Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the 16S rRNA gene

Background. It is widely assumed that the uterine cavity in non-pregnant women is a sterile body environment under physiological conditions. We have previously shown that some women with overt dysbiosis of the vaginal microbiome, present with a polymicrobial Gardnerella vaginalis-dominated covering the endometrium, casting doubt over the paradigm of the sterilityof the human uterus. We therefore aimed to assess the putative presence of a uterine microbiome in a series of non-pregnant women through deep sequencing of the V1-2 hypervariable region of the 16S ribosomal RNA (rRNA) gene. Methods. We sampled the endometrial surface by use of a transcervical device designed to avoid contamination from the vagina and endocervix in nineteen non-pregnant women with reproductive failure in the absence of uterine anomalies on hysteroscopy. Following DNA extraction, the V1-2 region of the 16S rRNA gene was targeted using the 27F and 338R primers. By use of the Illumina MiSeq platform, 16S rRNA gene amplicon sequences were identified and annotated by use of the Ribosomal Database Project. Results. Out of 183 unique 16S rRNA gene amplicon sequences, 15 operational taxonomic units or phylotypes were present in all samples, possibly representing the uterine core microbiome, dominated by Bacteroides xylanivorans, Bacteroides thetaiotaomicron, Bacteroides fragilis, and Pelomonas. Accordingly, three bacterial phyla, Proteobacteria, Firmicutes and Bacteroidetes, were consistently present. In some women, the endometrial community was also characterized by a single abundant species co-occurring with the core microbiota, in particular Lactobacillus crispatus, Lactobacillus iners, and Prevotella amnii, while in two women the community was largely different. Discussion. Our findings are, albeit not necessarily generalizable, consistent with the presence of a unique microbiome residing on the endometrium of the human non-pregnant uterus in women of reproductive age. A majority of women showed a rather similar endometrial community, dominated by only a few Bacteroides and Pelomonas phylotypes. Consistent with our current understanding of the human microbiome, the uterine microbiome is likely to have a previously unrecognized role in uterine physiology and human reproduction. Further study is therefore warranted to document community ecology and dynamics of the uterine microbiota, as well as the role of the uterine microbiome in health and disease.