{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T03:37:17Z","timestamp":1776310637384,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T00:00:00Z","timestamp":1646611200000},"content-version":"vor","delay-in-days":53,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["19H01021"],"award-info":[{"award-number":["19H01021"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["20K21834"],"award-info":[{"award-number":["20K21834"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP21km0405211"],"award-info":[{"award-number":["JP21km0405211"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP21ek0109413"],"award-info":[{"award-number":["JP21ek0109413"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP21gm4010006"],"award-info":[{"award-number":["JP21gm4010006"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP21km0405217"],"award-info":[{"award-number":["JP21km0405217"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP21ek0410075"],"award-info":[{"award-number":["JP21ek0410075"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"name":"JST Moonshot R&D","award":["JPMJMS2021"],"award-info":[{"award-number":["JPMJMS2021"]}]},{"name":"JST Moonshot R&D","award":["JPMJMS2024"],"award-info":[{"award-number":["JPMJMS2024"]}]},{"DOI":"10.13039\/100007449","name":"Takeda Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007449","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Bioinformatics Initiative of Osaka University Graduate School of Medicine"},{"DOI":"10.13039\/501100004206","name":"Osaka University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004206","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Microbiome is an essential omics layer to elucidate disease pathophysiology. However, we face a challenge of low reproducibility in microbiome studies, partly due to a lack of standard analytical pipelines. Here, we developed OMARU (Omnibus metagenome-wide association study with robustness), a new end-to-end analysis workflow that covers a wide range of microbiome analysis from phylogenetic and functional profiling to case\u2013control metagenome-wide association studies (MWAS). OMARU rigorously controls the statistical significance of the analysis results, including correction of hidden confounding factors and application of multiple testing comparisons. Furthermore, OMARU can evaluate pathway-level links between the metagenome and the germline genome-wide association study (i.e. MWAS-GWAS pathway interaction), as well as links between taxa and genes in the metagenome. OMARU is publicly available (https:\/\/github.com\/toshi-kishikawa\/OMARU), with a flexible workflow that can be customized by users. We applied OMARU to publicly available type 2 diabetes (T2D) and schizophrenia (SCZ) metagenomic data (n\u00a0=\u00a0171 and 344, respectively), identifying disease biomarkers through comprehensive, multilateral, and unbiased case\u2013control comparisons of metagenome (e.g. increased Streptococcus vestibularis in SCZ and disrupted diversity in T2D). OMARU improves accessibility and reproducibility in the microbiome research community. Robust and multifaceted results of OMARU reflect the dynamics of the microbiome authentically relevant to disease pathophysiology.<\/jats:p>","DOI":"10.1093\/nargab\/lqac019","type":"journal-article","created":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T11:44:25Z","timestamp":1646653465000},"source":"Crossref","is-referenced-by-count":4,"title":["OMARU: a robust and multifaceted pipeline for metagenome-wide association study"],"prefix":"10.1093","volume":"4","author":[{"given":"Toshihiro","family":"Kishikawa","sequence":"first","affiliation":[{"name":"Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan"},{"name":"Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan"},{"name":"Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya 464-8681, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yoshihiko","family":"Tomofuji","sequence":"additional","affiliation":[{"name":"Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan"},{"name":"Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hidenori","family":"Inohara","sequence":"additional","affiliation":[{"name":"Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0311-8472","authenticated-orcid":false,"given":"Yukinori","family":"Okada","sequence":"additional","affiliation":[{"name":"Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan"},{"name":"Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan"},{"name":"Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan"},{"name":"Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan"},{"name":"Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,3,7]]},"reference":[{"key":"2022030711375268000_B1","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/s41591-020-01183-8","article-title":"Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals","volume":"27","author":"Asnicar","year":"2021","journal-title":"Nat. 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Microbiol."},{"key":"2022030711375268000_B7","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1136\/annrheumdis-2021-220687","article-title":"Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in japanese","volume":"80","author":"Tomofuji","year":"2021","journal-title":"Ann. Rheum. Dis."},{"key":"2022030711375268000_B8","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/s41587-020-0603-3","article-title":"A unified catalog of 204,938 reference genomes from the human gut microbiome","volume":"39","author":"Almeida","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"2022030711375268000_B9","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/s41587-018-0008-8","article-title":"1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses","volume":"37","author":"Zou","year":"2019","journal-title":"Nat. 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