An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria

摘要: 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 single nucleotide polymorphisms, from shotgun metagenomes. Our method leverages a database of >30,000 reference genomes we clustered into groups. These cover majority abundant in human microbiome but only small proportion microbes other environments, soil seawater. applied MIDAS to stool metagenomes 98 Swedish mothers their infants over one year used rare variants reveal extensive vertical transmission strains at birth colonization with unlikely derive mother later time points. This pattern was missed species-level analysis, because infant gut composition converges towards that adult time. also 198 globally distributed marine show many prevalent have population structure correlates geographic location. Strain-level genetic clearly dynamics are obscured when data analyzed higher taxonomic resolution.