Aims: This pilot study aimed to describe the majority and minority microbiota of saliva from individuals with advanced periodontitis, with or without type 2 diabetes mellitus (T2D), correlating the relative abundance of microorganisms with clinical parameters. Material/Methods: Six individuals diagnosed with periodontitis were included and classified according to their diagnosis of T2D. Salivary pH, number of teeth with active caries lesions, number of remaining teeth, periodontal and glycemic parameters were evaluated. V4 region amplicons of the 16S rRNA from salivary DNA were sequenced at Ion PGM. Amplicon sequence variants (ASVs) were compared according to the clinical parameters. Results: Correlation showed eight low-abundant bacteria significantly correlated with co-variables, either positively or negatively. The periodontitis-associated bacteria followed the increasing pH and number of remaining teeth. Conclusions: This survey provided potential minority microbiota correlations with clinical parameters, such as number of remaining teeth, FBG, and salivary pH. The ubiquity of some low abundant microorganisms in individuals with advanced periodontitis, exposed or not to type 2 DM, can reveal microbial signatures not yet explored.