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Recent advances in metagenomic sequencing and bioinformatics have enabled detailed characterization of these vital microbial communities. Studies in animal models have uncovered vital previously unrecognized roles for the microbiota in normal function of the immune responses, and when perturbed, in the pathogenesis of diseases of the gastrointestinal tract and lungs, but also at distant sites in the body including the brain. The composition of gut and respiratory microbiota can influence systemic inflammatory responses that mediate asthma, allergy, inflammatory bowel disease, obesity\u2010related diseases, and neurodevelopmental or neurodegenerative conditions. Experiments in mouse models as well as emerging clinical studies have revealed that therapeutic manipulation of the microbiota, using fecal microbiota transplantation, probiotics, or engineered probiotics represent effective nontoxic approaches for the treatment or prevention of <jats:italic>Clostridium difficile<\/jats:italic> infection, allergy, and autoimmune diseases and may enhance the efficacy of certain cancer immunotherapeutics. This review discusses how commensal bacteria can influence immune responses that mediate a range of human diseases and how the microbiota are being targeted to treat these diseases, especially those resistant to pharmacological therapies.<\/jats:p>","DOI":"10.1002\/eji.201948322","type":"journal-article","created":{"date-parts":[[2020,1,28]],"date-time":"2020-01-28T23:48:45Z","timestamp":1580255325000},"page":"326-337","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":57,"title":["The microbiota and immune\u2010mediated diseases: Opportunities for therapeutic intervention"],"prefix":"10.1002","volume":"50","author":[{"given":"Gillian","family":"Fitzgibbon","sequence":"first","affiliation":[{"name":"School of Biochemistry and Immunology Trinity Biomedical Sciences Institute Trinity College Dublin  Dublin 2 Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3646-8222","authenticated-orcid":false,"given":"Kingston H. 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