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Updated: Sep 20, 2025

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Published on: March 19, 2018

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

Isabella M Davidson¹, Elham Nikbakht¹, Larisa M Haupt^2,3,4

¹Faculty of Health Sciences & Medicine, Bond University, 14 University Drive, Robina QLD 4226, Gold Coast, Australia.

Journal of Assisted Reproduction and Genetics

|May 29, 2025

Summary

This study explored the vaginal microbiome in healthy women using nanopore sequencing. Results show a Lactobacillus-rich microbiome is common, but improved methods are needed for accurate fertility outcome analysis.

Keywords:

Lactobacillus 16S rRNA sequencing Bioinformatics Community state types (CSTs)Nanopore sequencing Vaginal microbiome

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Last Updated: Sep 20, 2025

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Published on: March 19, 2018

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

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Published on: April 14, 2016

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

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.