The Dynamics of the Female Microbiome: Unveiling Abrupt Changes of Microbial Domains across Body Sites from Preconception to Perinatal Phase
The maternal microbial ecosystem undergoes tremendous changes during pregnancy and the perinatal period. Surprisingly little is known about the extent of change in the maternal microbiomes beyond the vaginal cavity and their recovery after birth. In this study, we followed pregnant women (mpre, n = 30) into the postpartum period (1 month, mpost, n = 30) and profiled their oral, urinary, and vaginal microbiome, archaeome and mycobiome, and urinary metabolome. Results were compared to the microbiomes and metabolomes of non-pregnant women (np, n = 29). Overall, pregnancy status (np, mpre, mpost) had a smaller effect on the microbiomes than body site, but massive transitions were observed for the oral and urogenital (vaginal and urinary) microbiomes. While the oral microbiome fluctuates during pregnancy but rapidly stabilizes within the first month postpartum, the urogenital microbiome ischaracterized by a major shift from mpre to mpost, driven by a massive loss of Lactobacillus and thus a shift from vaginal community state type (CST) I (40% of women) to CST IV (85% of women). Although the urinary metabolome rapidly reached an np-like composition after parturition, except for lactose and oxalic acid, which were elevated during active lactation, the urinary microbiome reflected vaginal dysbiosis. Fungal and archaeal profiles were indicative of pregnancy status. Methanobacterium signatures were found exclusively in np women, and Methanobrevibacter showed opposite behavior during pregnancy in oral samples (increased) and in the vaginal cavity (decreased).   Our findings suggest that the massive rearrangement of the maternal microbiome and metabolome needs more attention from researchers and that potential interventions could be envisioned to optimize recovery and avoid long-term effects on maternal health and subsequent pregnancies.