Abstract Type 1 diabetes is an autoimmune disease that occurs spontaneously in non-obese diabetic mice, and the gut microbiota has been implicated in disease manifestation. The simple dietary variable, acidified drinking water, exaggerated or reduced diabetes incidence in some studies but not in our investigation. To elucidate the underlying basis of these discrepancies, we profiled the gut microbiome of diabetic mice that were transitioned from acid to neutral water. Quantitative polymerase reactions using primers specific for 16S rRNA genes validated the relative abundance of bacterial taxa longitudinally from 6 weeks of age to adults that overtly manifested diabetes. Among the 15 representative bacterial groups examined, only Lactobacillussp. remained low throughout the life of the mouse. The frequencies of the Firmicutes Ruminococcaceaeand the Bactereoidetesphylum members Anaerophagasp. and Paludibactersp. increased during maturation. The level of mucin-degrading Akkermansia muciniphila, implicated in diabetes protection remained low throughout the life of the mouse. The segmented filamentous bacteria could be detected in the gut of young mice and remained abundant in adult mice that developed full blown diabetes. The drinking water’s pH neither impacted the relative abundance of these bacterial taxa investigated herein nor diabetes incidence. Thus, the combination of microbiome profiling and quantitative real-time polymerase chain reactions facilitated validation of the signature gut bacterial taxa in autoimmune diabetes, which remain unperturbed by the pH of the drinking water. Supported by the University of Illinois at Chicago, Chicago.