Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective

Abstract

As investigations of low-biomass microbial communities have become more common, so too has the recognition of major challenges affecting these analyses. These challenges have been shown to compromise biological conclusions and have contributed to several controversies. Here, we review some of the most common and influential challenges in low-biomass microbiome research. We highlight key approaches to alleviate these potential pitfalls, combining experimental planning strategies and data analysis methods.

Keywords: batch effect; contamination; experimental design; low-biomass microbiome; microbiome.