Harrison Joshua G, John Calder W, Shuman Bryan, Alex Buerkle C
University of Wyoming, Laramie, WY, USA.
Mol Ecol Resour. 2021 Jan;21(1):30-43. doi: 10.1111/1755-0998.13247. Epub 2020 Sep 17.
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.
为了表征微生物群落和其他生态组合，生态学家通常对焦点分类群之间存在差异的基因座进行测序和比较。这些序列的计数传达了有关分类群的出现情况和相对丰度的信息，但由于测序过程的技术限制，无法提供其绝对丰度的直接测量值。组成数据中的相对丰度本质上是受限的，难以解释。将内标（ISDs；通俗地称为“加标”）纳入DNA库可以改善相对丰度数据带来的问题，并使绝对丰度得以近似估算。不幸的是，许多实验室和采样偏差会导致内标表现不佳或失效。在这里，我们讨论如何谨慎部署内标可以避免这些复杂情况，并成为旨在通过DNA测序表征生态组合的精心设计研究的一个组成部分。
