Department of Genetics, Stanford University, Stanford, CA, USA.
Department of Biology, Stanford University, Stanford, CA, USA.
Nat Biotechnol. 2024 Feb;42(2):328-338. doi: 10.1038/s41587-023-01754-3. Epub 2023 Apr 27.
To gain insight into the accuracy of microbial measurements, it is important to evaluate sources of bias related to sample condition, preservative method and bioinformatic analyses. There is increasing evidence that measurement of the total count and concentration of microbes in the gut, or 'absolute abundance', provides a richer source of information than relative abundance and can correct some conclusions drawn from relative abundance data. However, little is known about how preservative choice can affect these measurements. In this study, we investigated how two common preservatives and short-term storage conditions impact relative and absolute microbial measurements. OMNIgene GUT OMR-200 yields lower metagenomic taxonomic variation between different storage temperatures, whereas Zymo DNA/RNA Shield yields lower metatranscriptomic taxonomic variation. Absolute abundance quantification reveals two different causes of variable Bacteroidetes:Firmicutes ratios across preservatives. Based on these results, we recommend OMNIgene GUT OMR-200 preservative for field studies and Zymo DNA/RNA Shield for metatranscriptomics studies, and we strongly encourage absolute quantification for microbial measurements.
为了深入了解微生物测量的准确性，评估与样本状况、保存方法和生物信息学分析相关的偏差来源非常重要。越来越多的证据表明，测量肠道中微生物的总数和浓度，即“绝对丰度”，提供了更丰富的信息来源，并且可以纠正从相对丰度数据得出的一些结论。然而，关于保存剂选择如何影响这些测量的知识却知之甚少。在这项研究中，我们研究了两种常见的保存剂和短期储存条件如何影响相对和绝对微生物测量。OMNIgene GUT OMR-200 在不同储存温度之间产生的微生物分类变化较小，而 Zymo DNA/RNA Shield 产生的微生物转录组分类变化较小。绝对丰度定量揭示了两种不同的保存剂导致拟杆菌门/厚壁菌门比例变化的原因。基于这些结果，我们建议在野外研究中使用 OMNIgene GUT OMR-200 保存剂，在转录组学研究中使用 Zymo DNA/RNA Shield 保存剂，并强烈鼓励对微生物测量进行绝对定量。
