Cited by 9,116Genomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyGut microbiota and health

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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

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Langille, Morgan G I, Zaneveld, Jesse, Caporaso, J Gregory, McDonald, Daniel, Knights, Dan, Reyes, Joshua A, Clemente, Jose C, Burkepile, Deron E, Vega Thurber, Rebecca L, Knight, Rob, Beiko, Robert G, Huttenhower, Curtis·2013·Nature Biotechnology

DOI 10.1038/nbt.2676PMC PMC3819121

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Abstract

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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Authors: Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., Beiko, R. G., & Huttenhower, C.
Affiliations: Dalhousie University (CA)
Oregon State University (US)
Argonne National Laboratory (US)
University of Colorado Boulder (US)
University of Minnesota (US)
Harvard University (US)
Florida International University (US)
Howard Hughes Medical Institute (US)
Broad Institute (US)
Corresponding author: Huttenhower, Curtis
ORCID: Langille, Morgan G I
Zaneveld, Jesse
Caporaso, J Gregory
McDonald, Daniel
Knights, Dan
Burkepile, Deron E
Knight, Rob
Beiko, Robert G
Huttenhower, Curtis
Venue: Nature Biotechnology
Publisher: Springer Science and Business Media LLC
Published: 2013-08-25
Volume: 31
Issue: 9
Pages: 814-821
ISSN: 0733-222X (ISSN-L)
1087-0156
1546-1696
DOI: 10.1038/nbt.2676
PMC: PMC3819121
OpenAlex: W2110300022
Cited by: 9,116
References: 49
Citations by year: 2026: 420 · 2025: 552 · 2024: 736 · 2023: 743 · 2022: 1094 · 2021: 1216 · 2020: 1171 · 2019: 1037 · 2018: 882 · 2017: 528 · 2016: 392 · 2015: 216 · 2014: 112 · 2013: 6
FWCI: 108.48
Type: journal article
Language: en
Open access: green
europepmc.org
Licence: www.springer.com/tdm (tdm)
Locations: Nature Biotechnology (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion)
Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
Florida International University Digital Commons (Florida International University) (submittedVersion)
Funders: Howard Hughes Medical Institute
Crohn's and Colitis Foundation
National Institutes of Health
Canadian Institutes of Health Research
National Human Genome Research Institute (U01HG004866, R01HG005969, R01HG004872)
National Institute of General Medical Sciences (T32GM008759, T32GM080177, T32GM142607)
National Institute of Diabetes and Digestive and Kidney Diseases (P01DK078669)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords: PICRUSt, 16S rRNA, ancestral state reconstruction, Human Microbiome Project, reference genome, host-associated microbiota, environmental microbiota
MeSH terms: Bacteria, Genes, Bacterial, Genetic Markers, Humans, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Metagenomics, High-Throughput Nucleotide Sequencing, Microbiota

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