VMG II transport medium stabilises oral microbiome samples for Next-Generation Sequencing

Abstract

Next-Generation Sequencing is providing insights into the critical role of the oral microbiome in dental diseases. Application of this method can require the collection of dental plaque from large cohorts in field-type conditions, which necessitates a transport medium to preserve the microbiome composition. We evaluated the use of two transport media, VMG II and RNAprotect® Bacteria Reagent (Qiagen), for room temperature storage of dental plaque. VMG II has not previously been assessed for suitability to store microbiome samples intended for deep sequencing. We compared the microbiome composition of dental plaque (total n=23) stored in either VMG II or RNAprotect Bacteria at room temperature with immediately-frozen plaque. 454 sequencing of 16S gene amplicons was used to assess the plaque microbial composition. While the bacterial diversity recovered was similar between storage conditions (p>0.1), the abundance of bacteria was influenced by storage environment. Dental plaque stored in VMG II was most similar to immediately-frozen material, with only one of the 324 bacterial species being differentially abundant (Neisseria, p<0.001). In comparison, dental plaque stored in RNAprotect Bacteria had 24 differentially abundant species compared with the immediately-frozen samples and a significantly different phylogenetic structure (p<0.01). We have identified VMG II as a new transport medium for room temperature storage of dental plaque samples being subject to Next-Generation Sequencing that stabilises oral microbial DNA makeup.

Keywords: Next-Generation Sequencing; Oral microbiome; Storage; VMG II.