Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

eLife

Aitor Blanco-Míguez¹  Leonard Dubois¹  Francesco Asnicar¹  Mireia Valles-Colomer¹  Moreno Zolfo¹  Paolo Manghi¹  Francesco Beghini¹  Andrew Maltez Thomas¹  Nicola Segata²  Matthias Scholz³  Lauren J McIver⁴  Yancong Zhang⁵  George Weingart⁵  Sagun Maharjan⁵  Curtis Huttenhower⁵  Eric A Franzosa⁵  Ana Mailyan⁵ 

[1] Department CIBIO, University of Trento, Trento, Italy;Department CIBIO, University of Trento, Trento, Italy;IEO, European Institute of Oncology IRCCS, Milan, Italy;Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, San Michele all’Adige, Italy;Harvard T.H. Chan School of Public Health, Boston, United States;Harvard T.H. Chan School of Public Health, Boston, United States;The Broad Institute of MIT and Harvard, Cambridge, United States;

关键词: microbiome;    metagenomics;    microbial genomics;    computational analysis;    Human;    Other;   

DOI  :  10.7554/eLife.65088

来源: eLife Sciences Publications, Ltd

【 摘 要 】

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.

【 授权许可】

CC BY