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.