A Sensitivity Analysis of Methodological Variables Associated with Microbiome Measurements

The experimental methods employed during metagenomic sequencing analyses of microbiome samples significantly impact the resulting data and typically vary substantially between laboratories. In this study, a full factorial experimental design was used to compare the effects of a select set of methodological choices (sample, operator, lot, extraction kit, variable region, reference database) on the analysis of biologically diverse stool samples. For each parameter investigated, a main effect was calculated that allowed direct comparison both between methodological choices (bias effects) and between samples (real biological differences). Overall, methodological bias was found to be similar in magnitude to real biological differences, while also exhibiting significant variations between individual taxa, even between closely related genera. The quantified method biases were then used to computationally improve the comparability of datasets collected under substantially different protocols. This investigation demonstrates a framework for quantitatively assessing methodological choices that could be routinely performed by individual laboratories to better understand their metagenomic sequencing workflows and to improve the scope of the datasets they produce.