Shallow shotgun metagenomic sequencing of vaginal microbiomes with the Oxford Nanopore technology enables the reliable determination of vaginal community state types and broad community structures

The vaginal microbiome plays a crucial role in reproductive health, as it is associated with reproductive success and susceptibility to infection. Disruption of the microbiome can lead to conditions, such as bacterial vaginosis (BV), which impacts well-being and increases the likelihood of preterm birth. However, BV symptoms can differ between ethnicities or be asymptomatic, requiring microbiome characterisation for diagnosis. Traditionally, 16S sequencing has been used, but this method only detects prokaryotes. To overcome this limitation, the researchers employed shallow shotgun metagenomic sequencing (SMS) with Oxford Nanopore technology. Shallow SMS effectively characterised the vaginal microbiome and generated additional insights inaccessible with traditional methods, including methylation, detection of non-bacterial species, and characterisation of disrupted microbiome states. Oxford Nanopore-based shallow SMS proved to be a potential alternative method that reveals unique microbiome insights and could be applied to large-scale studies to advance women’s health research.

Sample type: DNA from swabs

Kits: Ligation Sequencing Kit and Native Barcoding Expansion