Background Despite diabetes mellitus and periodontal diseases are mutually exclusive, little is known about particular types of bacteria that may have exacerbated the development of diabetics’ periodontal inflammation. The purpose of this study was to compare the salivary microbiomes of individuals with type 2 diabetes (20–40 years old) who had gingivitis or periodontitis to those who did not. Additionally, we evaluated the relationship between the number of periodontopathogens and the amount of nitrate-reducing bacteria in their salivary microbiome. Methods Saliva was collected, DNA was isolated, the entire 16S ribosomal RNA gene was amplified, and sample libraries were prepared in accordance to the Oxford Nanopore MinION Technology procedure. The relative abundance and bacterial diversity in saliva samples that were pooled according to three groups; T2DM patients without periodontal disease (G1), T2DM patients with gingivitis (G2), and T2DM patients with periodontitis (G3), was measured using bioinformatic methods. Additionally, the relationships between the periodontopathic bacteria ( Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, and Fusobacterium spp.) and denitrifying community ( Haemophilus, Neisseria, Rothia, and Veillonella) were assessed. Results The salivary microbiota among people with type 2 diabetes and periodontal disease (gingivitis, G2; periodontitis, G3) showed more …