Toward accurate vaginal microbiome profiling: protocol, bioinformatics, and core microbiota characterisation

Area of Science:

• Microbiology
• Genomics
• Reproductive Health

Background:

• Assisted reproductive technologies (ART) success rates need improvement.
• The vaginal microbiome's role in fertility is increasingly recognized.
• Standardized methods are crucial for accurate microbiome assessment.

Purpose of the Study:

• To assess nanopore sequencing and bioinformatics for vaginal microbiota characterization.
• To analyze the core vaginal microbiota in healthy reproductive-age Australian women.

Main Methods:

• Utilized 16S rRNA sequencing with nanopore technology.
• Optimized PCR strategies and bioinformatic analysis pipelines.
• Compared different primer sets and bioinformatics tools for microbial identification.

Main Results:

• Identified Community State Type I (Lactobacillus crispatus dominance) as the most common (66%).
• Porechop with NanoCLUST showed accuracy in microbial identification.
• No Chlamydia trachomatis was detected using nanopore sequencing.

Conclusions:

• A Lactobacillus-rich vaginal microbiome is prevalent in healthy females.
• 16S rRNA sequencing has limitations for precise microbial detection.
• Metagenomics may offer improved accuracy for vaginal microbiome studies.