TOOLS AND RESOURCES Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 Francesco Beghini1†, Lauren J McIver2†, Aitor Blanco-Mı´guez1, Leonard Dubois1, Francesco Asnicar1, Sagun Maharjan2,3, Ana Mailyan2,3, Paolo Manghi1, Matthias Scholz4, Andrew Maltez Thomas1, Mireia Valles-Colomer1, George Weingart2,3, Yancong Zhang2,3, Moreno Zolfo1, Curtis Huttenhower2,3*, Eric A Franzosa2,3*, Nicola Segata1,5* 1Department CIBIO, University of Trento, Trento, Italy; 2Harvard T.H. Chan School of Public Health, Boston, United States; 3The Broad Institute of MIT and Harvard, Cambridge, United States; 4Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, San Michele all’Adige, Italy; 5IEO, European Institute of Oncology IRCCS, Milan, Italy Abstract 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 *For correspondence: phylogenetic profiling of metagenomes newly developed to build on the largest set of reference
[email protected] (CH); sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of
[email protected] (EAF); taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These
[email protected] (NS) methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and †These authors contributed IBD (1635 metagenomes and 817 metatranscriptomes).