{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:41:58Z","timestamp":1791852118955,"version":"4.3.4"},"reference-count":104,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01 AI167860"],"award-info":[{"award-number":["R01 AI167860"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["T32 DK007202"],"award-info":[{"award-number":["T32 DK007202"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000069","name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","doi-asserted-by":"publisher","award":["T32 AR064194"],"award-info":[{"award-number":["T32 AR064194"]}],"id":[{"id":"10.13039\/100000069","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","award":["GT15123"],"award-info":[{"award-number":["GT15123"]}],"id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,8,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Bacteroides fragilis,<\/jats:italic>\n                      a key member of the human gut microbiota, contributes to host health by maintaining intestinal homeostasis. Yet, it is also the most frequently isolated anaerobe in clinical infections. These contrasting roles raise questions about the genetic and ecological factors that explain why this common symbiont is disproportionately linked to infection. We analyzed 813 Division I\n                      <jats:italic toggle=\"yes\">B. fragilis<\/jats:italic>\n                      genomes, including 147 new isolates from intestinal and extra-intestinal sites. Infection-associated isolates spanned all phylogroups, indicating no pathogenic lineage. We identified 16 phylogroups, distinguished by genes associated with capsule biosynthesis and interbacterial competition. Additionally, differential metabolomic analysis identified 12 metabolites associated with isolation source, while a microbial genome-wide association study uncovered 44 genes enriched in isolates from extra-intestinal sites, providing the first population-scale markers tied to clinical recovery sites. These results do not implicate a pathogenic lineage; instead, they point to associational links between accessory modules and recovery from extra-intestinal sites under permissive host conditions. This work underscores how genomic diversity and ecological context may jointly shape the clinical impact of gut commensals.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        <jats:italic toggle=\"yes\">Bacteroides fragilis,<\/jats:italic>\n                        a human gut resident, is paradoxically one of the most frequent anaerobes recovered from bloodstream and abscess infections. The genetic features that enable frequent recovery from extra-intestinal sites remain poorly defined. Using comparative genomic and metabolomic analyses of strains from intestinal and extra-intestinal sources, we show that strains isolated from infections are phylogenetically dispersed rather than restricted to a single lineage. We observe lineage-linked differences in capsule loci and competition systems, which suggests constrained gene flow and lineage-specific adaptation within the gut. Additionally, a subset of genes and metabolites is enriched among extra-intestinal isolates. Together, these findings suggest that extra-intestinal survival among\n                        <jats:italic toggle=\"yes\">B. fragilis<\/jats:italic>\n                        strains reflects the interplay between species-wide genomic diversity and permissive host conditions, rather than the emergence of a single pathogenic lineage.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00306-26","type":"journal-article","created":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T13:00:17Z","timestamp":1784034017000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["Comparative genomic analysis of\n                    <i>Bacteroides fragilis<\/i>\n                    from intestinal and extra-intestinal sites"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5945-0215","authenticated-orcid":true,"given":"Renee E.","family":"Oles","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0168r3w48","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, University of California","place":["San Diego, USA"]},{"id":[{"id":"https:\/\/ror.org\/0168r3w48","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California","place":["San Diego, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8830-5161","authenticated-orcid":false,"given":"Marvic","family":"Carrillo Terrrazas","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0168r3w48","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, University of California","place":["San Diego, 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