Viome: Making Chronic Illness an Option

Revolutionizing the Functional Health Space!

We recently launched our new functional health practice, this is our first blog article ever as partners, and we felt that a discussion about Viome would be the best way to kick off our new endeavor.  Thanks to Dr. Helen Messier, Chief Medical Officer of Viome, for extending us a private practitioner consult, we now have a much deeper understanding of this wellness assessment and how it compares to other technology.  

Before we delve into the ins and outs of Viome, we would first like to thank you for joining us on our journey in creating Empowered To Heal.  Our mission is to help you empower yourself and unleash your full potential.  Our motivation for this work came from our own journeys with healing from complex, chronic health challenges.  Additionally, we both have our own private practices but decided to join forces as to pool our talents, diversify, and ultimately enhance the scope of our work.  Our goal is to play a part in revolutionizing the functional health space.  Enough about us, now let's delve right into the ins and outs of Viome. 

The Current Status Quo for Gut Testing

Before talking about specific advantages of Viome we first need to touch upon the current status quo in functional-based gut testing, which is PCR (Polymerase Chain Reaction).  PCR technology specifically sequences DNA as a means to identify gut microbes.  As practitioners we have known, respected, and used this technology to assess gut health in our work with clients for a long while now.   We have come to learn, however, that PCR technology, even with as advanced as it is, has some limitations that we feel Viome does not fall short with. These limitations are as follows:

  • DNA sequencing can pick up not only the alive and active microbes, but also dead and transient organisms passing through the GI tract within food particles, water, and air. This can result in many false positive results and unnecessary interventions that can further disrupt the delicate balance of the microbiome.

  • PCR testing is super useful when the goal is to identify specific pathogens that are suspected to be causing issues. The problem comes in, however, in that it looks at specific microbes solely in isolation versus within the context of the complex interactions amongst the entire microbiota. This can result in not providing a comprehensive enough picture from which to form an accurate clinical perspective. For example, some microbes in isolation can absolutely be harmful but yet these same microbes, within the context of the entire microbiome, may actually end up being a benefit in some way. To help illustrate this point Dr. Helen explained that there are specific, potentially pathogenic microbes that produce endotoxins (inflammatory metabolites) that some beneficial microbes consume to make useful by-products such as butyrate. Butyrate is a short-chain fatty acid that intestinal cells utilize as a main energy source. Moreover, bacteria able to synthesize short chain fatty acids such as butyrate have been found to be critical for gastrointestinal homeostasis, and their imbalance has been documented in diseases such like IBD (See: For this reason it is crucial to make sure the presence of potentially harmful microbes are evaluated within the context of the full ecosystem of the microbiome.

  • PCR technology also varies from lab to lab due to varying methods and primers used. This can lead to inconsistent results that create confusion for both practitioners and clients.

  • PCR technology often uses 16S sequencing. This can be problematic because the 16S gene is only a small segment of microbial DNA and can result in a substantial amount of false positives. A recent paper published by Robert C. Edgar pointed out that 16S sequencing can often result in a false positive rate upwards of 55% to 88% (See:

  • Lastly, PCR methodology does not assess the metabolites produced by microbes, which are end results of microbial activity. This can be an issue because microbes are not always in a pathogenic state. Evaluating the metabolites allows one to assess what microbes are doing in the gut, how their activity may be influencing downstream bodily functions, and whether or not they are causing harm.

Viome: New Kid on the Block!

Viome, however, uses meta-transcriptomic technology.  This method sequences all microbial RNA from the microbiome. Viome then matches these sequences to an extensive database of all sequenced organisms, that has been curated to remove false positives.  This technology offers an unprecedented visibility into the eco system living inside all of us.  Meaning, it is able to identify every alive and active microbe (bacteria, parasites, fungus, virus, and mycoplasma), how those microbes are interacting with one another, and the metabolites they are producing. 


It is also important to know that Viome only needs nanogram amounts of RNA to get an accurate picture of what is truly happening within the context of the microbiota.  This gives a much deeper look into what these microbes are doing inside of the gut, not just their presence.   Comparing meta-transcriptomic data with 16S data is like comparing apples to oranges.  It is not applicable.  Furthermore, Viome is constantly developing and continues to make additions to what the report will reveal. 

Soon to come, there will be markers indicating virulence factors as well as how microbes are specifically influencing life-sustaining functions such as detoxification, energy production, neurotransmitter and hormone synthesis, and much more.  Even without these soon-to-come markers, we find that the information provided by a Viome far surpasses any other gut testing on the market today.  

With our deeper understanding of Viome, we feel that meta-transcriptomic sequencing of all RNA (microbial and human) is vastly superior to the technologies we referenced as the status-quo.  To be clear, DNA is a set of genetic instructions that can be identified from both dead and alive organisms.  RNA, on the other hand, is what is produced by the expression of DNA.  RNA is only produced by alive and active organisms whose DNA is being expressed.  As we see it, the main advantages of meta-transcriptomics are as follows:

  • It compensates for transient organisms that can often be detected via PCR but yet are not inhabiting the GI tract or causing issues. This is true because there is simply not enough time for those organisms to produce enough RNA to qualify as relevant.

  • It looks at the entire microbiome and the complex relationship between microbes versus looking at pathogens in isolation. This a plus because possible pathogenic microbes are not always bad and don't always need to be addressed with heavy duty anti-microbial protocols. Obtaining a complete picture allows us to understand the relationships between microbes so that one can make better informed, personalized decisions when it comes to therapeutic interventions.

  • Because Viome has exclusive access to this technology, there is no potential for varying results from different laboratories. This technology was created at the prestigious Los Alamos National Lab, originally designed for national security. Viome is now the sole owner of this technology and uses it as a highly calibrated and customized tool against chronic and age-related conditions.

  • By looking at all the genetic expression and metabolites of alive and active microbes, the potential for false positives that can come with PCR methods has been significantly reduced. Gathering the amount of data that Viome does is actually a constant check and balance on itself. Moreover, for this test to miss a microbe, it would not only have to miss the genetic expression of the microbe but all the metabolites produced as well. The possibility of this happening is extremely slim.

A Window Into Intestinal Permeability and Metabolism

Another HUGE benefit of Viome is that by looking at RNA, we can look at human RNA that is being shed from the gut lining into the stool.  This can serve as a marker of intestinal permeability (aka: leaky gut).  Within Viome results, human RNA is reported as a percentile.  Dr. Helen carefully explained to us that ideally one would want to fall somewhere within 20% - 50% with some leeway for bio-individuality.  Scores above 50% can be indicative of inflammation, significant amounts of intestinal lining shedding, and slow motility due to factors such as pathogenic infections and bacterial dysbiosis.  Results below 20%, on the other hand, can be an indicator of improper cellular turnover within the gut due to poor nutrition and/or an over abundance of biofilms.  These two factors can prevent the proper recovery of intestinal cells.  

Moreover, Viome is NOT just a gut test.  It is also a dynamic metabolic assessment tool.  It allows us to learn how the microbiota and the rest of the body (outside of the GI tract), after digestion and absorption, process and assimilate the nutrients taken in by the foods we eat.  This is achieved via the glucose challenge portion of the test. 

This well-established methodology gives us insight into energy production, blood sugar regulation, and insulin resistance.  This information, combined with the microbiota data, allows Viome to provide the user with the most bio-individualized food list available to the general consumer today.  As clinicians, we can utilize the in-depth microbiota data combined with these bio-individualized food lists to bootstrap our healing protocols with clients.  Furthermore, this allows for much more accurate healing protocols.  

Unprecedented Amount of Data

This level of insight results in an amount of data that far surpasses human capability to synthesize and comprehend.  For this reason, Viome recruits the assistance of deep machine learning AI (artificial intelligence) to make sense of all this data.  The AI utilized by Viome contains all of the microbiome research that has been completed to date and they continue to add more each day.  This means that this AI has evaluated almost every piece of microbiome research that humans have conducted already.  It also learns by analyzing its own internal data that it gathers with each and every sample submitted for analysis.  Viome's model of yearly testing with optional retesting for reduced rates within the same year allows the AI to analyze multiple samples from you overtime.  This is helpful in identifying long-term patterns and trends within your gut health and metabolism.  Seeing patterns ahead of time awards us all the potential to proactively address dysfunction and metabolic chaos® long before it turns into dis-ease states.  

To wrap up all that has presented into a succinct list, Viome's benefits can be highlighted by the following:

  • Comprehensive look at every alive and active microbe and its metabolites

  • Identification of microbes to the strain level and the activity of those microbes

  • Soon-to-come virulence factors and analysis of how metabolites are influencing all bodily functions

  • A self-checking and continually evolving methodology that uses deep machine AI learning

  • Serves as an assessment of intestinal permeability and integrity of the epithelial lining of the gut

  • Bio-individualized food lists to help optimize the microbiome, boost overall health and wellness, and bootstrap healing protocols

  • More accurate and targeted healing protocols

  • Significant reduction in the potential for false positive results

  • Means to track efficacy of probiotic use, diet, and other health-promoting interventions

  • Available to everyone without the need for an order from a doctor

Viome is a wellness assessment versus a medical diagnostic test.  This holds true so they can provide the service to everyone without the need for a medical doctor's orders or the massive overhead costs of FDA approval.  Having said this, the data presented on the Viome report does require the ability to understand the nuances in relation to a person's health history and current challenges.  This is where the role of qualified, functional practitioner comes in.  For instance, Viome does not provide gut pathogen eradication protocols and accompanying therapeutic support as that is something that should always be overseen and guided by a qualified practitioner.  

In our practice, we offer a wide array of services that can assist our clients with understanding their Viome results as well as implementing targeted healing protocols. If you are interested in a more comprehensive approach, please see our "Work With Us" tab to review all options.