Mouse gut metagenomes at the early stage after weaning

We provide metagenomic sequencing data of 16 male C57BL/6 mouse gut microbiomes. To explore the potential maternal and cage mate effects at the early stage after weaning, we chose littermates of two different mother mice and housed them in different cages. Four of the mice (My*, V*, E*, S*) were littermates of one mother mouse, while the rest four (J, Ms, N, U) were littermates of another mother mouse. My* and V* were co-housed in cage 1. U and N were co-housed in cage 3. E*, S* were co-housed together with J, and Ms in cage 2. Samples were collected at the 1st, 2nd, 9th, and 10th day after weaning (weaned at 21 days after birth). Samples of the first two time points and the last two time points were pooled, respectively, and subjected independently to shotgun metagenomic sequencing by the BIGSEQ-500 platform .