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Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
Published on: March 19, 2018
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Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies
Rashmi Sinha1, Jun Chen2, Amnon Amir3
1Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland. sinhar@exchange.nih.gov chia.nicholas@mayo.edu.
Summary
The fecal occult blood test (FOBT) method offers optimal stability and reproducibility for fecal microbiome analysis. Standardized fecal sample collection is crucial for large population studies investigating gut microbiota and chronic diseases.
Area of Science:
- Microbiome Research
- Gut Microbiota Analysis
- Population Health Studies
Background:
- Accurate fecal microbiome analysis is critical for large-scale population studies.
- Developing valid sampling and analysis methods is increasingly important.
- Understanding gut microbiota's role in chronic disease requires reliable data.
Purpose of the Study:
- To compare the reproducibility, stability, and accuracy of seven fecal sampling methods.
- To evaluate nine common microbiome metrics across different collection techniques.
- To identify optimal fecal collection methods for 16S rRNA microbiome profiling.
Main Methods:
- Compared seven fecal sampling methods: no additive, RNAlater, 70% ethanol, EDTA, dry swab, and fecal occult blood test (FOBT).
- Utilized 16S rRNA microbiome profiling in two laboratories.
- Assessed technical reproducibility, ambient temperature stability, and accuracy of microbiome metrics.
Main Results:
- All methods demonstrated high reproducibility, with inter-individual variation being the primary source.
- FOBT and RNAlater showed the highest stability at ambient temperature for up to 4 days.
- Swab, FOBT, and 70% ethanol methods provided the greatest accuracy when samples were immediately frozen.
Conclusions:
- Fecal occult blood test (FOBT) provides optimal stability and reproducibility for 16S rRNA microbiome analysis.
- Standardized fecal sample collection and storage methods are essential for future large population studies.
- This research supports reliable gut microbiota investigations in chronic disease etiology.
