Impact of optimised sample preparation method on DNA recovery from subgingival plaque in a population with periodontitis

OBJECTIVE(S): This study aimed to evaluate whether an alternate sample preparation method could enhance DNA yield from subgingival plaque samples collected from patients with untreated periodontitis. DESIGN: Fifty-six consecutive participants with untreated periodontitis each provided two subgingival plaque samples from periodontal sites with probing pocket depth (PPD) > 5 mm. In the alternate method (AM), 1.4 mm ceramic beads were added to the sample prior to supernatant removal to protect the microbial pellet, after which samples were processed using a standardized extraction protocol and subjected to 16S rRNA gene sequencing (V3-V4 region). RESULTS: A total of 112 samples were analysed. DNA concentration (ng/µl) was significantly higher in the AM group (23.82 ± 23.31) compared to the standard method (SM) group (13.6 ± 17.07; p < 0.001). The DNA input in 2.5 µl was also significantly greater in the AM group (1156 ± 1139 ng vs. 277.96 ± 273.12 ng; p < 0.001). Shannon diversity was significantly higher in AM than SM (p = 6e-04). No significant differences in DNA yield or microbial diversity were observed between the two periodontal sites within each group. CONCLUSION: The alternate sample preparation method improved DNA concentration compared to standard sample preparation method of sub-gingival plaque analysis collected from patients with untreated periodontitis.