  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
microbiome-gut-brain axis. While our techniques to measure the presence and
abundance of these microbes have been steadily improving, the analysis of
microbiome data is non-trivial.
  Here, we present a perspective on the concepts and foundations of data
analysis and interpretation of microbiome experiments with a focus on the
microbiome-gut-brain axis domain. We give an overview of foundational
considerations prior to commencing analysis alongside the core microbiome
analysis approaches of alpha diversity, beta diversity, differential feature
abundance and functional inference. We emphasize the compositional data
analysis (CoDA) paradigm.
  Further, this perspective features an extensive and heavily annotated
microbiome analysis in R in the supplementary materials, as a resource for new
and experienced bioinformaticians alike.
