Microbial DNA identification from saliva – comparison of methods

Introduction: Microbial DNA can be extracted for example from samples of plaque, saliva, gingival liquid, mucosa, or teeth. In principle, all such DNA can be identified with the help of PCR. Objectives: This investigation aimed to design a method of DNA template preparation, and to compare direct DNA extraction and identification from saliva samples with the indirect approach of first culturing the samples. Methods: After ethical approval, Streptococcus mutans and S. sobrinus were identified directly (no bacterial culture, n = 34) and indirectly (with culture, n = 9) using DNA extracted from stimulated saliva samples. The samples were taken from 34 otherwise healthy adolescent dental patients, for whom also the caries status (DMF-T) was evaluated. DNA was extracted using the Wizard Genomic kit, measured with a spectrophotometer(A₂₆₀/₂₈₀), and identified with the help of PCR. T-test was used for statistical evaluation of the results. Results: Direct extraction resulted in higher concentration of DNA (571 ± 381 ng/µl) than extraction from cultured samples (439 ± 259 ng/µl). However, direct extraction shows a lower DNA purity (1.49 ± 0.23 ng/µl) than the cultured samples (2.02 ± 0.09 ng/µl). Conclusion: The DNA concentration is higher for direct DNA extraction than for extraction from cultured samples. In contrast, the purity of directly extracted DNA is lower than that from cultured samples. Nevertheless, both methods show satisfactory performance in microbial identification.