BackgroundKawasaki disease (KD) is a multi-systemic vasculitis that primarily affects children and has an unknown cause. Although an increasing number of studies linking the gut microbiota with KD, the unchallengeable etiology of KD is not available.MethodsHere, we obtained fecal and oral samples from KD patients and healthy controls, and then we use high-throughput sequencing to examine the diversity and composition of microbiota.ResultsResults showed that both in the gut and oral microbiota, the diversity of KD patients was significantly lower than that of the healthy controls. In the gut microbiota, a higher abundance ofEnterococcus(40.12%vsless than 0.1%),Bifidobacterium(20.71%vs3.06%),Escherichia-Shigella(17.56%vs0.61%),Streptococcus(5.97%vs0.11%) andBlautia(4.69%vs0.1%) was observed in the KD patients, and enrichment ofEnterococcusin the patients was observed. In terms of oral microbiota, the prevalence ofStreptococcus(21.99%vs0.1%),Rothia(3.02%vs0.1%), andEscherichia-Shigella(0.68%vs0.0%) were significantly higher in the KD patients, with the enrichment ofStreptococcusandEscherichia-Shigella. Additionally, significant differences in microbial community function between KD patients and healthy controls in the fecal samples were also observed, which will affect the colonization and reproduction of gut microbiota.ConclusionsThese results suggested that the dysbiosis of gut and oral microbiota are both related to KD pathogenesis, of which, the prevalence ofEnterococcusin the gut and higher abundance ofStreptococcusandEscherichia-Shigellain the oral cavity will be a potential biomarker of the KD. Overall, this study not only confirms that the disturbance of gut microbiota is a causative trigger of KD but also provides new insight into the oral microbiota involved in KD pathogenesis.