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Mucosal surfaces, particularly in the gut, are highly adapted to be able to tolerate a large population of microorganisms whilst still being able to produce a rapid and effective immune response against infection. The intestinal microbiome is not functionally independent from the host mucosa and can, through presentation of microbe-associated molecular patterns (MAMPs) and generation of microbe-derived metabolites, fundamentally influence mucosal barrier integrity and modulate host immunity. In a healthy gut there is an abundance of beneficial bacteria that help to preserve intestinal homoeostasis, promote protective immune responses, and limit excessive inflammation. The importance of the microbiome is further highlighted during dysbiosis where a loss of this finely balanced microbial population can lead to mucosal barrier dysfunction, aberrant immune responses, and chronic inflammation that increases the risk of disease development. Improvements in our understanding of the microbiome are providing opportunities to harness members of a healthy microbiota to help reverse dysbiosis, reduce inflammation, and ultimately prevent disease progression.<\/jats:p>","DOI":"10.1042\/bsr20203850","type":"journal-article","created":{"date-parts":[[2021,6,2]],"date-time":"2021-06-02T13:35:13Z","timestamp":1622640913000},"update-policy":"https:\/\/doi.org\/10.1042\/crossmark_policy","source":"Crossref","is-referenced-by-count":64,"title":["The role of the microbiome in gastrointestinal inflammation"],"prefix":"10.1042","volume":"41","author":[{"given":"David\u00a0J.","family":"Sanders","sequence":"first","affiliation":[{"name":"Department of Microbial Diseases, UCL Eastman Dental Institute, Royal Free Campus, University College London, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saskia","family":"Inniss","sequence":"additional","affiliation":[{"name":"Department of Microbial Diseases, UCL Eastman Dental Institute, Royal Free Campus, University College London, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory","family":"Sebepos-Rogers","sequence":"additional","affiliation":[{"name":"Department of Microbial Diseases, UCL Eastman Dental Institute, Royal Free Campus, University College London, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Farooq\u00a0Z.","family":"Rahman","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London NW1 2PG, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4691-5973","authenticated-orcid":false,"given":"Andrew\u00a0M.","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Microbial Diseases, UCL Eastman Dental Institute, Royal Free Campus, University College London, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"288","published-online":{"date-parts":[[2021,6,11]]},"reference":[{"key":"2021111620474794000_B1","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1038\/nature06245","article-title":"An ecological and evolutionary perspective on human-microbe mutualism and disease","volume":"449","author":"Dethlefsen","year":"2007","journal-title":"Nature"},{"key":"2021111620474794000_B2","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1038\/nature06244","article-title":"The human microbiome project","volume":"449","author":"Turnbaugh","year":"2007","journal-title":"Nature"},{"key":"2021111620474794000_B3","doi-asserted-by":"publisher","first-page":"e1002533","DOI":"10.1371\/journal.pbio.1002533","article-title":"Revised estimates for the number of human and bacteria cells in the body","volume":"14","author":"Sender","year":"2016","journal-title":"PLoS Biol."},{"key":"2021111620474794000_B4","doi-asserted-by":"publisher","first-page":"e00824","DOI":"10.1128\/mBio.00824-17","article-title":"First insights into the diverse human archaeome: specific detection of archaea in the gastrointestinal tract, lung, and nose and on skin","volume":"8","author":"Koskinen","year":"2017","journal-title":"mBio"},{"key":"2021111620474794000_B5","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1186\/s12915-020-00785-5","article-title":"A tissue level atlas of the healthy human virome","volume":"18","author":"Kumata","year":"2020","journal-title":"BMC Biol."},{"key":"2021111620474794000_B6","doi-asserted-by":"publisher","first-page":"e1000713","DOI":"10.1371\/journal.ppat.1000713","article-title":"Characterization of the oral fungal microbiome (mycobiome) in healthy individuals","volume":"6","author":"Ghannoum","year":"2010","journal-title":"PLoS Pathog."},{"key":"2021111620474794000_B7","doi-asserted-by":"publisher","first-page":"e00007","DOI":"10.1128\/mSystems.00007-18","article-title":"Asymptomatic intestinal colonization with protist blastocystis is strongly associated with distinct microbiome ecological patterns","volume":"3","author":"Nieves-Ramirez","year":"2018","journal-title":"mSystems"},{"key":"2021111620474794000_B8","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.cell.2016.01.013","article-title":"Are we really vastly outnumbered? 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