Journal
ELIFE
Volume 10, Issue -, Pages -Publisher
eLIFE SCIENCES PUBL LTD
DOI: 10.7554/eLife.65088
Keywords
-
Categories
Funding
- European Research Council (ERC-STG project) [MetaPG-716575]
- MIUR 'Futuro in Ricerca' [RBFR13EWWI_001]
- European H2020 program [ONCOBIOME-825410, MASTER-818368]
- National Cancer Institute of the National Institutes of Health [1U01CA230551]
- Premio Internazionale Lombardia e Ricerca 2019
- Harvard Chan Microbiome Analysis Core
- National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health [R24DK110499, U54DE023798]
- Cancer Research UK Grand Challenge award [C10674/A27140]
- Juvenile Diabetes Research Foundation [3-SRA-2016-141-Q-R]
- National Human Genome Research Institute of the National Institutes of Health [R01HG005220]
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Culture-independent analyses of microbial communities have advanced significantly in the past decade, particularly due to the emergence of Shotgun Metagenomics. bioBakery 3, a newly developed toolset, enhances the accuracy and scope of taxonomic, functional, and phylogenetic profiling in microbial community studies by providing an expanding set of reference sequences.
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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