The quest for absolute abundance: the use of internal standards for DNA-based microbial and community ecology

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Authors

Joshua Harrison, W. John Calder, Bryan N. Shuman, C. Alex Buerkle

Abstract

To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the technical limitations of the sequencing process. The relative abundances in compositional data are inherently constrained and difficult to interpret. The incorporation of internal standards (ISDs; colloquially referred to as ``spike-ins) into DNA pools can ameliorate the problems posed by relative abundance data and allow absolute abundances to be approximated. Unfortunately, many laboratory and sampling biases cause ISDs to underperform or fail. Here, we discuss how careful deployment of ISDs can avoid these complications and be an integral component of well-designed studies seeking to characterize ecological assemblages via sequencing of DNA.

DOI

https://doi.org/10.32942/osf.io/q7gy6

Subjects

Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Microbiology

Keywords

DNA barcoding, internal standard, metabarcoding, metagenomics, Microbiome, spike-in

Dates

Published: 2020-03-26 20:46

Last Updated: 2020-07-31 23:54

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License

CC-By Attribution-ShareAlike 4.0 International

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