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ConStrains identifies microbial strains in metagenomic datasets

2015; Nature Portfolio; Volume: 33; Issue: 10 Linguagem: Inglês

10.1038/nbt.3319

1546-1696

Chengwei Luo, Rob Knight, Heli Siljander, Mikael Knip, Ramnik J. Xavier, Dirk Gevers,

Probiotics and Fermented Foods

Different bacterial strains in a metagenome are distinguished using a method that detects SNPs in conserved genes. An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly similar sequences. We present ConStrains, an open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. The algorithm uses single-nucleotide polymorphism (SNP) patterns in a set of universal genes to infer within-species structures that represent strains. Applying ConStrains to simulated and host-derived datasets provides insights into microbial community dynamics.