Microbial differences and continuity across rectal, vaginal and endometrial sites in obese and normal-weight infertile women

Abstract Background This study characterizes microbial relationships and bacterial transfer across the rectal, vaginal and endometrial microbiomes upon embryo transfer, and evaluates the influence of obesity on site-specific profiles. The Tampere Infertility Microbiome Project (TIMP) included eighty-nine women with male-factor infertility undergoing IVF or ICSI. Participants were classified into normal-weight ( n = 45, BMI < 25 kg/m 2 ) and obese ( n = 44, BMI 30–35 kg/m 2 ) groups. A total of 267 rectal, vaginal and endometrial samples were collected upon fresh embryo transfer and analysed using next-generation sequencing. Results The anatomical site was the dominant determinant of microbial structure. Rectal samples showed the highest diversity and differed from Lactobacillus -dominated vaginal and endometrial communities ( p < 0.0001), which partially overlapped but exhibited distinct genera. Lactobacillus accounted for 61.3% of vaginal, 18.2% of endometrial and 1.7% of rectal communities. Higher vaginal abundance of Lactobacillus was associated with lower occurrences of Gardnerella , Prevotella and other non- Lactobacillus genera ( p = 0.001), suggesting a vaginal-endometrial association. Increased rectal abundances of Gardnerella and Prevotella corresponded to higher vaginal abundances of the same genera, suggesting a rectal-vaginal microbial relationship. Obesity was associated with a trend towards increased vaginal diversity and a higher prevalence of Gardnerella in obese versus normal-weight individuals (19% vs. 9%, p = 0.047). Conclusions Rectal microbiomes were diverse and distinct from vaginal and endometrial communities. Vaginal Lactobacillus dominance was associated with lower abundance of potentially pathogenic genera. Microbial continuity was most pronounced for Gardnerella and Prevotella . BMI-related variation appeared most pronounced in the vaginal microbiome, followed by the endometrium, whereas community-level differences between BMI groups were not statistically significant.