Alterations in the gut microbiome have increasingly been implicated in driving obesity and its associated diseases, but underlying mechanisms remain poorly defined. Herein, in addition to reviewing the field, we hypothesize that a highly significant causative factor of such inflammatory disease-associated microbiome alterations is a more aggressive microbiota that encroaches upon its host, with components having high potential to activate host pro-inflammatory gene expression in a manner that drives metabolic disease. We further hypothesize that a range of societal changes, including use of antibiotics and increasing consumption of food additives, have provoked such microbiota aggression and, consequently, may be contributing factors to the increased incidence of obesity and its associated diseases.