{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T16:59:41Z","timestamp":1792515581718,"version":"4.5.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2024,8,21]],"date-time":"2024-08-21T00:00:00Z","timestamp":1724198400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001602","name":"Science Foundation Ireland","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001602","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Centre Award to APC Microbiome Ireland","award":["12\/RC\/2273_P2"],"award-info":[{"award-number":["12\/RC\/2273_P2"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>There is an accumulation of evidence that the human gut microbiota plays a role in maintaining health, and that an altered gut microbiota (sometimes called dysbiosis) associates with risk for many noncommunicable diseases. However, the dynamics of disease-linked bacteria in the gut and other body sites remain unclear. If microbiome alterations prove causative in particular diseases, therapeutic intervention may be possible. Furthermore, microbial signature taxa have been established for the diagnosis of some diseases like colon cancer. We identified 163 disease-enriched and 98 disease-depleted gut microbiome signature taxa at species-level resolution (signature species) from 10 meta-analyses of multiple diseases such as colorectal cancer, ulcerative colitis, Crohn's disease, irritable bowel syndrome, pancreatic cancer, and COVID-19 infection. Eight signature species were enriched and nine were depleted across at least half of the diseases studied. Compared with signature species depleted in diseases, a significantly higher proportion of disease-enriched signature species were identified as extra-intestinal (primarily oral) inhabitants, had been reported in bacteremia cases from the literature, and were aerotolerant anaerobes. These findings highlight the potential involvement of oral microbes, bacteremia isolates, and aerotolerant anaerobes in disease-associated gut microbiome alterations, and they have implications for patient care and disease management.<\/jats:p>","DOI":"10.1093\/pnasnexus\/pgae352","type":"journal-article","created":{"date-parts":[[2024,9,4]],"date-time":"2024-09-04T01:40:48Z","timestamp":1725414048000},"source":"Crossref","is-referenced-by-count":11,"title":["Disease-associated microbiome signature species in the gut"],"prefix":"10.1093","volume":"3","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3563-9114","authenticated-orcid":false,"given":"Junhui","family":"Li","sequence":"first","affiliation":[{"name":"APC Microbiome Ireland, University College Cork , Cork T12 K8AF ,","place":["Ireland"]},{"name":"School of Microbiology, University College Cork , Cork T12 K8AF ,","place":["Ireland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5377-0824","authenticated-orcid":false,"given":"Paul W","family":"O\u2019Toole","sequence":"additional","affiliation":[{"name":"APC Microbiome Ireland, University College Cork , Cork T12 K8AF ,","place":["Ireland"]},{"name":"School of Microbiology, University College Cork , Cork T12 K8AF ,","place":["Ireland"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,8,21]]},"reference":[{"key":"2024093009483889500_pgae352-B1","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1084\/jem.20180448","article-title":"The gut microbiome: relationships with disease and opportunities for therapy","volume":"216","author":"Durack","year":"2019","journal-title":"J Exp Med."},{"key":"2024093009483889500_pgae352-B2","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1038\/s41591-019-0405-7","article-title":"Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation","volume":"25","author":"Thomas","year":"2019","journal-title":"Nat Med."},{"key":"2024093009483889500_pgae352-B3","article-title":"In production. Cross-cohort gut microbiome signatures of irritable bowel syndrome presentation and treatment","author":"Li","year":"2024","journal-title":"Adv Sci"},{"key":"2024093009483889500_pgae352-B4","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1053\/j.gastro.2022.03.054","article-title":"Metagenomic identification of microbial signatures predicting pancreatic cancer from a multinational study","volume":"163","author":"Nagata","year":"2022","journal-title":"Gastroenterology"},{"key":"2024093009483889500_pgae352-B5","doi-asserted-by":"crossref","first-page":"1784","DOI":"10.1038\/s41467-017-01973-8","article-title":"Meta-analysis of gut microbiome studies identifies disease-specific and shared responses","volume":"8","author":"Duvallet","year":"2017","journal-title":"Nat Commun."},{"key":"2024093009483889500_pgae352-B6","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.cell.2019.12.025","article-title":"Establishing or exaggerating causality for the gut microbiome: lessons from human microbiota-associated rodents","volume":"180","author":"Walter","year":"2020","journal-title":"Cell"},{"key":"2024093009483889500_pgae352-B7","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1016\/j.cell.2020.05.048","article-title":"The intermucosal connection between the mouth and gut in commensal pathobiont-driven colitis","volume":"182","author":"Kitamoto","year":"2020","journal-title":"Cell"},{"key":"2024093009483889500_pgae352-B8","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1177\/0022034520924633","article-title":"The bacterial connection between the oral cavity and the gut diseases","volume":"99","author":"Kitamoto","year":"2020","journal-title":"J Dent Res."},{"key":"2024093009483889500_pgae352-B9","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1016\/j.molmed.2023.08.006","article-title":"Microbiome-targeted interventions for the control of oral\u2013gut dysbiosis and chronic systemic inflammation","volume":"29","author":"Pacheco-Yanes","year":"2023","journal-title":"Trends Mol Med."},{"key":"2024093009483889500_pgae352-B10","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1126\/science.aan4526","article-title":"Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation","volume":"358","author":"Atarashi","year":"2017","journal-title":"Science"},{"key":"2024093009483889500_pgae352-B11","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1038\/s41575-021-00488-4","article-title":"The role of oral bacteria in inflammatory bowel disease","volume":"18","author":"Read","year":"2021","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"2024093009483889500_pgae352-B12","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1177\/00220345211049781","article-title":"Periodontitis salivary microbiota worsens colitis","volume":"101","author":"Qian","year":"2022","journal-title":"J Dent Res."},{"key":"2024093009483889500_pgae352-B13","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1038\/s41368-022-00183-3","article-title":"Periodontitis may induce gut microbiota dysbiosis via salivary microbiota","volume":"14","author":"Bao","year":"2022","journal-title":"Int J Oral Sci."},{"key":"2024093009483889500_pgae352-B14","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1038\/s41564-023-01350-w","article-title":"No evidence for a common blood microbiome based on a population study of 9,770 healthy humans","volume":"8","author":"Tan","year":"2023","journal-title":"Nat Microbiol."},{"key":"2024093009483889500_pgae352-B15","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/nrmicro.2017.157","article-title":"The human skin microbiome","volume":"16","author":"Byrd","year":"2018","journal-title":"Nat Rev Microbiol."},{"key":"2024093009483889500_pgae352-B16","doi-asserted-by":"crossref","first-page":"57","DOI":"10.4161\/viru.26514","article-title":"The complex pathogenesis of bacteremia","volume":"5","author":"Christaki","year":"2014","journal-title":"Virulence"},{"key":"2024093009483889500_pgae352-B17","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1053\/j.gastro.2018.04.028","article-title":"Association between bacteremia from specific microbes and subsequent diagnosis of colorectal cancer","volume":"155","author":"Kwong","year":"2018","journal-title":"Gastroenterology"},{"key":"2024093009483889500_pgae352-B18","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1093\/cid\/ciac259","article-title":"Bacteremia with anaerobic bacteria and association with colorectal cancer: a population-based cohort study","volume":"75","author":"Justesen","year":"2022","journal-title":"Clin Infect Dis."},{"key":"2024093009483889500_pgae352-B19","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s13099-021-00408-6","article-title":"Are hospitalized patients with inflammatory bowel disease at increased risk of invasive bacterial infections? 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