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Updated: May 7, 2026
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Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
Published on: April 14, 2016
Advancing our understanding of the human microbiome using QIIME
José A Navas-Molina1, Juan M Peralta-Sánchez, Antonio González
1Department of Computer Science, University of Colorado, Boulder, Colorado, USA.
Methods in Enzymology
|September 25, 2013
Summary
This study demonstrates the QIIME (Quantitative Insights Into Microbial Ecology) pipeline for analyzing mouse microbial communities using 16S rRNA gene sequences. It provides a recommended workflow and guidelines for microbial ecology research.
Area of Science:
- Microbial Ecology
- Bioinformatics
- Genomics
Background:
- High-throughput DNA sequencing and bioinformatics tools accelerate microbial ecology research.
- Understanding the human microbiome is advancing rapidly.
- QIIME is an open-source software package for microbial community analysis.
Purpose of the Study:
- To demonstrate the QIIME pipeline for analyzing microbial communities from mouse body sites.
- To provide a recommended QIIME analysis pipeline and guidelines.
- To showcase QIIME's analytical capabilities and integration with other tools like phyloseq and R.
Main Methods:
- Utilized QIIME (Quantitative Insights Into Microbial Ecology) software.
- Analyzed 16S rRNA gene sequences from mouse microbial communities.
- Generated sequence data using the Illumina MiSeq platform.
- Applied recommended QIIME pipeline for data analysis.
Main Results:
- Successfully analyzed microbial communities from various mouse body sites.
- Presented a robust QIIME pipeline for microbial community analysis.
- Illustrated QIIME's capacity for statistical analyses and interactive visualizations.
Conclusions:
- QIIME provides a comprehensive framework for microbial community analysis.
- The recommended QIIME pipeline facilitates critical decision-making in analysis.
- QIIME analysis can be expanded using complementary tools like phyloseq and R.
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