The gut microbiome has been proposed to play a causal role in obesity. Here, we review the historical context for this hypothesis, highlight recent key findings, and critically discuss issues central to further progress in the field, including the central epistemological problem for the field: how to define causality in the relationship between microbiota and obesity phenotypes. Definition of such will be critical for the field to move forward.
Keywords: Innate immunity; Microbiome; Microbiota; Non-alcoholic fatty liver disease; Obesity; Segmented filamentous bacteria; Type 2 diabetes.