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4bases’Paper of the Month – June 2022 -MinION, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting 

Our team’s reading recommendation for this month is ” MinION, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting “, an excellent scientific study conducted by S Komiya et al. 1and recently published in “BMC Medical Genomics”.

Bacterial vaginosis (BV) is a vaginal disorder that can affect women of reproductive age. This disorder is due to a disturbance of the vaginal microbiota that can be caused by several factors. It can have dramatic consequences on reproduction by causing infections, premature deliveries or even infertility. Unfortunately, conventional methods for diagnosing this disorder are not very reliable because they depend either on the skills of the examiner or on a difficult to perform bacterial culture. Therefore, it is crucial to develop a rapid and reliable tool for vaginal microbiota profiling. 

Next-generation sequencing is a tool that combines metagenomic sequencing and bioinformatics technologies to objectively identify bacterial communities without the need for bacterial culture, nor relying on the opinion of an expert. The goal of the study is to assess the rapidity and the reliability of the MinION nanopore sequencer, a recently developed next-generation sequencing platform, in identifying bacterial communities of the vagina. The interest in using the MinION nanopore sequencer lies in its unlimited theoretical read length, and hence its potential very high taxonomic resolution in bacterial profiling. 

This study demonstrates the ability of MinION sequencing to identify vaginal microbiota in a simple, rapid and reliable manner. Complete 16S ribosomal RNA (rRNA) gene sequencing using the MinION nanopore shows that no specific sample collection method is required, allowing for a minimally invasive procedure during diagnosis. Regarding the time required for the total analysis, 16S ribosomal RNA (rRNA) gene sequencing using the MinION nanopore identifies the microbial composition at the species level in a reasonable time of about 4 hours, which offers the additional advantage of a fast turnaround time for this workflow. MinION sequencing shows a very high resolution in the identification of bacterial taxonomy at the species level, a resolution that is not achievable by the conventional techniques used, which therefore do not allow the identification of bacterial composition at the species level.

Prior to MinION nanopore sequencing, vaginal samples were collected and then submitted to DNA extraction and two PCRs. The first PCR step was to amplify the nearly complete 16S rRNA genes and the second step was to extend the resulting amplicons from the first amplification with barcodes and adapters to prepare them for MinION nanopore sequencing. The effectiveness of this procedure was verified by analyzing a pre-characterized fictitious population sample of bacteria. 

Sequencing with the MinION nanopore has the ability to reveal the presence of the bacteria responsible for BV, even when conventional methods fail to identify this disorder. The fact that the MinION nanopore sequencer allows long term sequencing in a very short time with very high resolution identifying the vaginal microbiota, facilitates the screening of the vaginal microbiota. This opens up the possibility of establishing links between this vaginal composition and several problems related to women’s health.

1. Komiya, S. et al. MinION, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting. BMC Med Genomics 15, 68 (2022).

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