Presented by: Eric Franzosa
Culture-independent analyses of microbial communities have improved dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate given greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these resources, we present bioBakery 3: a set of integrated and improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes and metatranscriptomes developed using 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 associations in applications to CRC (1,262 metagenomes) and IBD (1,635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4,077 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. Phylogenetic analysis with PhyloPhlAn 3 supports both genomic and metagenomic data, by assigning genomes from isolate sequencing or metagenomic assemblies to species-level genome bins defined on >230,000 publically available sequences. It accurately reconstructs phylogenies at different resolutions (from strain-level to microbial tree-of-life) using maximally informative markers and, optionally, metagenomic assemblies and novel organisms. The bioBakery 3 implementation includes open-source software, documentation, training data, and cloud-deployable reproducible workflows to help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial communities.
Eric Franzosa – Poster Description (Audio Clip)
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