Dataset Information

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

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.

SUBMITTER: Beghini F

PROVIDER: S-EPMC8096432 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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

Beghini Francesco F McIver Lauren J LJ Blanco-Míguez Aitor A Dubois Leonard L Asnicar Francesco F Maharjan Sagun S Mailyan Ana A Manghi Paolo P Scholz Matthias M Thomas Andrew Maltez AM Valles-Colomer Mireia M Weingart George G Zhang Yancong Y Zolfo Moreno M Huttenhower Curtis C Franzosa Eric A EA Segata Nicola N

eLife 20210504

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 metagen ...[more]

PMID: 33944776

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Dataset Information

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

Publications

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

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