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Updated: Jan 9, 2026
12:37
Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
Published on: April 14, 2016
40.0K
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
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.
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.
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