{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T04:36:10Z","timestamp":1792816570128,"version":"4.5.0"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,2,14]],"date-time":"2025-02-14T00:00:00Z","timestamp":1739491200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["R01DK099076"],"award-info":[{"award-number":["R01DK099076"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["T32AI162624"],"award-info":[{"award-number":["T32AI162624"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Crohn\u2019s disease (CD) is characterized by an inflammatory response to gut microbiota. Macrophages and dendritic cells play an active role in CD inflammation. Specific microbiota have been implicated in the pathogenesis of ileal CD. We investigated the phagocyte-associated microbiome using an unbiased sequencing approach to identify potential pathobionts and elucidate the host response to these microbes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We collected ileal and colonic mucosal biopsies from CD patients and controls without inflammatory bowel disease (IBD), isolated lamina propria phagocytes (CD11b+ cells), and performed deep RNA sequencing (n\u2005=\u200537). Reads were mapped to the human genome for host gene expression analysis and a prokaryotic database for microbiome taxonomic and metatranscriptomic profiling. Results were confirmed in a second IBD cohort (n\u2005=\u200517). Lysed lamina propria cells were plated for bacterial culturing; isolated colonies underwent whole genome sequencing (n\u2005=\u200511).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Crohn\u2019s disease ileal phagocytes contained higher relative abundances of Escherichia coli, Ruminococcus gnavus, and Enterocloster spp. than those from controls. CD phagocyte-associated microbes had increased expression of lipopolysaccharide (LPS) biosynthesis pathways. Phagocytes with a higher pathobiont burden showed increased expression of pro-inflammatory and antimicrobial genes, including PI3 (antimicrobial peptide) and BPIFB1 (LPS-binding molecule). E. coli isolated from the CD lamina propria had more flagellar motility and antibiotic resistance genes than control-derived strains.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Lamina propria resident phagocytes harbor bacterial strains that may act as pathobionts in CD. Our findings shed light on the role of pathobionts and the immune response in CD pathogenesis and suggest new targets for therapies.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/ibd\/izae316","type":"journal-article","created":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T20:22:14Z","timestamp":1738009334000},"page":"1203-1219","source":"Crossref","is-referenced-by-count":5,"title":["Deep Sequencing of Crohn\u2019s Disease Lamina Propria Phagocytes Identifies Pathobionts and Correlates With Pro-Inflammatory Gene Expression"],"prefix":"10.1093","volume":"31","author":[{"given":"Gillian E","family":"Jacobsen","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, University of Miami Miller School of Medicine , Miami, FL ,","place":["USA"]},{"name":"Medical Scientist Training Program, University of Miami Miller School of Medicine , Miami, FL ,","place":["USA"]},{"name":"Department of Medicine, Crohn\u2019s and Colitis Center, University of 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,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria A","family":"Quintero","sequence":"additional","affiliation":[{"name":"Department of Medicine, Crohn\u2019s and Colitis Center, University of Miami Miller School of Medicine , Miami, FL ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunsu","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Medicine, Crohn\u2019s and Colitis Center, University of Miami Miller School of Medicine , Miami, FL ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oriana M","family":"Damas","sequence":"additional","affiliation":[{"name":"Department of Medicine, Crohn\u2019s and Colitis Center, University of Miami Miller School of Medicine , Miami, FL ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amar R","family":"Deshpande","sequence":"additional","affiliation":[{"name":"Department of 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