TY - JOUR TI - Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 AU - Beghini, Francesco AU - McIver, Lauren J AU - Blanco-Míguez, Aitor AU - Dubois, Leonard AU - Asnicar, Francesco AU - Maharjan, Sagun AU - Mailyan, Ana AU - Manghi, Paolo AU - Scholz, Matthias AU - Thomas, Andrew Maltez AU - Valles-Colomer, Mireia AU - Weingart, George AU - Zhang, Yancong AU - Zolfo, Moreno AU - Huttenhower, Curtis AU - Franzosa, Eric A AU - Segata, Nicola A2 - Turnbaugh, Peter A2 - Franco, Eduardo A2 - Brown, C Titus VL - 10 PY - 2021 DA - 2021/05/04 SP - e65088 C1 - eLife 2021;10:e65088 DO - 10.7554/eLife.65088 UR - https://doi.org/10.7554/eLife.65088 AB - Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies. KW - microbiome KW - metagenomics KW - microbial genomics KW - computational analysis JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -