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Changes in the structure of the gut microbiota alter the metabolome, specifically the production of secondary bile acids. Specific bile acids are able to initiate\n                    <jats:named-content content-type=\"genus-species\">C. difficile<\/jats:named-content>\n                    spore germination and also inhibit\n                    <jats:named-content content-type=\"genus-species\">C. difficile<\/jats:named-content>\n                    growth\n                    <jats:italic>in vitro<\/jats:italic>\n                    , although no study to date has defined physiologically relevant bile acids in the gastrointestinal tract. In this study, we define the bile acids\n                    <jats:named-content content-type=\"genus-species\">C. difficile<\/jats:named-content>\n                    spores encounter in the small and large intestines before and after various antibiotic treatments. Antibiotics that alter the gut microbiota and deplete secondary bile acid production allow\n                    <jats:named-content content-type=\"genus-species\">C. difficile<\/jats:named-content>\n                    colonization, representing a mechanism of colonization resistance. Multiple secondary bile acids in the large intestine were able to inhibit\n                    <jats:named-content content-type=\"genus-species\">C. difficile<\/jats:named-content>\n                    spore germination and growth at physiological concentrations and represent new targets to combat\n                    <jats:named-content content-type=\"genus-species\">C. difficile<\/jats:named-content>\n                    in the large intestine.\n                  <\/jats:p>","DOI":"10.1128\/msphere.00045-15","type":"journal-article","created":{"date-parts":[[2016,1,4]],"date-time":"2016-01-04T21:46:26Z","timestamp":1451943986000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":465,"title":["Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large 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