Optimising Vaginal Microbiome Profiling for Clinical Translation: A Comparative Assessment of Sample Storage Methods...

Area of Science:

• Microbiology
• Genetics
• Obstetrics

Background:

• Vaginal microbiome composition is linked to preterm birth (PTB) risk.
• 16S rRNA gene profiling identifies specific vaginal community state types (CSTs) associated with PTB.
• Standardized pre-analytical protocols are crucial for diagnostic profiling.

Purpose of the Study:

• To evaluate two vaginal swab storage methods for 16S rRNA microbial profiling.
• To validate a vagina-specific 16S rRNA gene database (VagDB) for enhanced annotation.
• To assess the reliability of vaginal microbiome profiling for PTB risk assessment.

Main Methods:

• Two storage methods (dry/immediate freezing vs. Amies-stabilisation/refrigeration) were compared using paired swabs from 22 high-PTB risk women.
• 16S rRNA gene (V4) PCR and Illumina sequencing were performed.
• Diversity, composition, CST allocation, and DNA yield were assessed; VagDB was used for annotation.

Main Results:

• Amies-stabilised samples yielded significantly higher DNA (p = 0.003) but did not alter microbial diversity or community structure.
• VagDB improved species-level resolution.
• Clustering by participant and CST was robust (p < 0.001) regardless of storage, with >90% CST concordance.

Conclusions:

• Routinely collected vaginal swabs in Amies medium with an 8-72h refrigeration window yield reliable microbiome data.
• These findings support integrating vaginal microbiome profiling into clinical PTB risk assessment.
• Standardized protocols and specialized databases enhance diagnostic utility.