Treating Bugs as Features: A compositional guide to the statistical analysis of the microbiome-gut-brain axis

There has been a growing acknowledgement of the involvement of the gut microbiome - the collection of microbes that reside in our gut - in regulating our mood and behaviour. This phenomenon is referred to as the microbiota-gut-brain axis. While our techniques to measure the presence and abundance of these microbes has been steadily improving, the analysis of microbiome data is non-trivial. Here, we present a guidebook for the analysis and interpretation of microbiome experiments with a focus on microbiome-gut-brain axis experiments. We give an overview of the types of approaches of microbiome analysis, including caveats and considerations. We emphasize the compositional data analysis (CoDA) paradigm. Further, this guidebook features an extensive and heavily annotated microbiome analysis in R in the supplementary materials, including a demonstration of volatility analysis and functional gut-metabolic and gut-brain module analysis as a resource for new and experienced bioinformaticians alike.