Diversity of vaginal microbiome and metabolome during genital infections Original paper

What was studied?

This original research article investigated vaginal microbiome and metabolome signatures across four clinical states—healthy controls, bacterial vaginosis, vulvovaginal candidiasis, and Chlamydia trachomatis infection—to define how microbial communities and metabolites shift during common genital infections. Using 16S rRNA sequencing and proton NMR spectroscopy, the authors evaluated how loss of Lactobacillus dominance, emergence of anaerobic taxa, and altered metabolic pathways contribute to dysbiosis. The study mapped both taxonomic and metabolic fingerprints, highlighting condition-specific microbial patterns such as the transition from Lactobacillus crispatus dominance to Lactobacillus iners prevalence and increased representation of Gardnerella, Prevotella, Megasphaera, Roseburia, and Atopobium. Integration of microbial and metabolic datasets revealed correlations between particular taxa and metabolites, providing a combined ecological view of vaginal health and disease.

Who was studied?

The study included 79 reproductive-aged women enrolled at an STI clinic in Italy. Participants were classified into four groups: healthy controls (n=21), women with bacterial vaginosis (n=20), women with Chlamydia trachomatis infection (n=20), and women with vulvovaginal candidiasis caused by Candida albicans (n=18). Clinical criteria such as Amsel scoring, Nugent grading, PCR confirmation of C. trachomatis, and culture-based identification of Candida species ensured accurate diagnostic categorization. Most Chlamydia-positive women were asymptomatic, reflecting typical epidemiologic patterns. The groups did not differ significantly in age or BMI, allowing clearer interpretation of microbiome and metabolome differences as linked to infection status rather than confounding demographics.

Most important findings

Across all infection groups, the vaginal microbiota shifted from L. crispatus-dominant communities toward L. iners-dominated states, which are less protective and more permissive to dysbiosis. Healthy participants showed high L. crispatus abundance, whereas women with bacterial vaginosis displayed profound depletion of Lactobacillus alongside marked increases in anaerobes including Gardnerella, Prevotella, Atopobium, Megasphaera and Sneathia. Candida infection produced a signature similar to BV, including elevated Gardnerella and Prevotella, and increased Faecalibacterium and Roseburia—taxa typical of the gut, suggesting translocation or ecological disruption. Chlamydia infection showed a moderate shift, featuring elevated Megasphaera, Atopobium and Faecalibacterium. At the metabolome level, lactate concentrations dropped sharply in all pathological groups, mirroring Lactobacillus loss. Short-chain fatty acids, biogenic amines and organic acids increased, especially in BV. VVC samples uniquely displayed elevated vaginal glucose, supporting Candida overgrowth. Strong correlations linked Lactobacillus abundance with lactate and amino acids, while anaerobic taxa correlated with acetate, formate, propionate and putrescine, all indicators of dysbiosis.

Key implications

The study demonstrates that each genital infection produces a distinct but overlapping dysbiosis signature, emphasizing the clinical utility of combined microbiome–metabolome profiling. Loss of L. crispatus and expansion of anaerobic genera create biochemical environments conducive to pathogen persistence. Identifying condition-specific microbial and metabolic markers may enhance diagnostic accuracy, inform treatment strategies and support development of microbiome-targeted therapeutics or probiotics. These findings underscore the dynamic interplay between microbial community structure and metabolic function in regulating vaginal health.

Citation

Ceccarani C, Foschi C, Parolin C, et al. Diversity of vaginal microbiome and metabolome during genital infections.Scientific Reports. 2019;9:14095. doi:10.1038/s41598-019-50410-x