DWGSIM (v 0.1.13) has been used to simulate shotgun metagenomics short reads from Illumina sequencing platforms. 52,8 millions of paired-ends reads were extracted from 32 genomes retrieved from NCBI database to simulate gut microbial communities. Per-base error rate per reads is set at 0.0001 on first and second read. Mutation rate is also set at 0.001 and fraction of these mutations that were indels is 0.1. Probability that an indel is extend is zero. Genome coverage ranges from 1X to 200X. Two mocks of 52,8 millions of paired-ends reads are available and the only difference between the two mocks are the genome covers. Description of these genomes (taxonomies, genomes length, number of reads and cover) are fully described in metadata files.