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Optimization of fecal sample processing for microbiome study - The journey from bathroom to bench
Wei-Kai Wu1, Chieh-Chang Chen2, Suraphan Panyod3
1Department of Internal Medicine, National Taiwan University Hospital Bei-Hu Branch, Taipei, Taiwan; Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan.
Summary
Standardizing gut microbiota research is crucial for understanding human health. This review offers a practical guide for fecal sample collection and DNA extraction to improve metagenomic analysis quality.
Area of Science:
- Microbiology
- Genomics
Background:
- Gut microbiota research is vital for human health.
- Lack of standardized protocols hinders metagenomic analysis quality.
Purpose of the Study:
- To provide suggestions for optimizing the research pipeline for fecal sample collection and DNA extraction.
- To address the need for standardized protocols in gut microbiota research.
Main Methods:
- Review of existing methodology studies on fecal sample collection and DNA extraction.
- Discussion of strategies for clinical metadata collection.
- Proposal of principles for fecal sample handling, storage, and aliquoting.
- Comparison of DNA stabilization buffers and extraction protocols.
Main Results:
- Identification of common confounders in microbiome research.
- Presentation of a DIY stool collection kit protocol.
- Evaluation of collection kits and DNA stabilization buffers.
- Analysis of DNA extraction protocol impacts on metagenomic data.
Conclusions:
- Standardized protocols are essential for reliable gut microbiota metagenomic analysis.
- Optimized sample collection and DNA extraction minimize experimental artifacts.
- Further quality control measures are needed for advancing microbiome research.
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