Background The female reproductive hormone, progesterone, is crucial in regulating the menstrual cycle and maintaining pregnancy. Despite known correlations between gut microbiota, sex hormones, and host phenotypes, the metabolic fates of progesterone in the human gut remain unclear. Results Here, an integrated multi-omics approach was employed to investigate gut microbiota-mediated progesterone metabolism. Fresh fecal samples were collected from infertile women with progesterone treatment (n = 14). Progesterone (1 mM) was amended into fecal cultures to enrich progesterone-metabolizing gut microbes, and the key players were identified through culturomics-based metagenomics analysis. Microbial functions were predicted by tracking temporal changes in metabolite profiles and microbial abundances. The prevalence of progesterone metabolism genes among gut microbiota was explored through functional genomics analysis. Pregnanolone was identified as the primary microbial metabolite of gut progesterone. Members of Enterobacteriaceae and Veillonellaceae were identified as crucial pregnanolone producers; progesterone metabolism genes were abundant in these bacterial families. Moreover, these bacterial families showed significant abundance differences among healthy women (n = 19) and women with miscarriages (n = 41). Conclusions This study provides potent therapeutic targets for improving progesterone bioavailability and demonstrates stereoselective production of neurosteroids using characterized bacterial strains and their corresponding metabolic pathways.

Multi-Omics Mapping of Gut Microbiota's Role in Progesterone Metabolism