TY - JOUR
T1 - Species-level functional profiling of metagenomes and metatranscriptomes
AU - Franzosa, Eric A.
AU - McIver, Lauren J.
AU - Rahnavard, Gholamali
AU - Thompson, Luke R.
AU - Schirmer, Melanie
AU - Weingart, George
AU - Lipson, Karen Schwarzberg
AU - Knight, Rob
AU - Caporaso, J. Gregory
AU - Segata, Nicola
AU - Huttenhower, Curtis
N1 - Funding Information:
The authors thank M. Wong, T. Sharpton, and the members of the HUMAnN user group for their feedback on the development and evaluation of HUMAnN2. Funding for this work was provided by NSF 1565100 (to J.G.C.); People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement PCIG13-GA-2013-618833 and by MIUR “Futuro in Ricerca” RBFR13EWWI_001 (to N.S.); NIH NIDDK U54DE023798, NSF MCB-1453942, NIH NIDDK P30DK043351; and NSF DBI-1053486 (to C.H.).
Publisher Copyright:
© 2018, The Author(s), under exclusive licence to Springer Nature America, Inc.
PY - 2018/11/1
Y1 - 2018/11/1
N2 - 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.
AB - 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.
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U2 - 10.1038/s41592-018-0176-y
DO - 10.1038/s41592-018-0176-y
M3 - Article
C2 - 30377376
AN - SCOPUS:85055773262
SN - 1548-7091
VL - 15
SP - 962
EP - 968
JO - Nature Methods
JF - Nature Methods
IS - 11
ER -