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Previous studies have linked the microbiome of distinct body habitats to obesity and infertility; however, the often-divergent results observed have left the role of the so-called "second genome" in obese infertile patients incompletely explored. Here, we present a prospective observational multicenter study of oral, gut, endometrial, and vaginal microbiota of infertile patients classified according to BMI. Patients collected saliva/fecal samples, while vaginal/endometrial fluid samples were collected in the clinic. Total bacterial DNA was extracted, and microbiota profiles were analyzed by 16S rRNA gene sequencing. Our results showed no differences in the Bacteroidetes/Firmicutes ratio (proposed obesity hallmark) in the gut microbiota between patients with obesity and normal weight; however, a tendency for higher levels of genera such as Escherichia-Shigella in normal-weight patients was observed; in comparison, patients with obesity possessed increased numbers of Parasutterella and Roseburia. In the reproductive tract, vaginal samples possessed a similar microbiota to endometrial fluid, both largely colonised by Lactobacillus, Gardnerella, and Streptococcus, supporting the hypothesis that uterine colonisation proceeds from vaginal bacteria ascension. Additionally, higher prevalence of a Streptococcus-dominated (>50%) endometrial microbiota was observed among patients with obesity. This first description of the human digestive and reproductive tract microbiota in infertile women with obesity may explain their poor reproductive outcomes. [ABSTRACT FROM AUTHOR]