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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
Published on: August 25, 2018
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Signal and noise in metabarcoding data
Zachary Gold1,2, Andrew Olaf Shelton2, Helen R Casendino3
1Cooperative Institute for Climate, Ocean, & Ecosystem Studies, UW, Seattle, Washington, United States of America.
Plos One
|May 11, 2023
Summary
Non-detections in metabarcoding data arise from amplification biases and stochastic sampling. Understanding these factors is key to accurately quantify species in environmental DNA and microbiome studies.
Area of Science:
- Molecular Ecology
- Bioinformatics
Background:
- Metabarcoding surveys species using DNA, crucial for health and conservation.
- Quantitative estimates require correcting for amplification biases.
Purpose of the Study:
- Investigate causes of non-detections in metabarcoding replicates.
- Develop methods to distinguish true biological signals from technical noise.
Main Methods:
- Analysis of simulated and empirical metabarcoding data.
- Modeling of amplification biases and stochastic sampling effects.
Main Results:
- Non-detection rates depend on DNA concentration and species-specific amplification efficiency.
- Deterministic PCR biases and stochastic amplicon sampling significantly impact data.
- Stochastic pre-PCR sampling of rare molecules remains a challenge for quantification.
Conclusions:
- Accurate quantitative metabarcoding necessitates estimating species-specific amplification efficiencies.
- Evaluating non-detection patterns is vital for reliable detection of rare targets.
