{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,8]],"date-time":"2026-11-08T09:13:51Z","timestamp":1794129231035,"version":"4.8.0"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2022,5,13]],"date-time":"2022-05-13T00:00:00Z","timestamp":1652400000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100007028","name":"Leona M. and Harry B. Helmsley Charitable Trust","doi-asserted-by":"publisher","award":["2018PG-CD007"],"award-info":[{"award-number":["2018PG-CD007"]}],"id":[{"id":"10.13039\/100007028","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Edmond J. Safra Center for Bioinformatics at Tel-Aviv University"},{"name":"Israeli Ministry of Science and Technology"},{"DOI":"10.13039\/501100006544","name":"Israeli Ministry of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006544","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background and Aims<\/jats:title>\n                    <jats:p>Escherichia coli is over-abundant in the gut microbiome of patients with inflammatory bowel disease [IBD]. Here, we aimed to identify IBD-specific genomic functions of diverse E. coli lineages.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We investigated E. coli genomes from patients with ulcerative colitis [UC], Crohn\u2019s disease [CD] or a pouch, and healthy subjects. The majority of genomes were reconstructed from metagenomic samples, including newly sequenced faecal metagenomes. Clinical metadata were collected. Functional analysis at the gene and mutation level were performed and integrated with IBD phenotypes and biomarkers.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Overall, 530 E. coli genomes were analysed. The E. coli B2 lineage was more prevalent in UC compared with other IBD phenotypes. Genomic metabolic capacities varied across E. coli lineages and IBD phenotypes. Host mucin utilisation enzymes were present in a single lineage and depleted in patients with a pouch, whereas those involved in inulin hydrolysis were enriched in patients with a pouch. E. coli strains from patients with UC were twice as likely to encode the genotoxic molecule colibactin than strains from patients with CD or a pouch. Strikingly, patients with a pouch showed the highest inferred E. coli growth rates, even in the presence of antibiotics. Faecal calprotectin did not correlate with the relative abundance of E. coli. Finally, we identified multiple IBD-specific non-synonymous mutations in E. coli genes encoding for bacterial cell envelope components.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Comparative genomics indicates that E. coli is a commensal species adapted to the overactive mucosal immune milieu in IBD, rather than causing it. Our results reveal mutations that may lead to attenuated antigenicity in some E. coli strains.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/ecco-jcc\/jjac071","type":"journal-article","created":{"date-parts":[[2022,5,13]],"date-time":"2022-05-13T12:46:04Z","timestamp":1652445964000},"page":"1584-1597","source":"Crossref","is-referenced-by-count":20,"title":["<i>Escherichia coli<\/i>\n                    Strains from Patients with Inflammatory Bowel Diseases have Disease-specific Genomic Adaptations"],"prefix":"10.1093","volume":"16","author":[{"given":"Vadim","family":"Dubinsky","sequence":"first","affiliation":[{"name":"Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University , Tel Aviv , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leah","family":"Reshef","sequence":"additional","affiliation":[{"name":"Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University , Tel Aviv , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keren","family":"Rabinowitz","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Rabin Medical Center , Petah-Tikva , Israel"},{"name":"Felsenstein Medical Research Center, Rabin Medical Center , Petah Tikva , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nir","family":"Wasserberg","sequence":"additional","affiliation":[{"name":"Sackler Faculty of Medicine, Tel-Aviv University , Tel Aviv , Israel"},{"name":"Colorectal Unit, Division of Surgery, Rabin Medical Center , Petah-Tikva , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iris","family":"Dotan","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Rabin Medical Center , Petah-Tikva , Israel"},{"name":"Sackler Faculty of Medicine, Tel-Aviv University , Tel Aviv , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5129-5652","authenticated-orcid":false,"given":"Uri","family":"Gophna","sequence":"additional","affiliation":[{"name":"Shmunis School of Biomedicine and Cancer Research, George S. 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