Introduction Recently, gut microbiota has been described as being involved in the health and diseases of the host, and together with diet and drugs may influence metabolic health. Yet, there is still no answer which type of treatment plays the most important role in the interplay of gut microbiota and type of treatment for type 2 diabetes (T2DM). An attempt was made to answer the question of which factors have the most significant impact on the intestinal microbiome in the context of metformin or metformin+insulin use in treatment of the patients with T2DM. Thus the aim of the study was to compare the gut microbiome profiles of patients with T2DM and two of the most traditional treatment methods. Methods T2DM patients treated by metformin (Met) and metformin+insulin (Met+Ins), with the treatment duration of 5–10 years were enrolled. Biochemically blood glucose and glycated hemoglobin (HbA1c), lipids and kidney function were investigated and the quantitative and qualitative examination of the fecal intestinal flora were performed through the next-generation sequencing. Results There were no significant differences in the study of the gut microbiome: the dominant bacterial phyla were Firmicutes and Verrucomicrobia , while Bacteroidetes and Proteobacteria shared smaller proportions in both groups. However, the group Met+Ins had worse metabolic control in terms of blood glucose and HbA1c in comparison with the Met group. Conclusion As there are no differences in gut microbiome in T2DM patients treated with metformin only or metformin plus insulin, adding insulin in the treatment of T2DM may delay late diabetic complications development.

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