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Almost every part of our body has a coevolved microbial community. The expressed microbial genes comprise the various microbiomes that play important roles in normal physiology and development. The various microbiomes are separate, yet often connected, with the species composition of one affecting others. The female reproductive system microbiomes (eg, vaginal, placental, and mammary/milk) remain less well explored than the gut microbiome although they comprise a large proportion of the female microbial network. This review examines the evidence for interconnectivity between the female reproductive microbiomes, other maternal microbiomes, and developing infant microbiomes and the potential roles of each in health and disease. Disruptions in maternal microbiomes may be linked to pregnancy complications and maternal, fetal, and neonatal health. The diversity of the vaginal microbiome’s makeup, which appears to vary across ethnicity, has led researchers to reconsider the idea of a “healthy” or “normal” vaginal microbial community. Less is known about the possible placental microbiome, although an association between the placenta’s bacterial makeup and preterm labor and other pregnancy complications is being investigated. The mammary/milk microbiome appears to be influenced by maternal characteristics and may play a role in inoculating the infant but may also be affected by the infant’s oral microbiome. Probiotic therapies such as “vaginal seeding” offer potential health benefits but require more rigorous testing. Exploring the reproductive microbiomes in detail and pairing this information with an individual’s detailed medical history will provide a more complete picture of the status and importance of the microbial network to health.