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Nat Methods DOI:10.1038/s41592-018-0176-y

Species-level functional profiling of metagenomes and metatranscriptomes.

Publication TypeJournal Article
Year of Publication2018
AuthorsFranzosa, EA, McIver, LJ, Rahnavard, G, Thompson, LR, Schirmer, M, Weingart, G, Lipson, KSchwarzber, Knight, R, J Caporaso, G, Segata, N, Huttenhower, C
JournalNat Methods
Date Published2018 Nov

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that 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 faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types.


Alternate JournalNat. Methods
PubMed ID30377376
PubMed Central IDPMC6235447
Grant ListP30 DK043351 / DK / NIDDK NIH HHS / United States
U54 DE023798 / DE / NIDCR NIH HHS / United States