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Technical advances in massive parallel sequencing have allowed the characterization of the whole reproductive tract microbiome in all the compartments beyond the vagina. The microbiota in the uterine cavity seem to be a continuum from the microbiota in the vagina, but several works have reported significant differences between vaginal and endometrial microbiota, highlighting the relevance of assessing the upper genital tract microbiota to better understand the potential roles of bacteria in the physiological and pathological processes taking place in the uterine cavity, including embryo implantation, pregnancy maintenance, and other gynecological diseases. However, the study of the endometrial microbiota, as with other low-biomass microbiota, presents important hurdles because, due to the small amount of starting material, they are easily contaminated by exogenous bacterial DNA. For this reason, careful and appropriate investigation of the endometrial microbiota is of outstanding importance to detect uterine dysbiosis that may impact the reproductive function. [ABSTRACT FROM AUTHOR]