartolomaeus
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site, 10785, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Till Birkner
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Sarah Dwyer
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elena M Turek
- National Heart and Lung Institute, Imperial College London, London, UK
| | - A William Musk
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Perth, WA, Australia
- Department of Respiratory Medicine Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Jennie Hui
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Michael Hunter
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Alan James
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Department of Respiratory Medicine Sir Charles Gairdner Hospital, Perth, WA, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Marc-Emmanuel Dumas
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- U1283 INSERM / UMR8199 CNRS, Institut Pasteur de Lille, Lille University Hospital, European Genomic Institute for Diabetes, University of Lille, Lille, France
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Sarah Filippi
- Department of Mathematics, Imperial College London, London, UK
| | - Michael J Cox
- University of Birmingham College of Medical and Dental Sciences, 150183, Institute of Microbiology and Infection, Birmingham, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sofia K Forslund
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany.
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site, 10785, Berlin, Germany.
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany.
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany.
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London, UK.
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Kwon JE, Jo SH, Song WS, Lee JS, Jeon HJ, Park JH, Kim YR, Baek JH, Kim MG, Kwon SY, Kim JS, Yang YH, Kim YG. Investigation of metabolic crosstalk between host and pathogenic Clostridioides difficile via multiomics approaches. Front Bioeng Biotechnol 2022; 10:971739. [PMID: 36118584 PMCID: PMC9478559 DOI: 10.3389/fbioe.2022.971739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/11/2022] [Indexed: 11/23/2022] Open
Abstract
Clostridioides difficile is a gram-positive anaerobic bacterium that causes antibiotic-associated infections in the gut. C. difficile infection develops in the intestine of a host with an imbalance of the intestinal microbiota and, in severe cases, can lead to toxic megacolon, intestinal perforation, and even death. Despite its severity and importance, however, the lack of a model to understand host-pathogen interactions and the lack of research results on host cell effects and response mechanisms under C. difficile infection remain limited. Here, we developed an in vitro anaerobic-aerobic C. difficile infection model that enables direct interaction between human gut epithelial cells and C. difficile through the Mimetic Intestinal Host–Microbe Interaction Coculture System. Additionally, an integrative multiomics approach was applied to investigate the biological changes and response mechanisms of host cells caused by C. difficile in the early stage of infection. The C. difficile infection model was validated through the induction of disaggregation of the actin filaments and disruption of the intestinal epithelial barrier as the toxin-mediated phenotypes following infection progression. In addition, an upregulation of stress-induced chaperones and an increase in the ubiquitin proteasomal pathway were identified in response to protein stress that occurred in the early stage of infection, and downregulation of proteins contained in the electron transfer chain and ATP synthase was observed. It has been demonstrated that host cell energy metabolism is inhibited through the glycolysis of Caco-2 cells and the reduction of metabolites belonging to the TCA cycle. Taken together, our C. difficile infection model suggests a new biological response pathway in the host cell induced by C. difficile during the early stage of infection at the molecular level under anaerobic-aerobic conditions. Therefore, this study has the potential to be applied to the development of future therapeutics through basic metabolic studies of C. difficile infection.
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Affiliation(s)
- Ji-Eun Kwon
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Sung-Hyun Jo
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Won-Suk Song
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Jae-Seung Lee
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Hyo-Jin Jeon
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Ji-Hyeon Park
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Ye-Rim Kim
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Ji-Hyun Baek
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Min-Gyu Kim
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Seo-Young Kwon
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, Konkuk University, Seoul, South Korea
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
- *Correspondence: Yun-Gon Kim,
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4
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Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly. mSystems 2020; 5:5/1/e00620-19. [PMID: 32019832 PMCID: PMC7002114 DOI: 10.1128/msystems.00620-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A major function of the gut microbiota is to provide colonization resistance, wherein pathogens are inhibited or suppressed below infectious levels. However, the fraction of gut microbiota required for colonization resistance remains unclear. We used culturomics to isolate a gut microbiota culture collection comprising 1,590 isolates belonging to 102 species. This culture collection represents 34.57% of the taxonomic diversity and 70% functional capacity, as estimated by metagenomic sequencing of the fecal samples used for culture. Using whole-genome sequencing, we characterized species representatives from this collection and predicted their phenotypic traits, further characterizing isolates by defining nutrient utilization profiles and short-chain fatty acid production. When screened with a coculture assay, 66 species in our culture collection inhibited Clostridioides difficile Several phenotypes, particularly, growth rate, production of SCFAs, and the utilization of mannitol, sorbitol, or succinate, correlated with C. difficile inhibition. We used a combinatorial community assembly approach to formulate defined bacterial mixes inhibitory to C. difficile We tested 256 combinations and found that both species composition and blend size were important in inhibition. Our results show that the interaction of bacteria with one another in a mix and with other members of gut commensals must be investigated to design defined bacterial mixes for inhibiting C. difficile in vivo IMPORTANCE Antibiotic treatment causes instability of gut microbiota and the loss of colonization resistance, thus allowing pathogens such as Clostridioides difficile to colonize and causing recurrent infection and mortality. Although fecal microbiome transplantation has been shown to be an effective treatment for C. difficile infection (CDI), a more desirable approach would be the use of a defined mix of inhibitory gut bacteria. The C. difficile-inhibiting species and bacterial combinations identified herein improve the understanding of the ecological interactions controlling colonization resistance against C. difficile and could aid in the design of defined bacteriotherapy as a nonantibiotic alternative against CDI.
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5
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Anonye BO, Hassall J, Patient J, Detamornrat U, Aladdad AM, Schüller S, Rose FRAJ, Unnikrishnan M. Probing Clostridium difficile Infection in Complex Human Gut Cellular Models. Front Microbiol 2019; 10:879. [PMID: 31114553 PMCID: PMC6503005 DOI: 10.3389/fmicb.2019.00879] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/05/2019] [Indexed: 12/11/2022] Open
Abstract
Interactions of anaerobic gut bacteria, such as Clostridium difficile, with the intestinal mucosa have been poorly studied due to challenges in culturing anaerobes with the oxygen-requiring gut epithelium. Although gut colonization by C. difficile is a key determinant of disease outcome, precise mechanisms of mucosal attachment and spread remain unclear. Here, using human gut epithelial monolayers co-cultured within dual environment chambers, we demonstrate that C. difficile adhesion to gut epithelial cells is accompanied by a gradual increase in bacterial numbers. Prolonged infection causes redistribution of actin and loss of epithelial integrity, accompanied by production of C. difficile spores, toxins, and bacterial filaments. This system was used to examine C. difficile interactions with the commensal Bacteroides dorei, and interestingly, C. difficile growth is significantly reduced in the presence of B. dorei. Subsequently, we have developed novel models containing a myofibroblast layer, in addition to the epithelium, grown on polycarbonate or three-dimensional (3D) electrospun scaffolds. In these more complex models, C. difficile adheres more efficiently to epithelial cells, as compared to the single epithelial monolayers, leading to a quicker destruction of the epithelium. Our study describes new controlled environment human gut models that enable host-anaerobe and pathogen-commensal interaction studies in vitro.
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Affiliation(s)
- Blessing O. Anonye
- Microbiology and Infection Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Jack Hassall
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jamie Patient
- Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Usanee Detamornrat
- Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Afnan M. Aladdad
- Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Stephanie Schüller
- Norwich Medical School, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, United Kingdom
- Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Felicity R. A. J. Rose
- Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Meera Unnikrishnan
- Microbiology and Infection Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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6
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Less Is More: Genome Reduction and the Emergence of Cooperation-Implications into the Coevolution of Microbial Communities. Int J Genomics 2019; 2019:2659175. [PMID: 30911537 PMCID: PMC6398007 DOI: 10.1155/2019/2659175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/06/2019] [Indexed: 11/18/2022] Open
Abstract
Organisms change to adapt to the environment in which they live, evolving with coresiding individuals. Classic Darwinism postulates the primal importance of antagonistic interactions and selfishness as a major driver of evolution, promoting an increase of genomic and organism complexities. Recently, advancements in evolutionary ecology reshaped this notion, showing how leakiness in biological functions favours the adaptive genome reduction, leading to the emergence of codependence patterns. Microbial communities are complex entities exerting a gargantuan influence on the environment and the biology of the eukaryotic hosts they are associated with. Notwithstanding, we are still far from a comprehension of the ecological and evolutionary mechanisms governing the community dynamics. Here, we review the implications of genome streamlining into the unfolding of codependence within microbial communities and how this translates to an understanding of ecological patterns underlying the emerging properties of the community.
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7
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Ooijevaar RE, Terveer EM, Verspaget HW, Kuijper EJ, Keller JJ. Clinical Application and Potential of Fecal Microbiota Transplantation. Annu Rev Med 2018; 70:335-351. [PMID: 30403550 DOI: 10.1146/annurev-med-111717-122956] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fecal microbiota transplantation (FMT) is a well-established treatment for recurrent Clostridioides difficile infection. FMT has become a more readily available and useful new treatment option as a result of stool banks. The current state of knowledge indicates that dysbiosis of the gut microbiota is implicated in several disorders in addition to C. difficile infection. Randomized controlled studies have shown FMT to be somewhat effective in treating ulcerative colitis, irritable bowel syndrome, and hepatic encephalopathy. In addition, FMT has been beneficial in treating several other conditions, such as the eradication of multidrug-resistant organisms and graft-versus-host disease. We expect that FMT will soon be implemented as a treatment strategy for several new indications, although further studies are needed.
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Affiliation(s)
- R E Ooijevaar
- Department of Gastroenterology and Hepatology, and Department of Medical Microbiology and Infection Control, VU University Medical Center, 1181 HZ, Amsterdam, The Netherlands
| | - E M Terveer
- Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - H W Verspaget
- Department of Gastroenterology and Hepatology and Centralized Biobanking Facility, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - E J Kuijper
- Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - J J Keller
- Department of Gastroenterology and Hepatology and Centralized Biobanking Facility, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands.,Department of Gastroenterology and Hepatology, Haaglanden Medical Center, 2597 AX, The Hague, The Netherlands;
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Lazar V, Ditu LM, Pircalabioru GG, Gheorghe I, Curutiu C, Holban AM, Picu A, Petcu L, Chifiriuc MC. Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer. Front Immunol 2018; 9:1830. [PMID: 30158926 PMCID: PMC6104162 DOI: 10.3389/fimmu.2018.01830] [Citation(s) in RCA: 297] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 07/24/2018] [Indexed: 12/12/2022] Open
Abstract
The microbiota consists of a dynamic multispecies community of bacteria, fungi, archaea, and protozoans, bringing to the host organism a dowry of cells and genes more numerous than its own. Among the different non-sterile cavities, the human gut harbors the most complex microbiota, with a strong impact on host homeostasis and immunostasis, being thus essential for maintaining the health condition. In this review, we outline the roles of gut microbiota in immunity, starting with the background information supporting the further presentation of the implications of gut microbiota dysbiosis in host susceptibility to infections, hypersensitivity reactions, autoimmunity, chronic inflammation, and cancer. The role of diet and antibiotics in the occurrence of dysbiosis and its pathological consequences, as well as the potential of probiotics to restore eubiosis is also discussed.
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Affiliation(s)
- Veronica Lazar
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Lia-Mara Ditu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Gratiela Gradisteanu Pircalabioru
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Irina Gheorghe
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Carmen Curutiu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Alina Maria Holban
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Ariana Picu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- National Institute for Diabetes, Nutrition and Metabolic Diseases Prof. Dr. N. Paulescu, Bucharest, Romania
| | - Laura Petcu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- National Institute for Diabetes, Nutrition and Metabolic Diseases Prof. Dr. N. Paulescu, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
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9
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Rosa CP, Brancaglion GA, Miyauchi-Tavares TM, Corsetti PP, de Almeida LA. Antibiotic-induced dysbiosis effects on the murine gastrointestinal tract and their systemic repercussions. Life Sci 2018; 207:480-491. [DOI: 10.1016/j.lfs.2018.06.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 06/20/2018] [Accepted: 06/28/2018] [Indexed: 02/07/2023]
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10
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Comparison of Different Strategies for Providing Fecal Microbiota Transplantation to Treat Patients with Recurrent Clostridium difficile Infection in Two English Hospitals: A Review. Infect Dis Ther 2018; 7:71-86. [PMID: 29450831 PMCID: PMC5840108 DOI: 10.1007/s40121-018-0189-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Indexed: 12/13/2022] Open
Abstract
Fecal microbiota transplant (FMT) has emerged as a highly efficacious treatment for difficult cases of refractory and/or recurrent Clostridium difficile infection (CDI). There have been many well-conducted randomized controlled trials and thousands of patients reported in case series that describe success rates of approximately 90% following one or more FMT. Although the exact mechanisms of FMT have yet to be fully elucidated, replacement or restoration of a 'normal' microbiota (or at least a microbiota resembling those who have never had CDI) appears to have a positive effect on the gut dysbiosis that is thought to exist in these patients. Furthermore, despite being aesthetically unappealing, this 'ultimate probiotic' is a particularly attractive solution to a difficult problem that avoids repeated courses of antibiotics. The lack of clarity about the exact mechanism of action and the 'active ingredient' of FMT (e.g., individual or communities of bacteria, bacteriophage, or bioactive molecules such as bile acids) has hindered the ability to produce a standardized and well-characterized FMT product. There is no standard method to produce material for FMT, and there are a multitude of factors that can vary between institutions that offer this therapy. Only a few studies have directly compared clinical efficacy in groups of patients who have been treated with FMT prepared differently (e.g., fresh vs. frozen) or administered by different route (e.g., by nasojejunal tube, colonoscopy or by oral administration of encapsulated product). More of these studies should be undertaken to clarify the superiority or otherwise of these variables. This review describes the methods and protocols that two English NHS hospitals independently adopted over the same time period to provide FMT for patients with recurrent CDI. There are several fundamental differences in the methods used, including selection and testing of donors, procedures for preparation and storage of material, and route of administration. These methods are described in detail in this review highlighting differing practice. Despite these significant methodological variations, clinical outcomes in terms of cure rate appear to be remarkably similar for both FMT providers. Although both hospitals have treated only modest numbers of patients, these findings suggest that many of the described differences may not be critical factors in influencing the success of the procedure. As FMT is increasingly being proposed for a number of conditions other than CDI, harmonization of methods and techniques may be more critical to the success of FMT, and thus it will be important to standardize these as far as practically possible.
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11
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Cookson WOCM, Cox MJ, Moffatt MF. New opportunities for managing acute and chronic lung infections. Nat Rev Microbiol 2017; 16:111-120. [PMID: 29062070 DOI: 10.1038/nrmicro.2017.122] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lung diseases caused by microbial infections affect hundreds of millions of children and adults throughout the world. In Western populations, the treatment of lung infections is a primary driver of antibiotic resistance. Traditional therapeutic strategies have been based on the premise that the healthy lung is sterile and that infections grow in a pristine environment. As a consequence, rapid advances in our understanding of the composition of the microbiota of the skin and bowel have not yet been matched by studies of the respiratory tree. The recognition that the lungs are as populated with microorganisms as other mucosal surfaces provides the opportunity to reconsider the mechanisms and management of lung infections. Molecular analyses of the lung microbiota are revealing profound adverse responses to widespread antibiotic use, urbanization and globalization. This Opinion article proposes how technologies and concepts flowing from the Human Microbiome Project can transform the diagnosis and treatment of common lung diseases.
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Affiliation(s)
- William O C M Cookson
- Asmarley Centre for Genomic Medicine, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London SW3 6LY, UK
| | - Michael J Cox
- Asmarley Centre for Genomic Medicine, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London SW3 6LY, UK
| | - Miriam F Moffatt
- Asmarley Centre for Genomic Medicine, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London SW3 6LY, UK
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12
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Perna canaliculus and the Intestinal Microbiome. Mar Drugs 2017; 15:md15070207. [PMID: 28665349 PMCID: PMC5532649 DOI: 10.3390/md15070207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 06/21/2017] [Accepted: 06/26/2017] [Indexed: 12/28/2022] Open
Abstract
Natural medicines are often an attractive option for patients diagnosed with chronic conditions. Three main classes of bioactives that have been reported from marine mussel extracts include proteins, lipids and carbohydrates. Commercially, the most relevant species of marine mollusks belong to two genera, Perna and Mytilus. Specifically, the Perna canaliculus species has been repeatedly demonstrated to harbor anti-inflammatory compounds such as omega-3 polyunsaturated fatty acids (ω-3 PUFAs) that can ameliorate pro-inflammatory conditions, or proteins that can promote thrombin inhibitory activity. Recent clinical studies have posited that extracts from green-lipped mussels may lead to prebiotic activity in the intestinal microbiome that in turn has been reported to improve symptoms of osteoarthritis of the knee. Prebiotics have been reported to favorably interact with the intestinal microbiome through the proliferation of beneficial bacteria in the gut, suppressing exogenous and endogenous intestinal infections and promoting homeostasis by balancing local pro- and anti-inflammatory actions. Bioactive compounds from Perna canaliculus are functional foods and, in this regard, may positively interact with the intestinal microbiome and provide novel therapeutic solutions for intra-intestinal and extra-intestinal inflammatory conditions.
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Zhao J, Nian L, Kwok LY, Sun T, Zhao J. Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology. Eur J Clin Microbiol Infect Dis 2017; 36:1463-1472. [PMID: 28455781 DOI: 10.1007/s10096-017-2955-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/28/2017] [Indexed: 12/30/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) may cause potentially lethal infections. Increasing evidence suggests that the gut microbiota is associated with human health. Yet, whether patients with MRSA infections carry specific signatures in their fecal microbiota composition has not been determined. Thus, this study aimed to compare the fecal microbiota profile of MRSA-positive patients (n=15) with individuals without MRSA infection (n=15) by using the PacBio single molecule, real-time (SMRT) DNA sequencing system and real-time quantitative polymerase chain reaction (qPCR). Mann-Whitney tests and unweighted UniFrac principal coordinate analysis (PCoA) showed that the profile of fecal microbiota was apparently different between the two populations. Both the community richness and diversity were reduced in the MRSA-positive group (p<0.050). The genera Acinetobacter and Enterococcus were highly enriched in the MRSA-positive group, whereas less short-chain fatty acid (SCFA)-producing bacteria, including Butyricimonas, Faecalibacterium, Roseburia, Ruminococcus, Megamonas and Phascolarctobacterium, were detected in the MRSA-positive group. At species level, the species Acinetobacter baumannii and Bacteroides thetaiotaomicron were prevalent in the MRSA-positive group, whereas opposite trends were observed in 17 other species, such as Faecalibacterium prausnitzii, Lactobacillus rogosae, Megamonas rupellensis and Phascolarctobacterium faecium. Positive correlations were observed between Acinetobacter baumannii and erythrocyte sedimentation rate (ESR) (R=0.554, p=0.001), as well as hypersensitive C reactive protein (hsCRP) (R=0.406, p=0.026). Faecalibacterium prausnitzii was negatively associated with ESR (R=-0.545, p=0.002), hsCRP (R=-0.401, p=0.028) and total bile acids (TBA) (R=-0.364, p=0.048). In conclusion, the fecal microbiota structure was different between MRSA-positive and -negative patients. The increase in potential pathogens with the reduction of beneficial populations, such as SCFA-producing bacteria, in MRSA-positive patients may affect prognosis.
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Affiliation(s)
- J Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongoli, 010018, China
| | - L Nian
- The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, 010018, China
| | - L Y Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongoli, 010018, China
| | - T Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongoli, 010018, China
| | - J Zhao
- The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, 010018, China.
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Li J, Liu Y, Kim E, March JC, Bentley WE, Payne GF. Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology. Free Radic Biol Med 2017; 105:110-131. [PMID: 28040473 DOI: 10.1016/j.freeradbiomed.2016.12.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/06/2016] [Accepted: 12/20/2016] [Indexed: 12/20/2022]
Abstract
The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O2 for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H2O2) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this electrochemical tool for in vitro redox-probing.
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Affiliation(s)
- Jinyang Li
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - Yi Liu
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - Eunkyoung Kim
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - John C March
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - Gregory F Payne
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA.
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15
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Mirza A, Mao-Draayer Y. The gut microbiome and microbial translocation in multiple sclerosis. Clin Immunol 2017; 183:213-224. [PMID: 28286112 DOI: 10.1016/j.clim.2017.03.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/03/2017] [Accepted: 03/07/2017] [Indexed: 02/07/2023]
Abstract
Individuals with multiple sclerosis (MS) have a distinct intestinal microbial community (microbiota) and increased low-grade translocation of bacteria from the intestines into the circulation. The observed change of intestinal bacteria in MS patients regulate immune functions involved in MS pathogenesis. These functions include: systemic and central nervous system (CNS) immunity (including peripheral regulatory T cell function), the blood-brain barrier (BBB) permeability and CNS-resident cell activity. This review discusses the MS intestinal microbiota implication on MS systemic- and CNS-immunopathology. We introduce the possible contributions of MS low-grade microbial translocation (LG-MT) to the development of MS, and end on a discussion on microbiota therapies for MS patients.
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Affiliation(s)
- Ali Mirza
- Department of Microbiology and Immunology, University of Michigan School of Medicine, 4258 Alfred Taubman Biomedical Sciences Research Bldg. 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200, United States; Department of Neurology, University of Michigan School of Medicine, 4258 Alfred Taubman Biomedical Sciences Research Bldg. 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200, United States
| | - Yang Mao-Draayer
- Department of Neurology, University of Michigan School of Medicine, 4015 Alfred Taubman Biomedical Sciences Research Bldg. 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200, United States.
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Borgia G, Maraolo AE, Foggia M, Buonomo AR, Gentile I. Fecal microbiota transplantation for Clostridium difficile infection: back to the future. Expert Opin Biol Ther 2016; 15:1001-14. [PMID: 26063385 DOI: 10.1517/14712598.2015.1045872] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Clostridium difficile infection (CDI) is a leading cause of diarrhea in the industrialized world. The estimated costs of this infection are impressive: over 3.2 billion dollars annually in the US. The introduction of fecal microbiota transplantation (FMT) to clinical practice can be considered a Copernican Revolution. The rationale of this approach consists of correcting the imbalance of the organisms dwelling in the gut by reintroducing a normal flora. AREAS COVERED This review focuses on the indication for FMT in CDI; it examines in-depth the most relevant aspects of the techniques used, and the safety and efficacy of this new 'old' therapy. EXPERT OPINION Authoritative guidelines about the management of CDI strongly recommend FMT for multiple recurrent episodes of infection by C. difficile unresponsive to repeated antibiotic treatment. The cure rates are about 90%, with no serious adverse events having been reported. The main concerns are the long-term outcomes, lack of a standardized procedure for the delivery of donor material, and a cultural barrier to the transplantation of fecal microbiota. A promising solution to some of these problems could be the use of a more acceptable administration route of fecal material, namely, oral capsules.
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Affiliation(s)
- Guglielmo Borgia
- University of Naples "Federico II", Department of Clinical Medicine and Surgery, Section of Infectious Diseases, Naples , Italy +39(0)81 7463178 ; +39(0)81 7463190 ;
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Forster SC, Browne HP, Kumar N, Hunt M, Denise H, Mitchell A, Finn RD, Lawley TD. HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes. Nucleic Acids Res 2015; 44:D604-9. [PMID: 26578596 PMCID: PMC4702862 DOI: 10.1093/nar/gkv1216] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/28/2015] [Indexed: 02/07/2023] Open
Abstract
The Human Pan-Microbe Communities (HPMC) database (http://www.hpmcd.org/) provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota. Over the past decade, the application of metagenome sequencing to elucidate the microbial composition and functional capacity present in the human microbiome has revolutionized many concepts in our basic biology. When sufficient high quality reference genomes are available, whole genome metagenomic sequencing can provide direct biological insights and high-resolution classification. The HPMC database provides species level, standardized phylogenetic classification of over 1800 human gastrointestinal metagenomic samples. This is achieved by combining a manually curated list of bacterial genomes from human faecal samples with over 21000 additional reference genomes representing bacteria, viruses, archaea and fungi with manually curated species classification and enhanced sample metadata annotation. A user-friendly, web-based interface provides the ability to search for (i) microbial groups associated with health or disease state, (ii) health or disease states and community structure associated with a microbial group, (iii) the enrichment of a microbial gene or sequence and (iv) enrichment of a functional annotation. The HPMC database enables detailed analysis of human microbial communities and supports research from basic microbiology and immunology to therapeutic development in human health and disease.
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Affiliation(s)
- Samuel C Forster
- Host Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton 3168, Australia Department of Molecular and Translational Sciences, Monash University, Clayton 3800, Australia
| | - Hilary P Browne
- Host Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Nitin Kumar
- Host Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Martin Hunt
- Pathogen Informatics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Hubert Denise
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Alex Mitchell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Trevor D Lawley
- Host Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
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Schreiber F, Arasteh JM, Lawley TD. Pathogen Resistance Mediated by IL-22 Signaling at the Epithelial-Microbiota Interface. J Mol Biol 2015; 427:3676-82. [PMID: 26497621 DOI: 10.1016/j.jmb.2015.10.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 02/08/2023]
Abstract
Intestinal colonization resistance to bacterial pathogens is generally associated, among other factors, with mucosal homeostasis that preserves the integrity of the intestinal barrier. Mucosal homeostasis depends on physical and molecular interactions between three components: the resident microbiota, the epithelial layer and the local immune system. The cytokine IL-22 helps to orchestrate this three-way interaction. IL-22 is produced by immune cells present beneath the epithelium and is induced by bacteria present in the intestine. IL-22 stimulates the epithelial cells via the IL-22RA1-IL-10R2 receptor complex inducing changes in the expression of genes involved in the maintenance of epithelial barrier integrity, with a variety of functions in pathogen resistance such as mucus layer modifications and hydration, tight junction fortification and the production of a broad range of bactericidal compounds. These mechanisms of pathogen resistance, in turn, affect the microbiota composition and create an environment that excludes pathogens. Here we highlight the role of IL-22 as key mediator in the give-and-take relationship between the microbiota and the host that impacts pathogen resistance.
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Affiliation(s)
- Fernanda Schreiber
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.
| | - Julia Maryam Arasteh
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.
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Fecal microbiota transplantation restores dysbiosis in patients with methicillin resistant Staphylococcus aureus enterocolitis. BMC Infect Dis 2015; 15:265. [PMID: 26159166 PMCID: PMC4498521 DOI: 10.1186/s12879-015-0973-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 05/29/2015] [Indexed: 12/31/2022] Open
Abstract
Background Nosocomial Methicillin-resistant Staphylococcus aureus (MRSA) enteritis is rare but can be fatal unless it is detected at an early stage and treated effectively. Dysbiosis of the gut is one of the leading reasons of MRSA enteritis. Fecal microbiota transplantation (FMT) is a burgeoning treatment to rectify this imbalance. But the impact of FMT on MRSA enterocoitis is still unknown yet. Methods A total of 5 patients diagnosed as MRSA enteritis during the early postoperative period were given vancomycin 2 g/day for 3 days and FMT for three continuous days as a standard treatment. Result There was a 100 % clinical response rate that all the symptoms resulting from MRSA enterocolitis disappeared and MRSA in the feces eliminated clearly. The microbiota profile in feces of the patients also regained balance. Conclusion FMT can be a preferential measure to restore the dysbiosis caused by MSRA enterocolitis.
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Clostridium butyricum combined with Bifidobacterium infantis probiotic mixture restores fecal microbiota and attenuates systemic inflammation in mice with antibiotic-associated diarrhea. BIOMED RESEARCH INTERNATIONAL 2015; 2015:582048. [PMID: 25802855 PMCID: PMC4352745 DOI: 10.1155/2015/582048] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 02/02/2015] [Indexed: 12/22/2022]
Abstract
Antibiotic-associated diarrhea (AAD) is one of the most common complications of most types of antibiotics. Our aim was to determine the efficacy of Clostridium butyricum, Bifidobacterium infantis, and their mixture for AAD treatment in mice. AAD models were administered with single probiotic strain and probiotic mixture for short term and long term to evaluate the changes of the composition and diversity of intestinal microbiota, histopathology of the colon, and the systemic inflammation. Our data indicated that long-term probiotic therapy, but not short-term course, exerted beneficial effects on the restoration of the intestinal microbiota, the recovery of the tissue architecture, and attenuation of systemic inflammation. All predominant fecal bacteria reached normal level after the long-term probiotic mixture treatment, while IL-10, IFN-γ, and TNF-α also returned to normal level. However, the efficacy for AAD was time dependent and probiotic strain specific. Short-term administration of probiotic strains or mixture showed no apparent positive effects for AAD. In addition, the beneficial effects of C. butyricum combined with B. infantis probiotic mixture were superior to their single strain. This research showed that supplementation with C. butyricum combined with B. infantis probiotic mixture may be a simple and effective method for AAD treatment.
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Febinia C, Ha C, Le C, Holmes A. The role of the gut microbiome in host systems. MICROBIOLOGY AUSTRALIA 2015. [DOI: 10.1071/ma15005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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Impacts of infection with different toxigenic Clostridium difficile strains on faecal microbiota in children. Sci Rep 2014; 4:7485. [PMID: 25501371 PMCID: PMC4265774 DOI: 10.1038/srep07485] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/27/2014] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence suggests that altered intestinal microbial composition and function result in an increased risk of Clostridium difficile-associated diarrhoea (CDAD); however, the specific changes of intestinal microbiota in children suffering from CDAD and their associations with C.difficile strain toxigenicity are poorly understood. High-throughput pyrosequencing showed that reduced faecal bacterial diversity and dramatic shifts of microbial composition were found in children with CDAD. The Firmicutes/Bacteroidetes ratio was increased significantly in patients with CDAD, which indicated that dysbiosis of faecal microbiota was closely associated with CDAD. C. difficile infection resulted in an increase in lactate-producing phylotypes, with a corresponding decrease in butyrate-producing bacteria. The decrease in butyrate and lactate buildup impaired intestinal colonisation resistance, which increased the susceptibility to C. difficile colonisation. Strains of C.difficile which were positive for both toxin A and toxin B reduced faecal bacterial diversity to a greater degree than strains that were only toxin B-positive, and were associated with unusually abundant Enterococcus, which implies that the C. difficile toxins have different impacts on the faecal microbiota of children. Greater understanding of the relationships between disruption of the normal faecal microbiota and colonisation with C. difficile that produces different toxins might lead to improved treatment.
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Bakken JS. Staggered and tapered antibiotic withdrawal with administration of kefir for recurrent Clostridium difficile infection. Clin Infect Dis 2014; 59:858-61. [PMID: 24917658 DOI: 10.1093/cid/ciu429] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Daily administration of the probiotic kefir given in combination with a staggered and tapered antibiotic withdrawal regimen may resolve recurrent Clostridium difficile infection as effectively as fecal microbiota transplantation.
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Affiliation(s)
- Johan S Bakken
- Section of Infectious Disease, St Luke's Hospital, Duluth, Minnesota
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McCune V, Struthers J, Hawkey P. Faecal transplantation for the treatment of Clostridium difficile infection: a review. Int J Antimicrob Agents 2014; 43:201-6. [DOI: 10.1016/j.ijantimicag.2013.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 10/09/2013] [Indexed: 12/18/2022]
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Pham TAN, Lawley TD. Emerging insights on intestinal dysbiosis during bacterial infections. Curr Opin Microbiol 2013; 17:67-74. [PMID: 24581695 PMCID: PMC3969284 DOI: 10.1016/j.mib.2013.12.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 12/18/2022]
Abstract
Diverse enteric pathogens often induce significant perturbations to the microbiota or thrive during dysbiosis. Infection-associated dysbiosis is commonly characterized by decreased diversity and metabolic function. The dysbiotic microbiota may act as a pathogenic community to perpetuate host pathology. Pathogens can exploit dysbiosis for host colonization, genome evolution, and transmission. Bacteriotherapy represents a potential viable strategy to restore intestinal homeostasis.
Infection of the gastrointestinal tract is commonly linked to pathological imbalances of the resident microbiota, termed dysbiosis. In recent years, advanced high-throughput genomic approaches have allowed us to examine the microbiota in an unprecedented manner, revealing novel biological insights about infection-associated dysbiosis at the community and individual species levels. A dysbiotic microbiota is typically reduced in taxonomic diversity and metabolic function, and can harbour pathobionts that exacerbate intestinal inflammation or manifest systemic disease. Dysbiosis can also promote pathogen genome evolution, while allowing the pathogens to persist at high density and transmit to new hosts. A deeper understanding of bacterial pathogenicity in the context of the intestinal microbiota should unveil new approaches for developing diagnostics and therapies for enteropathogens.
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Affiliation(s)
- Tu Anh N Pham
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Trevor D Lawley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom.
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Moore T, Rodriguez A, Bakken JS. Fecal microbiota transplantation: a practical update for the infectious disease specialist. Clin Infect Dis 2013; 58:541-5. [PMID: 24368622 DOI: 10.1093/cid/cit950] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fecal microbiota transplantation (FMT) has been shown to be a superior therapeutic modality for the treatment of recurrent Clostridium difficile infection (RCDI). Recently the US Food and Drug Administration (FDA) determined that human stool should be classified as a biological agent and its use should be regulated to ensure patient safety. Consequently, the FDA determined that prescribers of FMT must possess an approved investigational new drug (IND) permit to administer FMT for the purpose of conducting research or treating any gastrointestinal condition other than RCDI. Although an IND is not required for use of FMT to treat RCDI, an IND is strongly encouraged and may ultimately be required. This article provides step-by-step guidance to infectious disease specialists on how to navigate the regulatory requirements and successfully obtain an IND before they can begin to use FMT as part of their clinical practice.
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Affiliation(s)
- Thomas Moore
- Infectious Disease Consultants (IDC) of Kansas, Wichita
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