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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
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VMG II transport medium stabilises oral microbiome samples for Next-Generation Sequencing
Christina J Adler1, Abbe White2, Michelle Bockmann2
1Institute of Dental Research, Faculty of Dentistry, The University of Sydney, New South Wales 2145, Australia; The Westmead Millennium Institute for Medical Research, The University of Sydney, New South Wales 2145, Australia.
Journal of Microbiological Methods
|November 21, 2017
Summary
VMG II is a new transport medium for preserving oral microbiome samples at room temperature. This method is suitable for dental plaque storage for Next-Generation Sequencing, maintaining microbial DNA stability.
Area of Science:
- Microbiology
- Genomics
- Dental Science
Background:
- Next-Generation Sequencing (NGS) reveals the oral microbiome's role in dental diseases.
- Field collection of dental plaque requires stable transport media for microbiome analysis.
- Previous assessments of transport media for NGS-based microbiome studies are limited.
Purpose of the Study:
- To evaluate VMG II and RNAprotect® Bacteria Reagent for room temperature storage of dental plaque.
- To compare their efficacy in preserving oral microbiome composition for NGS.
- To identify a suitable transport medium for large-scale field studies.
Main Methods:
- Dental plaque samples (n=23) were stored in VMG II, RNAprotect® Bacteria, or immediately frozen.
- Microbiome composition was analyzed using 454 sequencing of 16S gene amplicons.
- Bacterial diversity, abundance, and phylogenetic structure were compared across storage conditions.
Main Results:
- Bacterial diversity was similar across all storage conditions (p>0.1).
- VMG II storage showed high similarity to immediately-frozen samples, with only one differentially abundant species (Neisseria, p<0.001).
- RNAprotect® Bacteria resulted in 24 differentially abundant species and significantly different phylogenetic structure (p<0.01) compared to frozen samples.
Conclusions:
- VMG II is a suitable transport medium for room temperature storage of dental plaque for NGS.
- VMG II effectively stabilizes oral microbial DNA, preserving microbiome composition.
- This finding supports the use of VMG II in large cohort field studies of the oral microbiome.
