This is a Preprint and has not been peer reviewed. This is version 2 of this Preprint.
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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: 2020-03-27 07:46
Last Updated: 2020-08-01 09:54
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