MICROBIAL GENES

The human microbiome consists of microbes with pan-ecological evolutionary origins, yet a systematic gene-level analysis of microbial life across ecologies is lacking. We quantified the gene content from 14,183 samples across 17 ecologies - 6 human-associated, 7 non-human-host associated (e.g. mouse gut), and 4 in other environmental niches (e.g. soil). At 30% amino acid identity, we identified 117,629,181 non-redundant genes across all samples, 66% of which were singletons, only being observed in one sample. We quantified the genetic similarity and "uniqueness" between different ecologies, showing that sites like the human vaginal and skin ecologies had low genetic alpha-diversity yet high beta-diversity, indicating few species but high pangenomic variation. We further identified a set of 1,864 sequences conserved across all ecologies, which indicates an overwhelming gene-level conservation to microbial life despite extreme taxonomic variation. However, using 90% amino acid clustering..