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Updated: Jan 9, 2026

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

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

Published on: April 14, 2016

A QIIME2-based workflow for multi-amplicon 16S rRNA profiling.

Armando G Licata¹, Marica Zoppi¹, Chiara Dossena¹

¹Integrated Biology of Rare Tumors, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.

Microbiology Resource Announcements

|December 9, 2025

Summary

This summary is machine-generated.

We developed an open-source QIIME2 pipeline for 16S multi-amplicon sequencing. Our robust workflow offers comparable taxonomic accuracy and sequencing depth, making it a strong alternative for semiconductor sequencing data.

Keywords:

16S RNA QIIME bioinformatics multi‑amplicon sequencing open‑source software pediatric tumors stool microbiome

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Last Updated: Jan 9, 2026

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

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Published on: April 14, 2016

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

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Published on: August 29, 2014

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
Bioinformatics
Genomics

Background:

16S rRNA gene sequencing is crucial for microbial community analysis.
Existing pipelines may have limitations for specific sequencing technologies.
Standardization of multi-amplicon sequencing workflows is needed.

Purpose of the Study:

To present an open-source QIIME2 pipeline for 16S multi-amplicon sequencing.
To benchmark the pipeline's performance against proprietary software.
To validate the pipeline for semiconductor-based sequencing data.

Main Methods:

Development of an open-source QIIME2 pipeline.
Utilized 16S multi-amplicon sequencing.
Benchmarking performed using a mock microbial community.
Comparison with proprietary sequencing analysis software.

Main Results:

The QIIME2 pipeline demonstrated comparable sequencing depth to proprietary software.
Achieved high taxonomic accuracy with an F1-Score of 0.875.
The multi-region amplicon approach outperformed single amplicons.

Conclusions:

The developed pipeline is a robust and accurate tool for 16S sequencing.
It provides a reliable open-source alternative for analyzing semiconductor sequencing data.
Multi-region amplicon sequencing enhances microbial community analysis.