Species-level functional profiling of metagenomes and metatranscriptomes

Functional profiling from metagenomic or metatranscriptomic (“meta’omic”) sequencing provides insight into the molecular activities of microbial communities. These analyses are typically carried out using comprehensive search of sequencing reads, which is time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed a tiered meta’omic search strategy (HUMAnN2) which enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community’s known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is 3x faster and produces more accurate gene family profiles (89% vs. 67%). We apply HUMAnN2 to clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species’ genomic vs. transcriptional contributions, and strain profiling. Finally, we introduce “contributional diversity” to explain patterns of ecological assembly across different microbial community types.