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Quantifying bias introduced by sample collection in relative and absolute microbiome measurements
Dylan G Maghini1, Mai Dvorak2, Alex Dahlen3
1Department of Genetics, Stanford University, Stanford, CA, USA.
Nature Biotechnology
|April 27, 2023
Summary
Choosing the right sample preservative is crucial for accurate gut microbiome studies. OMNIgene GUT is recommended for field studies, while Zymo DNA/RNA Shield is better for metatranscriptomics, both improving microbial measurements.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Accurate microbial measurements are essential for understanding gut health.
- Sources of bias include sample condition, preservation methods, and bioinformatic analyses.
- Absolute microbial abundance offers richer insights than relative abundance.
Purpose of the Study:
- To investigate the impact of two common preservatives (OMNIgene GUT and Zymo DNA/RNA Shield) on microbial measurements.
- To assess how short-term storage conditions affect relative and absolute microbial abundance.
- To identify preservative-specific biases in gut microbiome data.
Main Methods:
- Comparison of OMNIgene GUT OMR-200 and Zymo DNA/RNA Shield.
- Evaluation of relative and absolute microbial abundance measurements.
- Analysis of metagenomic and metatranscriptomic data under varying storage conditions.
Main Results:
- OMNIgene GUT OMR-200 showed lower metagenomic taxonomic variation across storage temperatures.
- Zymo DNA/RNA Shield exhibited lower metatranscriptomic taxonomic variation.
- Absolute abundance quantification identified distinct causes for variable Bacteroidetes:Firmicutes ratios between preservatives.
Conclusions:
- OMNIgene GUT OMR-200 is recommended for field-based microbiome studies.
- Zymo DNA/RNA Shield is suitable for metatranscriptomics research.
- Absolute microbial quantification is strongly encouraged for robust microbiome analyses.
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