Characterisation of the Vaginal Microbiota Using Culturomics and Metagenomics Suggests Transplantation of Gut Microbiota Into the Vagina During Bacterial Vaginosis

Abstract

Background: Bacterial vaginosis is a very common vaginal disorder, with a gynaeco-obstetrical impact, but remains poorly understood. Current antibiotic treatment most often fails. Our objective was to exhaustively map the bacterial community present in bacterial vaginosis and normal flora, using not only a molecular approach but also a highly efficient culture approach, culturomics. Vaginal bacterial diversity was evaluated using both strategies for 24 Caucasian French women, including 7 cases of bacterial vaginosis, and 10 rural Senegalese women, including 5 cases of bacterial vaginosis. An additional 16 specimens (three cases of bacterial vaginosis and 13 normal flora) obtained during the follow-up visits of five French women with bacterial vaginosis were analysed using metagenomics.Results: The combination of culturomics and metagenomics reveals the richness and diversity of vaginal microbiota. Our data demonstrated that compared to healthy women, those with bacterial vaginosis present a shift in vaginal flora. The microbiota of the bacterial vaginosis group can be easily distinguished from that of healthy group by their increased bacterial diversity, abundance of Bacteroidales and Leptotrichiaeceae, and depletion of Proteobacteria and Lactobacillaceae species. In addition, a complex of 10 genera was associated with bacterial vaginosis: Gardnerella, Atopobium, Snethia, Aerococcus, Prevotella, Gemella, Facklamia, Porphyromonas, Mycoplasma, and Urinacoccus. Overall, the microbial population detected in bacterial vaginosis flora was largely similar to the bacterial communities found in gut microbiota. The two approaches showed a diverse vaginal microbiota that was largely non-overlapping, with only 146 common species. Furthermore, culturomics extends the repertoire of human-associated bacteria with the isolation of 27 new bacterial species.Conclusions: This study provides the most representative topology of the vaginal microbiota of normal flora and bacterial vaginosis and suggests the transplantation of gut microbiota into the vagina during bacterial vaginosis. Several sets of clinically relevant anaerobic bacteria and new species were also isolated from the human vagina, confirming that some previously “uncultivated” species may be cultivated using an appropriate strategy. Exhaustive characterisation of vaginal microbiota will enable a better understanding and management of bacterial vaginosis. Obtaining isolates will allow us to explore the bacterial interactions of the vaginal microbiota and will serve as a basis for the potential development of bacteriotherapy to prevent or treat vaginal dysbiosis.

Culturomics in Unraveling the Upper Female Reproductive Tract Microbiota

“…They proliferate slowly, necessitate specific nutrients, are easily outcompeted by more aggressive species, and perish in the presence of oxygen. 25 Traditional agar plate cultivation often falls short for these delicate bacteria. However, initiating their growth in nutrient-rich anaerobic liquid media can create a conducive environment for them.…”

Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms

“…Next, it utilizes matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) or NGS for species identification. 159 Initially developed to uncover novel bacterial species in the gut microbiota, culturomics has broadened its application to various microbiotas, including those in the human vagina 160,161 and urinary system. 162 Through the use of diverse culture media and appropriate negative controls, culturomics mitigates the inherent depth and DNA extraction biases associated with metagenomics-based microbiome analyses.…”

Culturomics to Investigate the Endometrial Microbiome: Proof-of-Concept

“…Previous studies highlight certain challenges in a successful culturomics set-up. Fastidious anaerobic species, such as Fusobacterium nucleatum and Peptostreptococcus anaerobius , often grow very slowly, require special nutrients, are rapidly grown over by other species, and die in the presence of oxygen [ 15 ]. As a result, most of these species are not suitable for standard cultivation on agar plates.…”

“…However, this technique also showed its utility on vaginal microbiota. Since the application of culturomics at least 15 new species from the vaginal tract haven been reported [ 13 , 15 ].…”