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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Open accessAbstract
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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“the prediction of bacterial gene functions based on 16S rRNA gene sequences using PICRUSt 27 revealed some functional diversity among the 3 groups in accordance with the difference in gut microbiota composition (Figure IIIH in the online-only Data Supplement).”
From Bacteroides vulgatus and Bacteroides dorei Reduce Gut Microbial Lipopolysaccharide Production and Inhibit Atherosclerosis (2018) · cites this paper as [27]
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PICRUSt2 for prediction of metagenome functions
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Metadata
- 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
- Venue
- Nature Biotechnology
- Published
- 2013-08-25
- Volume
- 31
- Issue
- 9
- Pages
- 814-821
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- 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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