Supporting data for the paper: "An integrated catalog of reference genes in the human gut microbiome".

Here we sequenced 249 fecal samples from European adults, leading to a total of 760 samples in the Metagenome of the Human Intestinal Tract (MetaHIT) project. All 6.4TB whole-genome shotgun sequencing data from 1267 fecal samples in MetaHIT, the Human Microbiome Project (HMP) and our diabetes study on Chinese adults were processed with the MOCAT pipeline. The resulting gene catalogs were merged using CD-HIT and complemented with genes from 511 sequenced human gut-related prokaryotic genomes that were present in our gut metagenomes. The final high-quality integrated reference catalog of the human gut microbiome contains 9,879,896 non-redundant genes. The genes were phylogenetically annotated according to 3449 bacterial and archaeal genomes and draft genomes from NCBI, and functionally annotated using orthologous groups from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) databases. In addition, 11 samples from the Chinese cohort were re-extracted using the MetaHIT DNA extraction protocol and shotgun-sequenced to compare with the original data generated by a slightly different DNA extraction protocol.