CosmosID Reveals the Microbes Inside Your Mouth

Dr Bonnie 360 uses CosmosID to reveal the microbes in her mouth and sequence her oral microbiome.

Like the shoemaker with badly repaired shoes, I am a dentist with advanced periodontal disease. My research on the oral microbiome taught me to to ask if oral microbes played a part in my poor oral health. CosmosID reveals the microbes (bacteria and fungi) inside my mouth. Their product can do the same for your mouth too.

For many years I have struggled with serious gum disease despite consistent brushing, flossing, and rinsing. I have tried all sorts of toothbrushes, a myriad of toothpastes and many rinses, all to no avail. I have consulted “dental” experts, “oral pathology” experts and “periodontal disease” experts, but nothing helped.

A new understanding of the oral microbiome is shaping how we think about caries, periodontal and other oral diseases. Oral disease may be a factor in diseases far removed from the mouth. These include heart and lung disease, cancer, Alzheimer’s and some autoimmune diseases. We dentists used to believe that oral diseases were caused by a small number of specific pathogens. However, we now think of the oral microbiome as an ecosystem of bacterial, fungal, and viral communities in oral microbiome equilibrium.

What if there was a way to reveal the microbes inside our mouths?

Screen Shot 2019-06-18 at 12.25.36 PM
Different ‘omics techniques used to characterize microbial communities.

Advances in ‘omics studies (metabolomics, transcriptomics, genomics, etc.) have provided researchers with new technologies to characterize microbiomes. Having already done gut microbiome profiling for my “leaky” gut, I was curious if there were any companies out there that could do the same for my oral microbiome or “leaky” mouth.

CosmosID reveals the microbes in your mouth with NGS

I had previously tried an oral DNA sampling test. However, that company’s PCR technology is now outdated. Newer technologies such as the Next Generation Sequencing (NGS) are offered by CosmosID. I decided to try CosmosID after a recommendation by a good friend and respected periodontist, Dr. Alvin Danenberg.

The instructions were straightforward. I swabbed the inside of my cheek and mixed the swab into the blue vial of clear liquid. The whole process took about 3 minutes. Unlike gut microbiome testing, which requires a fecal sample for testing (yuck), the oral microbiome test was quick and painless. The only reservation I had was whether a simple cheek swab could provide any insight into my oral microbiome. Nevertheless, I sent the vials back to the lab and waited patiently to receive my results. Would CosmosID reveal the microbes living in my mouth?

My comprehensive oral microbiome

To my pleasant surprise, the results from the CosmosID test were much more comprehensive than my previous PCR tests. The test identified 261 strains of bacteria, 6 species of fungi, and 23 viruses within my oral microbiome. I was impressed to see the test included the often overlooked, yet abundant, fungal and viral components in my oral cavity.

Example of fungal and bacteria species in oral cavity

You can decide, using the “Bacteria” drop down, to view information on fungi, viruses, protists, and even antibacterial resistant bacteria. CosmosID databases are organized phylogenetically and contain hundreds of millions of marker gene sequences.

The markers represent both coding and non-coding sequences uniquely identified by taxon and/or distinct nodes of phylogenetic trees. Cosmos created the tree structure based on genomic relatedness of organisms rather than predetermined taxonomy based on phenotype. This allows CosmosID to have a high degree of accuracy in identifying microorganisms based on their DNA in metagenomic samples. It also helps identify the closest match to genomes that do not have strain level references in the database (if, for example, they have never been sequenced before).


Visual diagrams reveal microbe relationships

Since the taxonomic information above can be confusing, CosmosID also offers visual diagrams. I was most amazed by this aspect of CosmosID. That is, I could organize so many bacteria, fungi, and viruses into colorful, visually appealing, and comprehensive diagrams.

Such as the diagrams shown below:

Example of COSMOS ID Test Results

In order to get actionable information, simply listing what is in my oral microbiome is not enough. I needed to compare my sample to a healthy cohort. The platform can compare within and between large cohorts. However, the size of the healthy comparison cohort is limited, so that we must take the results with some caution.

With the help of CosmosID’s chief science officer, Dr. Nur A Hasan, I compared my oral microbiome data to datasets (n=34) derived from buccal mucosa, saliva, tongue, throat, supra- and subgingival plaque of healthy individuals. We noticed that I have a higher relative abundance of Streptococcus mutans. This species is associated with oral diseases such as dental caries and gum disease. I also contained high ratios of Actinomyces timonensis, viral Streptococcus phages, and fungal Nosema bombycis. Additionally, the Shannon species alpha diversity index of my sample is similar to that of my buccal mucosa, but lower than saliva and higher than supragingival plaque (see figure below). The Shannon index measures the number of species in a sample but scales them based on the evenness of the community.  

Alpha Diversity from COSMOS ID

More technical analyses

A Principal Coordinate analysis is based on beta diversity (i.e., diversity dissimilarities based on microbial composition and abundance). My samples (red circles below) revealed that my oral microbiome didn’t cluster with any of the buccal mucosa, saliva, tongue, throat, supra- and subgingival plaque samples, as they did within each sample type. This also makes sense since the sample I sent in was merely a swab of the inside of my cheek.

Principle Coordinate Analysis from COSMOS ID

Due to many genetic, immune regulatory, and environmental factors, the oral microbiome composition alters on a daily, even hourly, basis. So, it is hard to say if the differences in my oral microbiome contribute to my periodontal disease. However, we could harness the oral microbial profiling specificity for future salivary diagnostics and biomarker testing for systemic diseases.

CosmosID offers a new way of reveling the microbes in our mouths, that is, our oral microbiomes. With such tools we can usher in a new era of oral well-being. Perhaps resolving leaky mouth is key to cultivating better overall systemic health!

Curious to learn more about the mouth? Want to learn more ways to maintain microbial balance in the mouth?

Check out our ebook on the oral microbiome!

Have you ever tried a microbiome testing company? Let us know in the comments below!

Written by: Bonnie Feldman, DDS, MBA, Hailey Motooka, BS, Sarah Hinton


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