BACKGROUND: Next generation sequencing techniques revealed significant variations present within the microbial community of the lower genital tract in healthy women. However, there is a paucity of data characterizing the microbiota of the female upper genital tract; which controversially remains frequently described as a sterile site.

METHODS/RESULTS: This study collected Fallopian tubes from women undergoing total hysterectomy or salpingectomy-oophorectomy for benign disease or prophylaxis. Histopathology revealed unremarkable features for all Fallopian tubes, and provided menstrual cycle staging of paired endometrial samples. Samples were interrogated for the presence of microorganisms using traditional culture techniques and a two-step next generation sequencing technology approach to exploit the V8 and V9 regions of the 16S rRNA gene.

Both culture and pyrosequencing revealed that the Fallopian tube is not a sterile site. Bacteria were isolated from 50% of cultured samples, and 100% of samples returned positive PCR results. Only 68% of the culture isolates could be confidently identified using automated diagnostic equipment in a clinical microbiology laboratory. Monomicrobial communities were identified only for cultured isolates (50%). Pyrosequencing revealed that all communities were polymicrobial.  Lactobacillus spp. were not present in all groups, nor were they the most dominant isolates. Distinct differences in the microbial communities were evident for left compared to right Fallopian tubes, ampulla versus isthmus, pre and post menopausal tissue, and in secretory phase Fallopian tubes with and without Mirena intrauterine devices in situ (all p > 0.05).

CONCLUSIONS: The female upper genital tract is not sterile. Distinct microbial community profiles in the Fallopian tubes of healthy women suggest that this genital tract site supports a resident commensal microflora.