Supporting data for the dynamics and stabilization of the Human gut microbiome during the first year of life.

Here we performed metagenomic shotgun sequencing on fecal samples from 98 full-term Swedish infants (new born, 4-months and 12-months old) and their mothers; assembled gut microbial genomes and constructed reference gene catalogs from the cohort. We generated 1.52 Tb paired-end reads of high-quality sequences (average 3.99 Gb per sample). A gene catalog was constructed for each time point based on de novo assembly and metagenomic gene prediction; and functionally annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. We also assembled a total of 4,356 microbial genomes (>0.9 MB) de novo; by binning assembled contigs according to abundance variations across samples. These de novo assembled genomes were complemented by 1,147 genomes from the National Center for Biotechnology Information (NCBI) Bacteria/Archaea genome database. All genomes were subsequently clustered into 690 unique metagenomic operational taxonomic units (MetaOTUs) that were equivalent to species-level classifications. Of these, 373 were annotated to species, the remaining 317 represent novel species related to known species. We constructed the metaOTUs profile by mapping reads to our metaOTUs sequences.