Species-level functional profiling of metagenomes and metatranscriptomes

Eric A. Franzosa, Lauren J. McIver, Gholamali Rahnavard, Luke R. Thompson, Melanie Schirmer, George Weingart, Karen Schwarzberg Lipson, Rob Knight, James G Caporaso, Nicola Segata, Curtis Huttenhower

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)962-968
Number of pages7
JournalNature Methods
Volume15
Issue number11
DOIs
StatePublished - Nov 1 2018

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Metagenome
Genes
Metagenomics
Microbiota
Metabolism

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Franzosa, E. A., McIver, L. J., Rahnavard, G., Thompson, L. R., Schirmer, M., Weingart, G., ... Huttenhower, C. (2018). Species-level functional profiling of metagenomes and metatranscriptomes. Nature Methods, 15(11), 962-968. https://doi.org/10.1038/s41592-018-0176-y

Species-level functional profiling of metagenomes and metatranscriptomes. / Franzosa, Eric A.; McIver, Lauren J.; Rahnavard, Gholamali; Thompson, Luke R.; Schirmer, Melanie; Weingart, George; Lipson, Karen Schwarzberg; Knight, Rob; Caporaso, James G; Segata, Nicola; Huttenhower, Curtis.

In: Nature Methods, Vol. 15, No. 11, 01.11.2018, p. 962-968.

Research output: Contribution to journalArticle

Franzosa, EA, McIver, LJ, Rahnavard, G, Thompson, LR, Schirmer, M, Weingart, G, Lipson, KS, Knight, R, Caporaso, JG, Segata, N & Huttenhower, C 2018, 'Species-level functional profiling of metagenomes and metatranscriptomes', Nature Methods, vol. 15, no. 11, pp. 962-968. https://doi.org/10.1038/s41592-018-0176-y
Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G et al. Species-level functional profiling of metagenomes and metatranscriptomes. Nature Methods. 2018 Nov 1;15(11):962-968. https://doi.org/10.1038/s41592-018-0176-y
Franzosa, Eric A. ; McIver, Lauren J. ; Rahnavard, Gholamali ; Thompson, Luke R. ; Schirmer, Melanie ; Weingart, George ; Lipson, Karen Schwarzberg ; Knight, Rob ; Caporaso, James G ; Segata, Nicola ; Huttenhower, Curtis. / Species-level functional profiling of metagenomes and metatranscriptomes. In: Nature Methods. 2018 ; Vol. 15, No. 11. pp. 962-968.
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