Gut microbiota impacts bone via Bacteroides vulgatus-valeric acid-related pathways

We performed integrative analyses in a Chinese cohort of peri-/post-menopausal women (n = 517) with metagenomics (n = 499), targeted metabolomics (n = 500) and whole-genome sequencing (n = 500) to identify novel microbiome-related biomarkers for bone health. We also performed metagenomics in a US whites cohort for validation (n = 59).The characteristics of the cohorts, genome-wide association study (GWAS) data, concentrations of serum short chain fatty acids (SCFAs), relative abundance of gut microbiota and gut microbiota-associated functional KEGG modules are shown in this dataset.The sequencing data of the Chinese cohort (whole genome sequencing and metagenomics) can be found in “Genome Sequence Archive for Human” (https://ngdc.cncb.ac.cn/gsa-human, accession No. HRA004900). The metagenomic sequencing data can be found in “Sequence Read Archive” (https://www.ncbi.nlm.nih.gov/sra, accession No. PRJNA986283 and PRJNA1011937).