BackgroundAlthough recent studies have indicated that gut microbiome dysbiosis was significantly associated with the onset of type 2 diabetes mellitus (T2DM), information on the role of blood microbiome in T2DM development is scarce.MethodsFifty incident T2DM cases and 100 matched non‐T2DM controls were selected from a prospective cohort study of “135.” The composition of the blood microbiome was characterized using bacterial 16S ribosomal RNA (16S rRNA) gene sequencing from pre‐diagnostic blood sample. The amplicons were normalized, pooled, and sequenced on the Illumina MiSeq instrument using a MiSeq Reagent Kit PE300 v3 kit.ResultsTotally, 3 000 391 and 6 244 227 high‐quality sequences were obtained from T2DM patients and non‐T2DM controls, respectively. The mean diversity of the blood microbiome (Simpson, Chao1 and Shannon indices) was not different between two groups at baseline. At genus level, the Aquabacterium, Xanthomonas, and Pseudonocardia were presented with lower abundance, while Actinotalea, Alishewanella, Sediminibacterium, and Pseudoclavibacter were presented with higher abundance among T2DM cases compared to those in non‐T2DM controls. As the results shown, participants carried the genus Bacteroides in blood were significantly associated with a decreased risk for T2DM development, with 74% vs 88% (adjusted OR: 0.367, 95% CI: 0.151‐0.894). However, participants carried the genus Sediminibacterium have an increased risk for T2DM, with adjusted OR (95% CI) being 14.098 (1.358, 146.330).ConclusionsBlood microbiome may play an etiology role in the development of T2DM. These findings would be useful to develop microbiota‐based strategies for T2DM prevention and control.