{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T21:30:32Z","timestamp":1778275832228,"version":"3.51.4"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,11]],"date-time":"2023-05-11T00:00:00Z","timestamp":1683763200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008762","name":"Genome Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008762","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Genome Quebec"},{"DOI":"10.13039\/501100001804","name":"Canada Research Chairs","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001804","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Microbiome studies have become routine in biomedical, agricultural\u00a0and environmental sciences with diverse aims, including diversity profiling, functional characterization, and translational applications. The resulting complex, often multi-omics datasets demand powerful, yet user-friendly bioinformatics tools to reveal key patterns, important\u00a0biomarkers, and potential\u00a0activities. Here we introduce MicrobiomeAnalyst 2.0 to support comprehensive statistics, visualization, functional interpretation, and integrative analysis of data outputs commonly generated from microbiome studies. Compared to the previous version, MicrobiomeAnalyst 2.0 features three new modules: (i) a Raw Data Processing module for amplicon data processing and taxonomy annotation that connects directly with the Marker Data Profiling module for downstream statistical analysis; (ii) a Microbiome Metabolomics Profiling module to help dissect associations between community compositions and metabolic activities through joint analysis of paired microbiome and metabolomics datasets; and (iii) a Statistical Meta-Analysis module to help identify consistent signatures by integrating datasets across multiple studies. Other important improvements include added support for multi-factor differential analysis and\u00a0interactive visualizations for popular graphical outputs,\u00a0updated methods for functional prediction and correlation analysis, and expanded taxon set libraries based on the latest literature. These new features are demonstrated using a multi-omics dataset from a recent type 1 diabetes study. MicrobiomeAnalyst 2.0 is freely available at microbiomeanalyst.ca.<\/jats:p>","DOI":"10.1093\/nar\/gkad407","type":"journal-article","created":{"date-parts":[[2023,5,11]],"date-time":"2023-05-11T15:50:46Z","timestamp":1683820246000},"page":"W310-W318","source":"Crossref","is-referenced-by-count":507,"title":["MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data"],"prefix":"10.1093","volume":"51","author":[{"given":"Yao","family":"Lu","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, McGill University , Quebec , Canada"}]},{"given":"Guangyan","family":"Zhou","sequence":"additional","affiliation":[{"name":"Institute of Parasitology, McGill University , Quebec , Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7555-736X","authenticated-orcid":false,"given":"Jessica","family":"Ewald","sequence":"additional","affiliation":[{"name":"Institute of Parasitology, McGill University , Quebec , Canada"}]},{"given":"Zhiqiang","family":"Pang","sequence":"additional","affiliation":[{"name":"Institute of Parasitology, McGill University , Quebec , Canada"}]},{"given":"Tanisha","family":"Shiri","sequence":"additional","affiliation":[{"name":"Institute of Parasitology, McGill University , Quebec , Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2040-2624","authenticated-orcid":false,"given":"Jianguo","family":"Xia","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, McGill University , Quebec , Canada"},{"name":"Institute of Parasitology, McGill University , Quebec , Canada"},{"name":"Department of Animal Science, McGill University , Quebec , Canada"}]}],"member":"286","published-online":{"date-parts":[[2023,5,11]]},"reference":[{"key":"2023070505023889600_B1","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","article-title":"Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases","volume":"569","author":"Lloyd-Price","year":"2019","journal-title":"Nature"},{"key":"2023070505023889600_B2","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1038\/s41586-019-1236-x","article-title":"Longitudinal multi-omics of host-microbe dynamics in prediabetes","volume":"569","author":"Zhou","year":"2019","journal-title":"Nature"},{"key":"2023070505023889600_B3","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1038\/nrg3182","article-title":"The human microbiome: at the interface of health and disease","volume":"13","author":"Cho","year":"2012","journal-title":"Nat. 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