During our conversation, Naveen and I discuss what would happen if you could create a digital scan of your body at home to understand what your cells are actually doing on a molecular level, and then receive a nutrition plan of exactly which “healthy” foods to eat more of, minimize, or completely avoid to decrease inflammation, improve recovery, and optimize your cells.
This is precisely what Naveen’s company Viome does. Unlike measuring DNA, which is stagnant and doesn’t change, Viome looks at ribonucleic acid (RNA) and measures which microbial, mitochondrial, and human genes are being expressed—what your cells are actually doing.
Originally, Viome utilized their technology, which was developed over 15 years by the US Governmental Lab at Los Alamos, NM, to understand the gut microbiome and learn how this foundational system operated and impacted our overall health. But, because this technology can be applied to any cell in the body, Viome has now expanded to look at mitochondrial health and the function of your human immune cells—fully digitizing the human body. This new at-home blood test is called Health Intelligence.
Being one of the first in the world (since it just launched) to actually get my hands on the Health Intelligence results, I figured I’d share them with you. So for today’s article, a guest post by the Viome science team, you’ll see my mitochondrial, immune cell, and microbiome scores, learn how you’ll be able to monitor your health in the future to maximize longevity, and much more.
The World’s First Health Intelligence Service
Ben’s scores were solid overall. With longitudinal improvements in areas like gut lining health and microbial inflammatory activity, it’s no surprise that (besides GI scores) he would like to focus on new scores available from Viome Health Intelligence service, which offers the new Human Gene Expression (blood test) scores and integrative scores drawing from both human (cellular, mitochondrial) and microbial perspectives to reveal new areas that contribute to his health.
So, let’s dive into each of Ben’s internal functions that we tested.
Mitochondrial Health: 52
Mitochondrial health is one of the new, breakthrough integrative functional scores in Viome Health Intelligence that assesses the efficiency of the functions of your mitochondria that are required to meet your body’s energy and metabolic demands. In addition to analyzing microbial and human gene expression, Viome also analyzes the gene expression from your mitochondria. It includes 2 important pathway scores: Mitochondrial Biogenesis and Energy Production Pathways.
If your Mitochondrial Health score is not optimal, it could mean that your cells are not receiving enough energy to function efficiently, resulting in accelerated aging, and poor metabolism, cardiovascular, and brain health. Mitochondria are considered the powerhouse of the cell, supplying energy for basic cellular functions like care and repair of cells in the body. Each cell contains hundreds to thousands of mitochondria that have their own DNA, known as mitochondrial DNA.
What this means for Ben: Alongside following his food recommendations, Ben could consider 4 supplement ingredients that could help this score: Quercetin, Magnesium, Curcumin, and Vitamin C. Quercetin is a polyphenol found in foods such as onions, apples, grapes, and berries. It has been suggested that quercetin plays a role in the induction of mitochondrial biogenesis pathway elements, including activators of mitochondrial DNA and protein synthesis. Besides serving as an anti-inflammatory agent, it can activate PGC-1 alpha and support mitochondrial health. Curcumin is another example of a PGC-1 alpha activator. Curcumin can improve mitochondrial health, cellular energy, and aging through activating several signaling pathways. It has been reported to increase the translocation of Nrf2 to the cell nucleus where it increases the expression of mitochondrial health enhancers PGC-1α and p-AMPK.
Mitochondrial Biogenesis Pathways: Average
Mitochondrial biogenesis is required for generating and maintaining the cellular functions and quantities of your mitochondria to meet your body’s energy and metabolic demands. This includes PGC1-alpha signaling, known as the master regulator of mitochondrial biogenesis. This score is part of Mitochondrial Health.
What this means for Ben: Ben’s score is above average, implying sufficient activity in mitochondria support functions. Ben’s oxidative stress is generally good and he’s getting the specific nutrients that may serve as cofactors needed for his specific mitochondrial biogenesis pathways (such as PGC1-alpha activators or NAD+ precursors). This may also indirectly contribute to Ben’s Energy Production score. The Viome app shows nutrients at the level of Mitochondrial Health score, which addresses it together with all of its pathway score components.
Energy Production Pathways: Average
The Energy Production Pathways score evaluates the efficiency of your cells’ ability to convert carbohydrates (glucose, fructose, etc.) or fats into energy molecules that fuel your cells (otherwise known as ATP). This score is part of the Mitochondrial Health Score.
What this score means for Ben: Ben’s score is at the low end of normal. This is totally fine, but it suggests that his mitochondrial metabolic activity could become even better from specific molecular targeting by vitamins/cofactors, or coenzyme supplements, such as CoQ10, NAD+ precursors, L-Carnitine, or various activators of AMPK (an activator of metabolic pathways, which stimulates mitochondrial ATP production).
Since Ben has many nutrients already listed for his mitochondrial health and energy support, and since his results are within the average range, he was not recommended NAD+ boosting supplements, which we can occasionally recommend to those with different score profiles in the form of Nicotinamide Riboside. Some opt for taking NMN, a more immediate NAD+ pathway precursor. Some of Ben’s foods are already rich in CoQ10 and NAD+ (muscle meats, salmon, sardines), but not high in purines, which Ben should avoid. These foods also provide other benefits, like healthy essential fatty acids (omega-3s). Foods or supplements that contain vitamin B3 (niacin) or nicotinate can also serve as natural precursors to NAD+, and Ben has a variety of such nutrients in his “superfoods,” “enjoy,” and other nutrient recommendation categories.
NAD+, CoQ10, and PQQ are PGC-1 alpha activators. Other activators of PGC-1 alpha include resveratrol, astaxanthin, curcumin, and white mulberry leaf. One natural and healthy way to increase NAD+ and PGC-1 alpha levels is by exercising, which is certainly not a problem for Ben.
There is also a possibility that Ben also has less efficient glucose utilization pathways due to over a dozen years on a low-carb or ketogenic diet, which trains the body to more efficiently use fat as a fuel, and may de-prioritize glucose utilization efficiency.
Cellular Health (49)
The Cellular Health score offers a complete picture of what is happening in the human body on the cellular and molecular level and takes into account the aging of your cells (senescence), cellular stress, cellular inflammation, along with the health of your mitochondria. If your Cellular Health score is not optimal or low, this can mean that your cellular functions are not performing efficiently, your energy production is low, or your cells are undergoing stress due to oxidative stress, inflammation, or environmental toxins. To improve this score, we may recommend antioxidants or anti-inflammatory food and supplements specifically for you.
To arrive at the Integrative Cellular Health score we combine multiple functional activities measured in the scores you see below along with many other additional health markers and pathways.
Cellular Senescence: 50 (Average)
As cells age, they stop dividing. We call this cellular senescence. These aging cells become dysfunctional, excreting more and more of their harmful byproducts into your body and the bloodstream, causing further cellular inflammation, damage, and stress throughout your body.
The Cellular Senescence score assesses processes involved in a progressive decline in your cells’ vital functions usually associated with cellular aging such as:
Cellular proteostasis (the ability to make, fold, deliver and degrade various proteins).
DNA damage markers and repair signaling.
Regulation of telomeres and cellular immortalization.
Oxidative and other stress-induced progressive functional decline.
Autophagy, stem-cell, and regenerative signaling decline. A score that is not optimal suggests that your body is not providing the needed cellular activities to remedy the stress processes, restore homeostasis, and rid cells of debris in an efficient manner.
What this score means for Ben: Ben’s score is about average, but it is connected to his Cellular Stress score, which is on the low side of average, possibly due to Ben’s couple decades of relatively extreme endurance sports (combined with a subpar diet for much of that time) and overall exercise-related inflammation. For example, increased cellular senescence is commonly observed in elite athletes. Certain supplements may help this score, such as Cat’s Claw, Astragalus, Chamomile, and Bacillus coagulans Probiotic strains such as BC-MTCC 5856, BC-SANK 70258, and BC-SNZ1969. Astragalus is an herb commonly used in traditional Chinese medicine known for its beneficial effects on senescence and immune pathways due to being rich in specific polysaccharides and other anti-aging compounds. For example, it can improve cellular longevity by protecting or increasing the length of your telomeres because a key ingredient in Astragalus activates the expression of TERT, which is the key enzyme needed to perform the telomere lengthening function.
Cellular Stress: 46
The Cellular Stress score measures pathway activities that either lead to, or are reflective of, cellular stress. Too much stress at a cellular level can contribute to damage and dysfunction, which can also expedite cellular aging.
Likely due to the exercise and athletic history-related stress discussed above, Ben’s score is on the low side of average, which indicates his body could benefit from support to mitigate some of the following areas:
Oxidative stress: Excessive reactive oxygen species (ROS) and insufficient antioxidant activities needed to remove them (including Sirtuins and NRF2).
Unfolded protein response (UPR) or Endoplasmic Reticulum (ER) stress can be caused by inflammation, high-fat diet, environmental exposures, or microbial sources of stress.
Genotoxic stress: DNA damage caused by toxins, which can elicit biochemical responses that either signal the need for quick repair or cell death (if the damage is too high).
Hypoxia-induced stress: Insufficient oxygenation levels in the blood, often accompanied by HIF1-alpha-pathway activation.
Stress-induced pro-apoptotic signaling, such as overly active p38/JNK or Calcium signaling pathways, all of which can cause otherwise healthy cells to die via programmed cell death, or apoptosis.
Antiviral or antimicrobial stress response (cells’ lowered ability to defend and sustain itself from foreign invaders).
What this score means for Ben: Cellular Stress has a wide range of supplement recommendations for Ben, including Astragalus, Horse Chestnut, Chamomile, Quercetin, Peppermint Leaf, and Ginger Extract. Horse chestnut seeds have been used traditionally to relieve bloating and poor circulation and contain Escin, a beneficial molecule that has been studied for its antioxidant properties. It also alleviates some digestive stress and helps some of Ben’s gut health.
Biological Age: 47 (Actual Age 38)
Ultimately we all want to live longer, healthier lives. Historically, youth has been measured by how many times you’ve circled the sun. But now that we can see how your cells, mitochondria, and gut microbiome are functioning and responding to stress, we can actually calculate your Biological Age.
Your Biological Age assesses the efficiency of your cellular activities and your gut microbial activities in order to determine how well you are aging in comparison with your chronological age. If your Biological Age is substantially higher than your chronological age, this means that at a cellular level, your body is aging faster compared with other people your age. Our comprehensive AI has analyzed data from more than 125,000 people to be able to match the molecular patterns from your data to people of different ages, which we use to predict your approximate biological age.
What this score means for Ben: Given that Ben’s biological age is a few years higher than his chronological age, this means that on a molecular level, his body is going through something that matches it more with that of a slightly older person, or it is handling things that make it appear as if it is aging faster compared with other people his age. Ben certainly doesn’t look like a 47-year-old, and many of his consumer-facing scores are in an average zone (where most customers usually fall). We also look at several hundred other scores that are not yet displayed to Viome users but are taken into account in calculating biological age. Additionally, biological age takes into account all human gene expression, mitochondrial gene expression, and gut microbial gene expression. The aging score is based on our machine learning model that we have patented and have published a paper on and is substantially better than any aging model published so far.
Given Ben’s training volume and focus on muscle/strength building, many of these growth factors may have an impact on his cells’ ability to manage stress and generate energy—as well as how they age. Continuing to take good care of his gut health may also help Ben improve this score.
That said, nutrient levels in your body can influence various metabolic pathways. Among the key parts of these pathways are proteins encoded by IGF-1, mTOR, sirtuins, AMPK, and many other genes. Changing levels of these proteins’ pathways have implications on longevity and your biological age. Notably, the gut microbiome also plays a role in aging by either supplying toxins, pathogenic factors, or beneficial nutrients like butyrate, vitamins, and spermidine (a known anti-aging compound).
Gut Microbiome Health: 51 (Average)
The Gut Microbiome Health score is the macro score that integrates over 20 microbial functional scores. This summarizes how your GI system is operating.
What this means for Ben: While his score is “average” at a score of 51, a score of 55 would put Ben in the ‘optimal’ range which includes just 12% of the overall population. This is very good and significantly better than in Ben’s last test placing him at 45! Because we know Ben is an overachiever, he will want to learn how to get into that top 12%. The larger the score (the more components or subscores it has) the harder it is to “move a needle” in it, so an improvement of 6 points is actually great news. This improvement is a result of Ben’s Digestive Efficiency and Gut Lining Health scores improving dramatically, Inflammatory Activity and Protein Fermentation scores improving significantly, and even his overall Gas Production score is better than it was before.
The reasons his Gut Microbiome Health score is not perfect lie in Metabolic Fitness and Active Microbial Diversity scores and the pathways scores they are composed of. Active Microbial Diversity is in the average zone, and it is not surprising, because when many complex carbohydrates needed to be avoided due to sulfide and other gas-producing effects, some of the prebiotic substrates were also less available in Ben’s Viome recommendations. Right now his recommendations look less restrictive and he may be able to get his diversity back up. For example, last year most cruciferous vegetables were on “Avoid” due to Ben’s high Sulfide Gas Production Pathways score, while now that score improved, and Ben can have these and other vegetables that may help this score (since they are on “Enjoy” or “Minimize” lists):
Metabolic Fitness is actually influenced in Ben’s case the most by his Bile Acid Metabolism Pathways score being not optimal, followed by Uric Acid and Oxalate Metabolism Pathway scores. These scores to various degrees also contribute to Digestive Efficiency and Gut Lining Health, which are affected by 2 more suboptimal scores: Methane Gas Production Pathways and LPS Biosynthesis Pathways.
Let’s look at several areas still needing support or improvement:
1. Methane Gas Production Pathways: High methane production has been linked with some motility issues in the gut (how your food moves along the digestive tract), as well as pro-inflammatory patterns that can negatively affect your intestinal lining.
What this means for Ben: We’re not surprised to see Ben’s methane production is high (it has been on all of his Viome tests). We commonly see this in athletes and the paleo community who have high protein fermentation due to eating very high-protein diets, which can overwhelm the digestive system and lead to increased methane production. However, proteins are not the only source of methane production. Microbes that have constantly appeared active in Ben (called Archaea) can make methane out of carbohydrates and even fats. It’s not possible to cut out all major food groups that can feed Ben’s methane producers, so in this case, the best ways to manage this score is to:
Review and follow his antimicrobial food and supplement recommendations to target the offenders (for example, one of Ben’s superfoods is Sage, which has antimicrobial properties).
Stick closely to all the beneficial functions and microbes-boosting recommendations.
Mitigate the GI effects of methane and other gases. For example:
Some probiotics can counter the activity of methanogens, such as a specific strain of Bacillus coagulans – species that is commonly available from multiple probiotic providers.
Ben’s overall recommendations include nutrients like Peppermint, which can help with gas, as well as enzymes that can help with protein and other macronutrient digestion and motility.
Otherwise, just be cognizant of where proteins and certain vegetables land on Viome food recommendations and follow your recommended servings. Another example is peppermint leaf extract.
Peppermint is a common herb often used for flavoring, but also has many health benefits. Peppermint leaf is a good source of menthol which is known to have a calming effect on gut motility and gas production pathways. See resources here, here, here, and here.
2. Uric Acid and Oxalate: Uric acid is a normal byproduct that comes from the breakdown of compounds called purines, which can be found in certain proteins like turkey, veal, bacon, and organ meats, as well as seafood and shellfish. Excessive amounts of uric acid can contribute to joint pain or gout.
What this means for Ben: Just like with Ben’s methane gas production score, we’re not surprised to see his uric acid production is high. Uric acid is a byproduct of purines, which are common in some protein-foods and spinach. Many of Ben’s foods to minimize or avoid are due to their contribution to uric acid production (i.e. spinach and crab).
The best way to manage this score is to be aware of certain animal food sources of purines, like crab, haddock, goat and trout, and certain vegetables, like spinach. Spinach is an example of an avoid food that addressed both Uric Acid Production Pathways and Oxalate Metabolism Pathways scores because besides being high in purines, spinach also has a high content of oxalates.
3. Bile Acid Metabolism Pathways. This score assesses the levels of activity of all metabolic pathways that include bile acids. Normally bile acids are made by the liver to help with fat digestion. Bile acids enter the colon in the form of bile salts. Your gut microbiota can change them back into bile acids, after which they can even be recycled back to the liver. If this activity is relatively high or excessive, it may be an indicator of your inability to break down fat or absorb nutrients properly, which can contribute to a pro-inflammatory environment or negative liver-related effects, as the microbiome’s bile acid pathways have been implicated in fatty deposits in the liver. A good score means these pathway activity levels are low in your sample.
What this means for Ben: Ben’s diet may be rich in lipids that provide a favorable environment to lipid- and bile- loving microbes like Bilophila, of which Ben has 3 strains: Bilophila sp. 4_1_30, Bilophila wadsworthia 3_1_6, and Bilophila wadsworthia ATCC 49260. This is something Ben had active in his results before. In fact, his score, though not optimal, has actually improved relative to his last test.
The best way to address this score is for Ben to watch the serving of fat and cholesterol in the Viome recommendations and split up fatty or oil-rich meals into smaller portions throughout the day, as opposed to large amounts in fewer meals. Also, lipase can be used as needed, which appears along with other digestive enzymes in Ben’s recommendations. Ben has also been recommended caraway fruit/seed, which can help with lipolysis and cholesterol metabolism. Curcumin can also help by downregulating adipokines such as resistin and leptin, thus potentially enhancing metabolic fitness.
4) LPS Biosynthesis Pathways. Lipopolysaccharide (LPS) is a highly inflammatory molecule that is associated with chronic inflammation.
What this means for Ben: LPS is a fairly large molecule and should not be able to pass through the gut lining into the bloodstream to circulate the body if the intestinal barrier is strong. So, if a person has a strong mucosal layer and intestinal lining—that is helpful for mitigating the negative effects of producing too much LPS.
The best way to deal with LPS in the ecosystem is by taking some of the following approaches:
Attack the microbes that make it, because even though they are not always pathogenic, they nevertheless aren’t the “good guys” either. One example is Escherichia coli (E. coli), and you can see multiple antimicrobial food and supplement recommendations, many of which mention E. coli or other microbes they suppress. For example, Nettle Leaf that we talked about in the context of Immune Health, and chamomile, which helps with gases, motility, and stress response. Both of these ingredients are also able to address your microbiome’s Inflammatory Activity score with their antioxidant and antimicrobial action against bacterial and eukaryotic opportunists.
NOTE: Each nutrient is prioritized for a person based on how many suboptimal scores and to what degree they are able to address, which is why you see some of these “many-to-many” relationships depicted on the score screens and the overall food and nutrient list.
Out-balance the LPS producers with beneficial foods and probiotics that diminish LPS effects and suppress the populations of LPS-producing microbes by outnumbering them, increasing acidity (lowering GI pH) and making the environment less favorable for them.
Taking care of the gut lining and overall inflammatory activities, which are addressed by:
2) Your avoid list, and to a lesser degree, minimize, because even excessive uric acid or oxalate in your spinach, or plant viruses, like pepper mild mottle virus in your bell pepper, could add to the inflammatory environment created by LPS production. Prolamin is another example of a potential inflammatory trigger, which belongs to the same category of compounds as gluten, and is the reason Quinoa is ‘Avoid’ for Ben.
NOTE: In following your recommendations it is really important to focus on your “Superfoods” and avoid your generic and personalized “Avoid” foods while keeping up the variety and “eating the rainbow.” Try to not eat your “Minimize” foods, unless you really crave them (in which case, stick to the allowed serving limits).
Inflammatory Activity: 39 (Average)
This score measures the activities of your microbes that can contribute to, or reflect, inflammation in your gut environment. Maintaining low levels of chronic inflammation is critical for longevity, especially for someone who generates inflammation during intense workouts.
This score has improved for Ben over time, reduced inflammatory activity being the goal within this score, with a more significant drop in his recent test.
Inflammation in your gut can be caused by harmful compounds your microbes can produce. In Ben’s case, these can be molecules like uric acid, methane, or LPS. Ben’s score is pretty average, indicating that there are relatively balanced pro-inflammatory activities, as opposed to anti-inflammatory or protective ones.
What this score means for Ben: His score improved from his previous test and is almost in the optimal category. This is great to see in someone who pushes their body as hard as Ben does. It indicates that his diet and recovery protocols are helping to balance and minimize inflammation in his gut.
Tip for Ben: Supplements such as curcumin, ginger extract, and quebracho extract may help in reducing inflammation in his gut environment. Curcumin is a polyphenolic molecule extracted from turmeric root, a spice commonly consumed in Asia. Curcumin is known to have a powerful effect on antioxidant and anti-inflammatory pathways and may alleviate inflammation by inhibiting inflammatory mediators such as IFN-gamma, NF-KB, IL-17, TNF-alpha, COX-2, iNOS, IL-1, IL-1beta, IL-6, IL-12, IL-4, lipoxygenase, and MPO. Avoiding the foods listed in the “avoid food list” may also help improve this score because many of these foods may increase inflammation in your gut.
Immune System Health: 50 & Immune System Activation: 48
More and more people are concerned with immunity in the current climate. Viome’s Immune System Health score integrates multiple sub-scores, such as Inflammatory Activity, Gut Lining Health, Immune System Activation, and Cellular Stress, to assess your immune response based on the inflammatory activities throughout your body, as well as inside of your gut. If this score is not optimal, it means—either from the microbial or human cellular side, or both—immune system support may be needed.
The nutrients we prioritize for people who need help with this score tend to address all the different areas involved. However, in Ben’s case, there’s a relatively modest amount of nutrients targeting this score specifically, because he is doing fine in terms of his Inflammatory Activity (GI), which improved since last year, and is doing good on his cellular Immune System Activation score. Recommendations that are there to support this health area address both microbial and cellular counterparts at once, e.g Nettle Leaf:
Nettle Leaf, also known as stinging nettle, is an herb that contains polyphenols—molecules known for their beneficial effects on immune and inflammation pathways. The antimicrobial effect of nettles against certain species of bacteria and yeast has been noted, although the mechanism is unclear. Research has also shown that its anti-inflammatory action could occur by inhibiting the release of proinflammatory mediators, acting against histamine receptors, and reducing the activity of inflammatory pathways via the inhibition of Cyclooxygenase-1 (COX-1), Cyclooxygenase-2 (COX-2), and hematopoietic Prostaglandin D2 synthase.
If the Immune System Activation score were not optimal, there can be 2 scenarios: 1) Too high of an immune system activity, which equates to inflammation, or 2) Immunity is too low and your immune system’s preparedness to pathogens needs support.
Ben’s Immune System Activation pathways score as strong and allow us to finish on a high note. Ben’s score is 48, which is “Good” because this score should stay in balance. When your Immune System Activation scores “Good,” it means there is just the right amount of immune system activation. The ratio of anti-inflammatory to pro-inflammatory responses are telling your immune system that it can relax.
A good score means you likely have optimal activity from your immune system, are not currently having to fight infection or respond to something that immune cells recognize as foreign (even if it is your own body cell components), and not having an allergic reaction or food sensitivity triggers.
Pathway themes combined into the Immune System Activation score include:
Antiviral or antibacterial defense response needed to combat any foreign threat to the body by specialized immune system cells.
Proinflammatory cytokine signaling (including IL-1, IL-6, IL-8, TNFalpha, and multiple pathways of activation of NF-kappa B gene expression).
Tissue remodeling and wound healing (this can occur even in the absence of any wounds when cellular conditions signal damage).
Histamine signaling an allergic response.
Prostaglandin Biosynthesis (COX2), which can lead to increased inflammation & pain in various parts.
What this means for Ben: His immune system is in great shape, and ready to respond when needed. Given his high exercise volume, which induces stress and can tax the system, Ben’s immune system appears to be doing very well. It is not overactive or underactive.
Ben is a person who executes at a very high level nutritionally as well as in his strength and aerobic training. But there are still definite areas where he can see improvements. He spent the first several decades of his life eating a subpar Standard American Diet, taking antibiotics, overtraining, and exposing himself to high levels of toxins, pollutants, EMF, and much more—so all things considered, he seems to be “bouncing back” quite nicely.
As you can see from this report, this is why regularly measuring your cellular function at the molecular level is so critical.
You can’t nourish your cells correctly if you don’t know how they are working and which areas need extra support. Once you gain a better understanding of how your immune cells, mitochondria, and gut microbiome are functioning, you can follow your nutritional guidance on the Viome Health Intelligence platform to begin optimizing your cells.
For more on Viome, check out some of Ben’s previous podcasts with our founder, Naveen Jain, and articles on other services Viome provides: