A guide to host genetic determinants of female microbiome composition across distinct anatomical niches

The female microbiome is a complex, dynamic and site‐specific ecosystem that plays a vital role in maintaining host health, influencing immune regulation, metabolism, reproductive function and dermatological health. While significant attention has been directed towards modifiable lifestyle and environmental influences, host genetics, including inherited genetic variants in immune, cell signalling, metabolic, hormonal pathways and epithelial structure/barrier integrity, are increasingly recognised as contributors to microbial composition across distinct anatomical niches in individuals. It is theorised that these factors influence core microbial communities, predisposing individuals to dysbiosis or enhanced resilience against potential pathogens. This review integrates current evidence on how host genetics shape the female vaginal, gut, oral and skin microbiomes. By evaluating these influences across body sites, critical research gaps limiting our understanding of inherited microbe–host interactions and their contribution to disease susceptibility and persistence are identified. Addressing these gaps is essential for advancing insights into microbial composition and for informing personalised health strategies to identify populations contributing to greater risk of microbiome‐associated negative health outcomes.