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

Abstract

Culture-independent analyses of microbial communities have advanced 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 (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. 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.

Patterns of transmission and horizontal gene transfer in the Dioscorea sansibarensis leaf symbiosis revealed by whole-genome sequencing

“…35 Coverage for every genome was calculated using BEDTools v2.27.1 genomecov command. 53 Taxonomic composition of samples was determined using Metaphlan 3, 7 Kraken v1.1.1 54 (using a custom database of bacterial and plastome sequences 8 ), and blastn 36 searches against the NCBI non-redundant nucleotide database (accessed 03/2020), summarized using BASTA and Krona. 55,56…”

An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies

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Comparative analysis of 16S rRNA gene and metagenome sequencing in pediatric gut microbiomes

“…Briefly, KneadData (v 0.7.10) was used to trim and filter raw sequence reads, and to separate human and 16S ribosomal gene reads from bacterial sequences in both fecal and oral samples. Samples that passed quality control were taxonomically profiled to the genus level using MetaPhlAn (v 3.0.7), which uses alignment to a reference database of "marker genes" to identify taxonomic composition (Beghini et al, 2020).…”