The incidence of type 1 diabetes (T1D), as with several other autoimmune diseases and conditions, began to notably rise in the latter half of the last century. Most cases of T1D are not solely attributable to genetics and therefore, environmental influences are proposed to account for the difference. Humans live today in general under much more hygienic conditions than their ancestors. Although human enteroviruses (HEV) have been strongly implicated as causative environmental agents of T1D, recent work has shown that the bacterial genera in the gut of diabetics compared with non-diabetics, can vary significantly. Here, we consider these data in light of our non-hygienic human past in order to discuss a possible relationship between the resident bacterial biome and acute infectious events by HEV, suggesting how this may have influenced T1D incidences in the past and the risk for developing T1D today.