The MetaGeneBank database is a unique bioinformatics resource for whole-genome sequencing metagenomes in human gut, which provides not only raw sequencing files, but also readily usable multiple-level processed data such as abundance tables for genes, microbiota and molecular functions in KEGG orthology (KO) database based on a unified bioinformatic processing pipeline. The current version of the database (release date 2020-01-02) contains links of raw whole-genome metagenomic sequencing reads in gzip format, details on samples and data-generation process, and multi-level processed data for a total of 4470 sequencing files (more than 12 TB) covering more than 10 types of diseases for human fecal specimens collected from 17 assays of 16 studies conducted in over 14 different countries. The sequences of the 14,823,828 non-redundant genes, corresponding phylogenetic and functional annotation results are also provided.