White spot lesions (WSLs) are common enamel infectious diseases in fixed orthodontic treatment, which might attribute to the dysbiosis of oral microbiome. However, the correlation of with oral bacteriome in WSLs still remains unrevealed. This study investigated the carriage of and how it shaped the bacterial community in disease or healthy supragingival plaque, to explore the potential role of interkingdom interaction in orthodontic WSLs. In this study, 31 patients with WSLs (WSLs) and 23 healthy patients (Health) undergoing fixed orthodontic treatment were enrolled. The supragingival microbiota in both groups were determined using 16S rRNA gene sequencing. Colonization and abundance of in the plaque were determined culture-dependent and -independent methods. Among WSLs patients, the correlation of and bacteriome was analyzed under QIIME2-based bioinformatics and Spearman's correlation coefficient. The raw reads were deposited into the NCBI Sequence Read Archive (SRA) database (Accession Number: SRP404186). Significant differences in microbial diversity as well as composition were observed between WSLs and Health groups. remarkably enriched in the WSLs group, while and significantly enriched in the Health group. In addition, 45% of WSLs patients were carriers but none in patients without WSLs. Among all WSLs patients, beta diversity and microbial composition were distinguished between carriers and non-carriers. In carriers, and significantly enriched whereas significantly depleted. The abundance of was positively associated with bacteria such as , while the negative correlation was detected between and several bacteria such as and Our study elucidated the distinguished supragingival plaque microbiome between orthodontic patients with and without WSLs. frequently existed and enriched in orthodontic derived WSLs. The carriage of shape plaque bacterial community in demineralized lesions and might play roles in WSLs pathogenesis.