Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
2021/05/04 by Francesco Beghini, Lauren J. McIver, Aitor Blanco‐Míguez +14 · 52 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Genomics and Phylogenetic Studies #Gut microbiota and health #Microbial Community Ecology and Physiology
paper · doi:10.7554/elife.65088
openalex publication_date 2021/05/04 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/29
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 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.
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