Microbial strain-level population structure and genetic diversity from metagenomes
University of Trento · Broad Institute · +1 more institution
Abstract
Among the human health conditions linked to microbial communities, phenotypes are often associated with only a subset of strains within causal microbial groups. Although it has been critical for decades in microbial physiology to characterize individual strains, this has been challenging when using culture-independent high-throughput metagenomics. We introduce StrainPhlAn, a novel metagenomic strain identification approach, and apply it to characterize the genetic structure of thousands of strains from more than 125 species in more than 1500 gut metagenomes drawn from populations spanning North and South American, European, Asian, and African countries. The method relies on per-sample dominant sequence variant…
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- References
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Authors
5Topics & keywords
- Biology
- Faecalibacterium prausnitzii
- Metagenomics
- Genetics
- Genetic diversity
- Population
- Strain (injury)
- Genetic variation
- Life in Land
Funding
- NSNational Science FoundationAwards: 1053486, DBI-1053486
- ECEuropean CommissionAwards: 707345, H2020, 618833
- MDMinistero dell’Istruzione, dell’Università e della RicercaAwards: FIR RBFR13EWWI, RBFR13EWWI, H2020
- LPLEO Pharma Research Foundation
- FCFondazione Cassa Di Risparmio Di Trento E RoveretoAwards: 2013.0239, Rif. Int.2014.0325, Rif. Int.2013.0239
- LPLEO Pharma
- NINational Institutes of HealthAwards: U54DE023798, DBI-1053486, R01HG005969, H2020
- H2Horizon 2020 Framework Programme
- ARArmy Research OfficeAwards: W911NF-11-1-0473, W911NF, W911NF-11
- HMH2020 Marie Skłodowska-Curie ActionsAward: H2020