Gene catalog and definitions of the MGS
PID
As a reference gene catalog, we used the Clinical Microbiomics Human Gut gene catalog (14,355,839 genes), which was created based on 12,170 nonpublic deep-sequenced human gut specimens (including 481 from infants), 9,428 publicly available metagenomes compiled from 43 countriesTo taxonomically annotate an MGS, we blasted its genes against the NCBI RefSeq genome database (2020-01-27) and used the rank-specific annotation criteria. Specifically, we assigned a taxon to an MGS if at least M % of its genes were mapped to the taxon and no more than D % of its genes were mapped to a different taxon. We only considered blast hits with an alignment length of ≥ 100 bp, a query coverage ≥ 50%, and a % identity ≥ PID. Here we define: PID = (95, 95, 85, 75, 65, 55, 50, 45); 