Characterising interactions between bacteria in human vaginal microbiomes

The human body is colonised by an immense number of microbial organisms inhabiting various tissues and body sites and although most microbiomes are beneficial for the host, environmental disturbances can lead to negative clinical consequences. Microenvironment disruption has been linked with various disorders in the vaginal tissue including Bacterial Vaginosis, HIV and other Sexually Transmitted Infections. Microbiome studies have proven a useful tool in characterising microorganisms associated with health and disease in humans. Amplicon data can provide information on the relationship between bacterial community composition and ecosystem function. This study aimed to identify correlations between members of the vaginal microbiomes from different individuals with gynaecological disorders, to gain insight into the microbial interactions that affect community assembly. Although positive and negative correlations between bacterial taxa may give us insight to bacterial relationships, they can be enhanced by exploring the metabolic properties of these taxa. A pipeline was designed here to allow cultivation-free, bioinformatics analysis on existing amplicon data from vaginal microbiome studies. QIIME (Quantitative Insights Into Microbial Ecology) and other purpose-written Python scripts were designed to complete taxonomy assignment, diversity and clustering analysis, as well as to assess the statistical significance of the correlations from the interactions observed. Analysis suggests strong correlations between various anaerobes, linked with dysbiosis in bacterial communities. A novel correlation between Dialister and Prevotella genera is presented, which can be reinforced by the presence of metabolic links. Succinate is a shared metabolite, that is a product of fermentation in Prevotella and a substrate for Dialister in propionate production. The findings identify links between the human microbiome and pathogenicity, thus providing insight into vaginal microbiome structure and composition, particularly so in the gynaecological syndrome of bacterial vaginosis. In conclusion, microbiome analyses studies show the prospect of new approaches to diagnosis and therapy.