Updated Metagenomic Species Pan-genomes (MSPs) of the human gastrointestinal microbiota

Gene catalog constructionThe methodology for creating the IGC2 catalog is described in the original papers: Li et al., 2014 and Wen et al., 2017
MSP creationReads from publicly available human gut metagenomes were aligned against the IGC2 catalog with the Meteor to produce a raw gene abundance table (10.4M genes quantified in >2000 samples). Then, co-abundant genes were binned in 1,989 Metagenomic Species Pan-genomes (MSPs, i.e. clusters of co-abundant genes that likely belong to the same microbial species) using MSPminer.
MSPs taxonomic annotationMSPs taxonomic annotation was performed by aligning MSP core and accessory genes against representative genomes of the Genome Taxonomy Database (GTDB r207) using blastn (task = megablast, word_size = 16). The 20 best hits for each gene were kept (--max-target-seq 20). Using an in-house pipeline, a species-level assignment was given if > 50% of the genes matched the representative genome of a given species, with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MSPs were assigned to a higher taxonomic level (genus to superkingdom), if more than 50% of their genes had the same annotation.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the MSPs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni). (2021-04-01)