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Antibiotics deplete the indigenous gut microbiota and change the metabolic environment in the gut to one favoring\n            <jats:named-content content-type=\"genus-species\">C. difficile<\/jats:named-content>\n            growth. Here we used metabolomics and transcriptomics to define the gut environment after antibiotics and during the initial stages of\n            <jats:named-content content-type=\"genus-species\">C. difficile<\/jats:named-content>\n            colonization and infection. We show that amino acids, in particular, proline and branched-chain amino acids, and carbohydrates decrease in abundance over time and that\n            <jats:named-content content-type=\"genus-species\">C. difficile<\/jats:named-content>\n            gene expression is consistent with their utilization by the bacterium\n            <jats:italic>in vivo<\/jats:italic>\n            . We employed an integrated approach to analyze the metabolome and transcriptome to identify associations between metabolites and transcripts. This highlighted the importance of key nutrients in the early stages of colonization, and the data provide a rationale for the development of therapies based on the use of bacteria that specifically compete for nutrients that are essential for\n            <jats:named-content content-type=\"genus-species\">C. difficile<\/jats:named-content>\n            colonization and disease.\n          <\/jats:p>","DOI":"10.1128\/msphere.00089-18","type":"journal-article","created":{"date-parts":[[2018,3,27]],"date-time":"2018-03-27T10:07:43Z","timestamp":1522145263000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":108,"title":["Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model"],"prefix":"10.1128","volume":"3","author":[{"given":"Joshua R.","family":"Fletcher","sequence":"first","affiliation":[{"name":"Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha","family":"Erwin","sequence":"additional","affiliation":[{"name":"Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina","family":"Lanzas","sequence":"additional","affiliation":[{"name":"Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Casey M.","family":"Theriot","sequence":"additional","affiliation":[{"name":"Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1286-4579(99)80054-9"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1086\/521859"},{"key":"e_1_3_2_4_2","volume-title":"Healthcare Cost and Utilization Project (HCUP) statistical briefs","author":"Lucado J","year":"2012","unstructured":"Lucado J, Gould C, Elixhauser A. 2012. 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High resolution mass spectrometry improves data quantity and quality as compared to unit mass resolution mass spectrometry in high-throughput profiling metabolomics. Metabolomics 4:132.","journal-title":"Metabolomics"},{"key":"e_1_3_2_84_2","doi-asserted-by":"publisher","DOI":"10.1186\/1758-2946-2-9"},{"key":"e_1_3_2_85_2","unstructured":"Oliveros JC. 2007\u20132015. Venny. An interactive tool for comparing lists with Venn\u2019s diagrams. http:\/\/bioinfogp.cnb.csic.es\/tools\/venny\/index.html."},{"key":"e_1_3_2_86_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw937"},{"key":"e_1_3_2_87_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005752"},{"key":"e_1_3_2_88_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-253"},{"key":"e_1_3_2_89_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0940-1"}],"container-title":["mSphere"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mSphere.00089-18","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mSphere.00089-18","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,8]],"date-time":"2022-03-08T04:05:40Z","timestamp":1646712340000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mSphere.00089-18"}},"subtitle":[],"editor":[{"given":"Sarah E. 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