Abstract: Objective To establish a systematic method for isolation and identification of aerobic and facultative anaerobic
bacteria in the oral cavity. Methods Samples of the saliva, dental plaque and periapical granulation tissue were collected from
20 subjects with healthy oral condition and from 8 patients with different oral diseases. The bacteria in the samples were
identified by morphological identification, VITEK automatic microorganism identification and 16s rRNA gene sequencing.
Results VITEK automatic microorganism identification and 16s rRNA gene sequencing showed an agreement rate of 22.39% in
identifying the bacteria in the samples. We identified altogether 63 bacterial genus (175 species), among which Streptococcus,
Actinomyces and Staphylococcus were the most common bacterial genus, and Streptococcus anginosus, Actinomyces oris,
Streptococcus mutans and Streptococcus mitis were the most common species. Streptococcus anginosus was commonly found in
patients with chronic periapical periodontitis. Streptococcus intermedius and Staphylococcus aureus were common in patients with
radiation caries, and in patients with rampant caries, Streptococcus mutans was found at considerably higher rate than other
species. Conclusion Aerobic and facultative anaerobic bacteria are commonly found in the oral cavity, and most of them are
gram-positive. 16s rRNA gene sequencing is more accurate than VITEK automatic microorganism identification in identifying
the bacteria.