Vaginal microbial profiling in a preterm birth high-risk cohort using shallow shotgun metagenomics

Preterm birth (PTB) is a significant health problem globally, with an estimate of 15 million cases annually. Approximately 10% neonates born early will die prematurely, while subset develop severe life-long morbidities. Unfortunately, preterm birth’s syndromic nature has evaded prevention strategies, and it continues to impose high burden on healthcare systems families. The role vaginal bacteria in triggering biomolecular causes PTB been recognised for years. However, translating this knowledge practical diagnostic therapeutic strategies remained elusive. New techniques high-throughput sequencing have improved our understanding the microbiome during pregnancy. Several multi-ethnic multi-geographical studies into identified five distinct bacterial profiles termed community state types (CSTs), one which positively associated dysbiosis increased risk PTB. In small pilot study first-trimester microbial DNA obtained from pregnant women at high-risk PTB, we compared CST generated using standard 16S amplicon shallow shotgun metagenomics (SSM). Both methods presence CSTs as reported previously, although metagenomic data showed greater taxonomic resolution more accurate assignation. These findings suggest that SSM cost-effective potentially superior alternative analysis.