The oral and vaginal cavities of the human body each contain a distinct collection of microbial communities.1 Furthermore, the oral microbiome can be further subdivided into gum/plaque or tongue, as each can host a unique collection of microbial species. As seen with all human microbiomes, these microbial communities are dynamic and can vary between individuals.2,3 From various research studies, the microbial compositions of both the oral and vaginal cavities have been correlated with several diseases and health states.4,5
To accurately study the human oral and vaginal microbiomes as close to their in vivo state as possible, appropriate sample collection and stabilization is needed. In our published white paper, DNA Genotek Inc. researchers validated 3 of their offered microbial collection devices for the study of the human vaginal and oral microbiomes (i.e., gum/plaque and tongue).
To collect the required microbiome samples, three swab-based DNA Genotek devices were used; OMNIgene™•ORAL devices (OMR-110 and OMR-120) were used to collect oral samples (gum/plaque and tongue, respectively) while the OMNIgene™•VAGINAL device (OMR-130) was used to collect vaginal samples. A significant advantage of these specific OMNIgene™ devices is that each can stabilize both DNA and RNA for downstream assays.
From their studies, the DNA Genotek researchers tested the OMNIgene™•ORAL (OMR-110 and OMR-120) and OMNIgene™•VAGINAL (OMR-130) devices on two parameters:
If the devices could stabilize microbial nucleic acids (both DNA and RNA) in fluctuating shipping temperatures and while stored at room temperature; and
If the bacterial profiles attained from samples collected from the devices remained stable under the same aforementioned transport and storage conditions.
To assess nucleic acid stability following storage at room temperature or after shipping at ambient temperature, gum/plaque and tongue samples were collected by 20 healthy individuals with OMNIgene™•ORAL devices (OMR-110 for gum/plaque microbial samples and OMR-120 for tongue microbial samples). Freeze-thaw cycles (-20°C to +30°C) were used to stimulate the fluctuating temperature conditions that can occur during shipping at ambient temperature. For the control storage condition, samples were stored at -80°C. Full details of the experimental setup can be found here. In summary, both devices demonstrated that DNA and RNA integrity was maintained when samples were kept at room temperature for up to 30 days and after shipping at ambient temperature (simulated by 3 freeze-thaw cycles).
Using the extracted nucleic acids, the bacterial profiles across different post-collection time points were generated to assess the preservation of bacterial profiles during 30-day storage at room temperature or following shipping at ambient temperature (again, simulated by multiple freeze-thaw cycles). Similar taxonomic profiles between samples were observed at the various time points, suggesting both OMNIgene™•ORAL devices capture and maintain microbial profiles during both tested conditions.
Following the same study design, the OMNIgene™•VAGINAL device (OMR-130) was used to collect paired vaginal samples from 20 healthy individuals. From these samples, the extracted DNA and RNA were assessed in terms of stability following storage at room temperature or after shipping at ambient temperature (simulated by multiple freeze-thaw cycles, as done previously). Once again, the extracted DNA and RNA were also used to study the similarity between the generated bacterial profiles at various time points.
As observed with OMNIgene™•ORAL devices, DNA and RNA integrity and bacterial taxonomic profiles were similarly maintained when samples were collected with the OMNIgene™•VAGINAL device, suggesting the OMNIgene™•VAGINAL device is capable of accurately preserving vaginal microbial nucleic acids and profiles from collected samples.
To further support their simulated tests, the DNA Genotek researchers also tested the performance of the OMNIgene™•ORAL and OMNIgene™•VAGINAL devices in a real-life sample shipping and laboratory processing condition. In this scenario, real samples were collected from volunteers in Ottawa, Canada and then shipped at ambient temperature to Diversigen—a subsidiary of OraSure Technologies Inc. and a sister company to DNA Genotek—located in Minneapolis, U.S. The collected samples were analyzed using Diversigen’s metagenomic sequencing services. To read about the specific findings from the real-life study, see the white paper here. The key takeaways from the white paper can be summarized as follows:
These devices can preserve high-quality microbial nucleic acids (both DNA and RNA) during both shipping at ambient temperature and extended storage at room temperature.
OMNIgene™•ORAL (OMR-110, OMR-120) and OMNIgene™•VAGINAL (OMR-130) devices maintain bacterial profile stability of samples during both shipping at ambient temperature and storage at room temperature for up to 30 days. The devices maintain neutral microbial profile of samples without introducing detectable bias.
OMNIgene™•ORAL (OMR-110, OMR-120) and OMNIgene™•VAGINAL (OMR-130) devices are validated tools for microbiome studies with the ability to accurately capture and stabilize complex microbial profiles from point of collection and onward.
To learn more about the OMNIgene™•ORAL and OMNIgene™•VAGINAL devices and how they can benefit your research workflow, send us an email at info@dnagenotek.com. We welcome interested parties to test out the devices for themselves; request a free trial today by clicking the button below.
References
1. Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature. doi: 10.1038/nature11234.
2. Lira-Junior R, Åkerman S, Klinge B, Boström EA, Gustafsson A. (2018). Salivary microbial profiles in relation to age, periodontal, and systemic diseases. PLoS One. doi: 10.1371/journal.pone.0189374.
3. Huang B, Fettweis JM, Brooks JP, Jefferson KK, Buck GA. (2014). The changing landscape of the vaginal microbiome. Clin Lab Med. doi: 10.1016/j.cll.2014.08.006.
4. Graves DT, Corrêa JD, Silva TA. (2019). The oral microbiota is modified by systemic diseases. J Dent Res. doi: 10.1177/0022034518805739.
5. White BA, Creedon DJ, Nelson KE, Wilson BA. (2011). The vaginal microbiome in health and disease. Trends Endocrinol Metab. doi: 10.1016/j.tem.2011.06.001.