The female upper reproductive tract harbors endogenous microbial profiles

Abstract

Introduction: The female reproductive tract harbours unique microbial communities (known as microbiota) which have been associated with reproductive functions in health and disease. While endometrial microbiome studies have shown that the uterus possesses higher bacterial diversity and richness compared to the vagina, the knowledge regarding the composition of the Fallopian tubes (FT) is lacking, especially in fertile women without any underlying conditions.

Methods: To address this gap, our study included 19 patients who underwent abdominal hysterectomy for benign uterine pathology, and 5 women who underwent tubal ligation as a permanent contraceptive method at Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA). We analyzed the microbiome of samples collected from the FT and endometrium using 16S rRNA gene sequencing.

Results: Our findings revealed distinct microbiome profiles in the endometrial and FT samples, indicating that the upper reproductive tract harbors an endogenous microbiome. However, these two sites also shared some similarities, with 69% of the detected taxa Being common to both. Interestingly, we identified seventeen bacterial taxa exclusively present in the FT samples, including the genera Enhydrobacter, Granulicatella, Haemophilus, Rhizobium, Alistipes, and Paracoccus, among others. On the other hand, 10 bacterial taxa were only found in the endometrium, including the genera Klebsiella, Olsenella, Oscillibacter and Veillonella (FDR <0.05). Furthermore, our study highlighted the influence of the endometrial collection method on the findings. Samples obtained transcervically showed a dominance of the genus Lactobacillus, which may indicate potential vaginal contamination. In contrast, uterine samples obtained through hysterescopy revealed higher abundance of the genera Acinetobacter, Arthrobacter, Coprococcus, Methylobacterium, Prevotella, Roseburia, Staphylococcus, and Streptococcus.

Discussion: Although the upper reproductive tract appears to have a low microbial biomass, our results suggest that the endometrial and FT microbiome is unique to each individual. In fact, samples obtained from the same individual showed more microbial similarity between the endometrium and FT compared to samples from different women. Understanding the composition of the female upper reproductive microbiome provides valuable insights into the natural microenvironment where processes such as oocyte fertilization, embryo development and implantation occur. This knowledge can improve in vitro fertilization and embryo culture conditions for the treatment of infertility.

Keywords: 16S rRNA gene; endometrium; fallopian tubes; microbes; microbiome; microbiota; upper reproductive tract.

Figure 1

Study design. In total 24 women participated in the study and 34 samples from the upper reproductive tract were retrieved. In the hysterectomy cohort (H), seven women provided both endometrial and Fallopian tube (FT) samples, and in the tubal ligation cohort (TL), three women provided both samples. The rest of the participants provided only one of the samples due to the tissue damage during laparoscopic procedure, non-sterile condition, or blood contamination.

Figure 2

The most abundant genera detected in the Fallopian tubes (FT) samples from patients underwent atotal laparoscopic hysterectomy with bilateral salpingo-oophorectomy (patients 1, 2, 3, 5, 9, 10, 11, 12, 13, 15, 16 and 17) or laparoscopic tubal ligation (patients 20, 21, 23 and 24). Percent-stacked barchart of those genera whose mean relative abundances were higher than 1% are represented.

Figure 3

The most abundant genera detected in the endometrial samples from patients undergoing a total laparoscopic hysterectomy with bilateral salpingo-oophorectomy (patients 1, 2, 3, 4, 6, 7, 8, 10, 12, 13, 14, 15, 18 and 19) or laparoscopic tubal ligation (patients 20, 22, 23 and 24). Percent-stacked barchart of those genera whose mean relative abundances were higher than 1% are represented.

Figure 4

Relative abundance of nine bacterial genera between samples obtained directly from the uterus (hysterectomy, H) (fertile women with fibroids) and transcervically when undergoing tubal ligation (TL) (fertile women without the disease). After multiple testing correction adjustment, the difference remained marginal (FDR=0.083 for all plots).

Figure 5

Venn diagram illustrating the bacterial genera present in the upper reproductive tract.

Figure 6

Diversity indices in Fallopian tubes (FT) and endometrial (E) samples. (A) Alpha-diversity metrics (i.e., Shannon, OTUs number [richness]) of endometrial and FT samples. (B) Beta-diversity represented by principal coordinate analysis (PCoA) based on Bray-Curtis distances (PERMANOVA, R2=0.024, p=0.720) between endometrial and FT samples.

Figure 7

Diversity indices in paired endometrial and FT samples. (A) Alpha-diversity metrics (i.e., Shannon, OTUs number [richness]) of endometrial and FT samples when the restricted group of patients with paired samples was selected. (B) Beta-diversity represented by principal coordinate analysis (PCoA) based on Bray-Curtis distances of patients with paired samples (PERMANOVA, R2 = 0.048, p=0.706).

Figure 8

Diversity indices each pair of the tissue samples corresponding to their respective patient. (A) Alpha-diversity metrics (i.e., Shannon, OTUs number) of paired endometrium and Fallopian tube (FT) samples from the same women (n=7), all values p >0.05. Each label indicates a patient (e.g. 1). (B) Beta-diversity represented by principal coordinate analysis (PCoA) based on Bray-Curtis distances of patients with paired samples (PERMANOVA, R^2 = 0.622, p=0.044). Each patient is indicated with one colour, where the two dots of the same colour represent individuals’ endometrial and FT samples.