Aims Type 2 diabetes mellitus (T 2 DM) has a rising prevalence and gut microbiota involvement is increasingly recognized. Diabetic nephropathy (DN) is a major complication of T 2 DM. The aim of the study was to understand the gut–kidney axis by an analysis of gut microbiota composition among biopsy-proven DN, T 2 DM without kidney disease, and healthy control. Methods Fecal samples were collected from 14 DNs, 14 age/gender-matched T 2 DMs without renal diseases (DM), 14 age and gender-matched healthy controls (HC) and household contacts (HH) of DM group. The microbiota composition was analyzed by 16sRNA microbial profiling approach. Results Substantial differences were found in the richness of gut microbiota and the variation of bacteria population in DM compared to HC, and DN compared to DM, respectively. DM could be accurately distinguished from age/gender-matched healthy controls by the variable of genus g_Prevotella_9 (AUC = 0.9), and DN patients could be accurately distinguished from age/gender-matched DM by the variables of two genera ( g_Escherichia-Shigella and g_Prevotella_9 , AUC = 0.86). The microbiota composition of HH group was close to that of HC group, and was different from DM group. Under the same diet, DM could be more accurately detected by the same genus ( g_Prevotella_9 , AUC = 0.92). Conclusion Gut microbiota composition was explored to be related to the occurrence of biopsy-proven DN from DM. DM could be distinguished from HC by detecting g_Prevotella_9 level in feces, while DN was different from DM by the variables of g_Escherichia-Shigella and g_Prevotella_9 , which potentially contributed to the physiopathological diagnosis of DN from DM.