The aim of the present pilot study was deciphering bacterial community changes in Zucker diabetic fatty rats (ZDF rats), a model of type 2 diabetes. Recent studies unmasked that the status of gastrointestinal tract microbiota has a marked impact on nutrition-related syndromes such as obesity and type-2 diabetes (T2D). In this study, samples taken from the gastrointestinal tracts (GI tracts) of ZDF and their lean littermates (ZL rats) were subjected to 16S rRNA gene sequence-based analysis to examine the characteristic bacterial communities, including those located in the stomach, duodenum, jejunum, ileum, cecum and feces. Results revealed that the Firmicutes/Bacteroidetes ratio was increased and greater numbers of Lactobacillus were detected along GI tracts in ZDF rats compared to ZL rats. In conclusion, this work is the first study to systematically characterize bacterial communities along ZDF rat GI tract and provides substantial evidence supporting a prospective strategy to alter the GI microbial communities improving obesity and T2D.