Microbial strain-level population structure and genetic diversity from metagenomes.

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 reconstruction within species-specific marker genes. It identified primarily sub

SUBMITTER: Truong DT 

PROVIDER: S-EPMC5378180 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature