{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T08:11:39Z","timestamp":1783584699456,"version":"3.55.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008782","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,3,4]],"date-time":"2021-03-04T00:00:00Z","timestamp":1614816000000}}],"reference-count":101,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2021,2,22]],"date-time":"2021-02-22T00:00:00Z","timestamp":1613952000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Approximately 30% of patients who have\n                    <jats:italic>Clostridioides difficile<\/jats:italic>\n                    infection (CDI) will suffer at least one incident of reinfection. While the underlying causes of CDI recurrence are poorly understood, interactions between\n                    <jats:italic>C<\/jats:italic>\n                    .\n                    <jats:italic>difficile<\/jats:italic>\n                    and commensal gut bacteria are thought to play an important role. In this study, an\n                    <jats:italic>in silico<\/jats:italic>\n                    pipeline was used to process 16S rRNA gene amplicon sequence data of 225 stool samples from 93 CDI patients into sample-specific models of bacterial community metabolism. Clustered metabolite production rates generated from post-diagnosis samples generated a high\n                    <jats:italic>Enterobacteriaceae<\/jats:italic>\n                    abundance cluster containing disproportionately large numbers of recurrent samples and patients. This cluster was predicted to have significantly reduced capabilities for secondary bile acid synthesis but elevated capabilities for aromatic amino acid catabolism. When applied to 16S sequence data of 40 samples from fecal microbiota transplantation (FMT) patients suffering from recurrent CDI and their stool donors, the community modeling method generated a high\n                    <jats:italic>Enterobacteriaceae<\/jats:italic>\n                    abundance cluster with a disproportionate large number of pre-FMT samples. This cluster also was predicted to exhibit reduced secondary bile acid synthesis and elevated aromatic amino acid catabolism. Collectively, these\n                    <jats:italic>in silico<\/jats:italic>\n                    predictions suggest that\n                    <jats:italic>Enterobacteriaceae<\/jats:italic>\n                    may create a gut environment favorable for\n                    <jats:italic>C<\/jats:italic>\n                    .\n                    <jats:italic>difficile<\/jats:italic>\n                    spore germination and\/or toxin synthesis.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1008782","type":"journal-article","created":{"date-parts":[[2021,2,22]],"date-time":"2021-02-22T13:38:51Z","timestamp":1614001131000},"page":"e1008782","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":18,"title":["Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1969-4906","authenticated-orcid":true,"given":"Michael A.","family":"Henson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,2,22]]},"reference":[{"issue":"4","key":"pcbi.1008782.ref001","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1038\/ajg.2013.4","article-title":"Guidelines for diagnosis, treatment, and prevention of Clostridium difficile infections","volume":"108","author":"CM Surawicz","year":"2013","journal-title":"The American journal of gastroenterology"},{"issue":"3","key":"pcbi.1008782.ref002","doi-asserted-by":"crossref","first-page":"337","DOI":"10.3390\/antibiotics4030337","article-title":"Colonization resistance of the gut microbiota against Clostridium difficile","volume":"4","author":"AE 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