Metagenome-Assembled Genomes of Bacteroides uniformis and Parabacteroides vulgatus
Bacteroides uniformis and Phocaeicola vulgatus (formely Bacteroides vulgatus) rank among the most prevalent and abundant members of the human gut microbiome, and are considered relevant emerging model organisms. Yet in spite of their purported relevance as core gut commensals, only comparatively few B. uniformis and P. vulgatus reference genomes are currently available. Here, we generated 13,877 novel B. uniformis and 8,274 P. vulgatus metagenome-assembled genomes (MAGs) of medium (=50% complete, =10% contaminated) or high (=90% complete, =5% contaminated) quality according to MIMAG criteria. Genomes were derived from a total of 23,527 publicly available metagenomes using a bespoke workflow of metagenomic assembly (using MEGAHIT), contig binning (using metaBAT2) and quality control (using CheckM2 and GUNC), followed by taxonomic classification (using GTDB-Tk v2) to identify MAGs of the two target lineages. The resulting MAG set is a subset of the genomic arm of the Searchable, Planetary-scale, Integrated, microbiome REsource (SPIRE).