Female reproduction and the microbiota in mammals: Where are we?

While it is generally accepted that the mammalian vagina contains a site-specific microbiota that plays relevant roles in genital and reproductive health, the existence of an extra-vaginal microbiota in the female reproductive tract (i.e. follicular fluid, oviduct, endometrium, and placenta) is, at least, a matter of controversy. Many conclusions in this field have failed to consider the technical limitations, biases, and confounding factors inherent to next-generation sequencing (NGS) approaches. While this creates uncertainty in the field, there is no doubt this subject is set to be the focus of new research efforts because of its scientific and practical connotations in female reproductive health. The current art state, its limitations, and gaps in our knowledge about the female reproductive tract's microbiota and, particularly, about the microbes of the extra-vaginal environment are presented in this review. Also are discussed possible relationships between the gut and oral microbiota and reproductive events. •The presence of an extra-vaginal microbiota in the female reproductive tract is controversial.•Knowledge about the microbiota beyond the gut and/or beyond the human species is limited.•Limitations and gaps in our understanding about the microbiome and reproduction with a critical point of view is discussed.•Microbiome in other bodily localizations (i.e.: gut, oral cavity) can affect reproductive events.