{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T17:44:24Z","timestamp":1792604664592,"version":"4.5.0"},"reference-count":45,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T00:00:00Z","timestamp":1760227200000},"content-version":"vor","delay-in-days":11,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["R01DK104662"],"award-info":[{"award-number":["R01DK104662"]}],"id":[{"id":"10.13039\/100000062","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":["R01DK123342"],"award-info":[{"award-number":["R01DK123342"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Comprehensive Physiology"],"published-print":{"date-parts":[[2025,10]]},"abstract":"ABSTRACT<\/jats:title>\n \n Background<\/jats:title>\n The gut microbiome plays an important role in human health and disease. Kidney Precision Medicine Project (KPMP) is a well\u2010phenotyped, kidney biopsy\u2010proven cohort of AKI and CKD patients. Comprehensive profiling of gut microbiota can uncover novel mechanistic, diagnostic, and therapeutic strategies for CKD and AKI patients.<\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n We performed metagenomic whole genome sequencing (mWGS; >\u200925 million reads) on KPMP stool samples. mWGS data of healthy controls from 4 published studies was used. Kraken2 and MetaPhlAn3 were used for taxonomic assignment, and HUMAnN3 for functional annotation.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n Kraken2 analysis showed significantly higher abundance of\n Ruminococcus bicirculans<\/jats:italic>\n in CKD (6.47) compared to AKI (1.82) and healthy individuals (2.42;\n p<\/jats:italic>\n \u2009=\u20090.01). Furthermore, the abundance of\n \n Gordonibacter pamelaeae<\/jats:italic>\n <\/jats:styled-content>\n increased in CKD (0.30) compared to AKI (0.07;\n p<\/jats:italic>\n \u2009=\u20090.05) and healthy individuals (0.03). The percent mean abundance of genus\n Chryseobacterium<\/jats:italic>\n was slightly higher in CKD (0.07) compared to AKI (0.05;\n p<\/jats:italic>\n \u2009=\u20090.05) but reduced compared to healthy individuals (0.20;\n p<\/jats:italic>\n \u2009<\u20090.001). MetaPhlAn3 identified alterations in\n Gordonibacter, Bacteroides<\/jats:italic>\n , and\n Faecalibacterium<\/jats:italic>\n with a significant increase in\n \n Clostridium asparagiforme<\/jats:italic>\n <\/jats:styled-content>\n in AKI (11.68) compared to CKD (0.03;\n p<\/jats:italic>\n \u2009=\u20090.06) and healthy (0.01;\n p<\/jats:italic>\n \u2009=\u20090.001) individuals.\n \n Roseburia hominis<\/jats:styled-content>\n ,\n Roseburia intestinalis<\/jats:styled-content>\n ,\n Dorea longicatena<\/jats:styled-content>\n <\/jats:italic>\n , and\n \n Gemmiger formicilis<\/jats:italic>\n <\/jats:styled-content>\n were significantly reduced in AKI compared to CKD and healthy individuals. LDA\/HUMAnN3 analysis showed a significant correlation between several metabolites and bacterial species in this KPMP population.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n Kidney biopsy\u2010proven CKD and AKI patients show a distinct gut microbiota profile compared to healthy individuals. This high\u2010quality dataset is a valuable resource for developing microbiome\u2010based diagnostics and therapies for CKD and AKI.<\/jats:p>\n <\/jats:sec>","DOI":"10.1002\/cph4.70058","type":"journal-article","created":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T03:49:46Z","timestamp":1760327386000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Metagenomic Profiling of Gut Microbiota in Kidney Precision Medicine Project Participants With\n CKD<\/scp>\n and\n AKI<\/scp>"],"prefix":"10.1002","volume":"15","author":[{"given":"Sanjeev","family":"Noel","sequence":"first","affiliation":[{"name":"Division of Nephrology, Department of Medicine Johns Hopkins University Baltimore Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shishir Kumar","family":"Patel","sequence":"additional","affiliation":[{"name":"Division of Nephrology, Department of Medicine Johns Hopkins University Baltimore Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"White","sequence":"additional","affiliation":[{"name":"Resphera Biosciences, LLC Baltimore Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deepak","family":"Verma","sequence":"additional","affiliation":[{"name":"Department of Oncology Johns Hopkins University Baltimore Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven","family":"Menez","sequence":"additional","affiliation":[{"name":"Division of Nephrology, Department of Medicine Johns Hopkins University Baltimore Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominic","family":"Raj","sequence":"additional","affiliation":[{"name":"Division of Renal Disease and Hypertension George Washington University School of Medicine and Health Sciences Washington DC 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