期刊
NATURE BIOTECHNOLOGY
卷 31, 期 9, 页码 814-+出版社
NATURE PORTFOLIO
DOI: 10.1038/nbt.2676
关键词
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资金
- Canadian Institutes of Health Research
- Canada Research Chairs program
- US National Science Foundation (NSF) [1130786]
- Howard Hughes Medical Institute
- US National Institutes of Health (NIH) [P01DK078669, U01HG004866, R01HG004872]
- Crohn's and Colitis Foundation of America
- Sloan Foundation
- NSF [CAREER DBI1053486]
- ARO [W911NF-11-1-0473]
- [NIH 1R01HG005969]
- Direct For Biological Sciences
- Div Of Biological Infrastructure [1053486] Funding Source: National Science Foundation
- Directorate For Geosciences
- Division Of Ocean Sciences [1130786] Funding Source: National Science Foundation
Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.
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