Bugs as features (part 2): a perspective on enriching microbiome–gut–brain axis analyses

The microbiome–gut–brain axis field is multidisciplinary, benefiting from the expertise of microbiology, ecology, psychiatry, computational biology, and epidemiology among other disciplines. As the field matures and moves beyond a basic demonstration of its relevance, it is critical that study design and analyses are robust and foster reproducibility. In this companion piece to Bugs as features (part 1), we present techniques from adjacent and disparate fields to enrich and inform the analysis of microbiome–gut–brain axis data. Emerging techniques built specifically for the microbiome–gut–brain axis are also demonstrated. All of these methods are contextualized to inform several common challenges: how do we establish causality; how can we integrate data from multiple ’omics techniques; how might we account for the dynamicism of host–microbiome interactions? This perspective is offered to experienced and emerging microbiome scientists alike to assist with these questions and others at the study conception, design, analysis, and interpretation stages of research.