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In addition to providing pre\u2010clinical models for the development of novel therapeutics and diagnostic biomarkers, mouse systems actively support microbiome studies by defining microbial contributions to normal development and homeostasis, as well as the role of microbes in promoting diseases such as inflammatory auto\u2010immune disorders, diabetes, metabolic syndrome, and susceptibility to infectious agents. Mice provide a genetically tenable host that can be reared under gnotobiotic (germ\u2010free) conditions, allowing colonization studies with human\u2010 or mouse\u2010origin defined or complex microbial communities to define specific <jats:italic>in vivo<\/jats:italic> effects. The protocols and background information detail key aspects to consider in designing host\u2010microbiome experiments with mouse models, and in developing robust systems that leverage gnotobiotic mice, microbial consortia, and specific environmental perturbations to identify causal effects <jats:italic>in vivo<\/jats:italic>. \u00a9 2018 by John Wiley &amp; Sons, Inc.<\/jats:p>","DOI":"10.1002\/cpim.48","type":"journal-article","created":{"date-parts":[[2018,4,16]],"date-time":"2018-04-16T14:11:42Z","timestamp":1523887902000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Gnotobiotic and Conventional Mouse Systems to Support Microbiota Based Studies"],"prefix":"10.1002","volume":"121","author":[{"given":"Richard","family":"Lavin","sequence":"first","affiliation":[{"name":"Massachusetts Host\u2010Microbiome Center, Department Pathology, Brigham &amp; Women's Hospital, Harvard Medical School, Boston  Massachusetts"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"DiBenedetto","sequence":"additional","affiliation":[{"name":"Massachusetts Host\u2010Microbiome Center, Department Pathology, Brigham &amp; 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