Evaluation of a nucleic acid preservation protocol for microbiome studies involving samples from the oral cavity

Purpose

The accuracy of oral microbiome research depends significantly on specimen sampling protocols, as well as their storage and preservation. Traditional methods, such as freezing, may not only involve logistical hurdles but can also impact the quality of microbial data, leading to difficulties in the comparability between different studies. This study evaluates the effectiveness of the room temperature nucleic acid preservation protocol using DNA/RNA Shield buffer as compared to standard freezing in preserving oral microbial communities over the course of 7 days.

Results

Comparative analyses based on 16S rRNA gene sequencing revealed a high overall consistency between the microbiome data retrieved by both preservation strategies. In terms of DNA yield, qPCR analysis showed a significant increase in bacterial DNA recovered from tongue swabs, dental pockets and saliva samples when using DNA/RNA Shield. In the taxonomic analyses, the Shield buffer preserved a higher abundance of Veillonella as compared to freezing. However, the compositional data was highly comparable between both protocols for all other taxonomic groups. While no major differences in microbial diversity were observed between both preservation methods for most samples, saliva samples stored in DNA/RNA Shield exhibited significantly higher diversity. Both preservation methods performed in a highly comparable manner in their ability to retrieve consistent biological readouts, such as site-specificity and health status.

Conclusion

Storing oral samples at room temperature in DNA/RNA Shield buffer provides a reliable and efficient alternative to freezing for preserving microbiome samples. Furthermore, it may enhance DNA yield while preserving microbial diversity in the samples.