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Anti-tumor necrosis factor-\u03b1 (TNF-\u03b1) agents are important treatments for IBD. We investigated whether microbiome changes at multiple sites can predict the effectiveness of such treatment in IBD. Stool, saliva, serum, and urine biosamples were collected from 19 IBD patients before (V1) and 3\u00a0months after (V2) anti-TNF-\u03b1 treatment, and 19 healthy subjects (control). Microbiota analysis was performed using extracellular vesicles (EVs; all four sample types) and next-generation sequencing (NGS; stool and saliva). The stool, using NGS analysis, was the only sample type in which \u03b1-diversity differed significantly between the IBD and control groups at V1 and V2. Relative to non-responders, responders to anti-TNF-\u03b1 treatment had significantly higher levels of <jats:italic>Firmicutes<\/jats:italic> (phylum), <jats:italic>Clostridia<\/jats:italic> (class), and <jats:italic>Ruminococcaceae<\/jats:italic> (family) in V1 stool, and <jats:italic>Prevotella<\/jats:italic> in V1 saliva. Non-responders had significantly higher V2 serum and urine levels of <jats:italic>Lachnospiraceae<\/jats:italic> than responders. Finally, <jats:italic>Acidovorax caeni<\/jats:italic> was detected in all V1 sample types in responders, but was not detected in non-responders. Microbiome changes at multiple sites may predict the effectiveness of anti-TNF-\u03b1 treatment in IBD, warranting further research.<\/jats:p>","DOI":"10.1038\/s41598-022-10450-2","type":"journal-article","created":{"date-parts":[[2022,4,15]],"date-time":"2022-04-15T21:18:37Z","timestamp":1650057517000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":41,"title":["Microbial changes in stool, saliva, serum, and urine before and after anti-TNF-\u03b1 therapy in patients with inflammatory bowel diseases"],"prefix":"10.1038","volume":"12","author":[{"given":"Yong Eun","family":"Park","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hye Su","family":"Moon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongeun","family":"Yong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hochan","family":"Seo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinho","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tae-Seop","family":"Shin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoon-Keun","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin Ran","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoo Na","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Young-Ho","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joo Sung","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jae Hee","family":"Cheon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,4,15]]},"reference":[{"key":"10450_CR1","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1007\/s00281-014-0454-4","volume":"37","author":"K Matsuoka","year":"2015","unstructured":"Matsuoka, K. & Kanai, T. 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