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Related Experiment Video

Updated: Dec 25, 2025

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

Benchmarking the MinION: Evaluating long reads for microbial profiling.

Robert Maximilian Leidenfrost¹, Dierk-Christoph Pöther², Udo Jäckel²

¹Department of Biotechnology and Chemistry, Mittweida University of Applied Sciences, Technikumplatz 17, 09648, Mittweida, Germany. robert.leidenfrost@hs-mittweida.de.

Scientific Reports

|March 22, 2020

Summary

This summary is machine-generated.

Nanopore DNA sequencing offers long reads for bacterial community analysis. This study benchmarks the MinION sequencer, achieving high accuracy for microbial community composition, aiding future data processing pipeline development.

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Area of Science:

Genomics
Bioinformatics
Microbiology

Background:

Nanopore DNA sequencing provides long reads, simplifying bacterial community analysis.
This technology is under continuous development, necessitating robust benchmarking for analysis protocols.

Purpose of the Study:

To assess the specificity and sensitivity of the MinION nanopore sequencer for microbial community composition.
To provide an open protocol and dataset for developing and benchmarking future bioinformatics pipelines.

Main Methods:

A dataset of twelve prokaryotic species across four samples was used in a blind study.
Taxonomic classification was performed directly on reads using Kraken, Kraken2, and Centrifuge.
Evaluation focused on specificity and sensitivity of nanopore sequencing for microbial identification.

Main Results:

High taxonomic assignment accuracy was achieved: up to 99.27% at genus level and 92.78% at species level.
True-positive classification of strains was enabled down to 25,000 genomes per sample.
Full genomic coverage was obtained for strains as low as 250,000 genomes per sample.

Conclusions:

Nanopore sequencing analysis effectively determines microbial community composition.
The presented data and protocol serve as a foundation for advancing nanopore-based microbial analysis.