An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.

ABSTRACT: We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content and single-nucleotide polymorphisms (SNPs), from shotgun metagenomes. Our method leverages a database of more than 30,000 bacterial reference genomes that we clustered into species groups. These cover the majority of abundant species in the human microbiome but only a small proportion of microbes in other environments, including soil and seawater. We applied MIDAS to stool metagenomes from 98 Swedish mothers and their infants over one year and used rare SNPs to track strains between hosts. Using this approach, we found that although species compositions of mothers and

SUBMITTER: Nayfach S 

PROVIDER: S-EPMC5088602 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature