BackgroundOur aim in this study was to better understand the causality of metformin and gut microbiome in the treatment of type 2 diabetes (T2D). MethodsThis study was conducted on individuals with newly diagnosed and treatment-naive T2D. We used 16S rRNA sequencing to assess the effect of metformin on composition and diversity of the gut microbiota. We also compared the differences in relative abundance of gut microbiome at the genus level in patients with treatment-naive T2D before and after 2 months of metformin treatment. Spearman’s rank correlation coefficient analysis was used to identify genus abundance in relation to blood glucose and related factors. ResultsMetformin significantly reduced blood glucose and levels of the related factors in treatment-naive individuals with T2D after 2 months of treatment. The 16S rRNA sequencing showed that metformin treatment altered composition and diversity of gut microbiome. Megamonas and Klebsiella in the T2D groups were significantly higher compared with the control group. Metformin treatment caused a significant reduction in Megamonas and Klebsiella. Spearman’s rank correlation coefficient analysis showed a significant positive correlation between Megamonas and blood glucose, glycated hemoglobin (A1C), serum fructosamine and alanine aminotranferase (ALT). Klebsiella showed a significant positive correlation between A1C and ALT. ConclusionMetformin reduces blood glucose in T2D by interacting with different gut bacteria, possibly Megamonas and Klebsiella pneumoniae.