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This study analyzed the alteration of oral microbial composition in healthy subjects after using dextranase-containing mouthwash (DMW; Mouthwash formulation I) and dextranase-and-nisin-containing mouthwash (DNMW; Mouthwash formulation II). Eighteen participants were recruited and were randomly allocated to two groups: G1 (DMW user; n = 8) and G2 (DNMW user; n = 10). The subjects were instructed to use the provided mouthwash regularly twice a day for 30 days. The bleeding on probing (BOP), plaque index (PI), probing depth (PBD), and gingival index (GI) were analyzed, and saliva samples were collected before (day 0) and after (day 30) the use of mouthwashes. The saliva metagenomic DNA was extracted and sequenced (next-generation sequencing, Miseq paired-end Illumina 2 × 250 bp platform). The oral microbial community in the pre-and post-treated samples were annotated using QIIME 2™. The results showed the PI and PBD values were significantly reduced in G2 samples. The BOP and GI values of both groups were not significantly altered. The post-treated samples of both groups yielded a reduced amount of microbial DNA. The computed phylogenetic diversity, species richness, and evenness were reduced significantly in the post-treated samples of G2 compared to the post-treated G1 samples. The mouthwash formulations also supported some pathogens’ growth, which indicated that formulations required further improvement. The study needs further experiments to conclude the results. The study suggested that the improved DNMW could be an adjuvant product to improve oral hygiene.