The gut microbiome plays a critical role in human immunity. From the moment a baby ingests its mother's milk, our body is designed to incorporate and synergize with the different strains of bugs and critters living within our digestive system.
The human gut contains about 100 trillion bacterial cells and comprises about 2.2-4.4 lbs of our bodyweight. With over 1000 strains ranging from Firmicutes and Bacteroidetes to Proteobacteria and Actinobacteria, the human body (~37 trillion cells) is, by the numbers, is more bacteria than it is human.
In understanding our health and the role bacteria plays in regulating it, we've come to appreciate just how important how we tend our garden of bugs really is. Factors such as gut biodiversity and strain balance play into how our body performs both physically and mentally. The Gut-Brain Axis, a complex network of cellular pathways between the gut and brain, can influence brain function and behavior through the production of neurotransmitters like serotonin and dopamine, and via the vagus nerve. Disruptions in the gut microbiome have been linked to both autoimmune disorders like T1D and multiple sclerosis, as well as mental health disorders like anxiety and depression.
That's why in my health pursuits I've taken an interest in learning more about my own gut. A few months ago I invested in an at-home gut health test from Viome. I chose their Gut Intelligence Test. It's an online service that tests a sample of your gut microbiome and uploads a comprehensive list of the strains living in your GI tract. From that list they're able to rank your gut health variables like digestive abilities, immune health and biodiversity. With those scores, it can also make recommendations for things like prebiotics, probiotics and vitamins and minerals to positively influence your gut flora.
Here, we'll go over my test results and what was found, as well as what recommendations were made and why.
As far as working with Viome, this was an incredibly easy process. Sample collection was simple, straight forward and not all that disgusting. It begins with them mailing you a collection box. You'll register it and make your sample collection. It's 2 vials with plastic swabs that you use to "scoop" after having gone to the bathroom.
You send it to their lab with the prepaid packaging and wait 2-3 weeks for results. My wait time was about 12 days.
After receiving your results, your health dashboard is populated with all your information; Your Health Scores is a numerical grade measured against the rest of Viome users.
Functional Scores include (with my scores):
Inflammatory Activity (Average)
This score measures the activities of your microbes that can contribute to or reflect inflammation in your gut environment.
Metabolic Fitness (Average)
This score represents active microbial organisms and functions that are associated with your blood sugar, insulin resistance, or weight control.
Digestive Efficiency (Average)
This score is a comprehensive microbial reflection of your gastrointestinal (GI) tract functions. The score consists of multiple activity patterns related to digestion, such as the movement of food, specific macronutrient breakdown ability, and your gut lining health from your first bite of food to the time it leaves your body.
Gut Lining Health (Average)
This score focuses on your gut lining (or intestinal barrier) and the health of the mucosal layer that protects it.
Protein Fermentation (Not Optimal)
This score reflects whether or not you are digesting your proteins properly.
Gas Production (Average)
This score is an assessment of your overall gas production activity by the microbes in your gut.
Gut Active Microbial Diversity (Average)
This score is your percentile for the total count of active microbial species detected and sequenced from your stool sample. Both microbial richness (number of microbes) and evenness (the balance of microbial species) in your gut microbiome play a role in determining the value of Gut Active Microbial Diversity.
Microbiome-Induced Stress (Average)
Your Microbiome-Induced Stress score offers insights about those microbial activities that can lead to stress or inflammatory response not only in your gut, but also in your body.
Each section has its own graph and write up to help you "digest" the information.
All of my "average" scores were on the lower end of average (except Microbial Diversity, YAY!). This made the perfectionist within me wince. But with all of my health improvements over the past 2 years I can only imagine how poor my scores would have been before.
My one "Not Optimal" score was for protein fermentation. It suggested that my gut microbes were over-utilizing amino acids from protein as fuel, which can increase the production of harmful byproducts.
From a diabetes perspective this makes sense. With my glucose utilization compromised, even with a well-regulated blood sugar, there is going to be a residual tendency to digest proteins in states of fasting (like when you sleep), and during times of high physical activity.
However there is digestive efficiency component to this score as well. Protein digestion begins when you first start chewing and continues down in your stomach. If the protein is not fully broken down through this process, your microbes will digest the excess protein available and may convert it into harmful byproducts. Byproducts like ammonia, hydrogen sulfide, ammonia, indoles, and phenols can irritate the gut lining and contribute to inflammation and other gastrointestinal symptoms.
All in all I was pleased with the results. It's clear I have more room to improve and I'd like to get each of the categories trending toward the optimal range. Yet, it's also comforting to know that my current baseline puts me in what I would call a neutral state. There doesn't seem to be any major obstacles being overcome in my daily digestion. Combine that with the quality of my diet and I see myself achieving the necessary improvements in the near future.
Then came the Pathway Activities (with my scores):
TMA Production (Average)
TMA is created in the gut by microbes when certain compounds, such as choline and carnitine, are present. TMA can then be converted into TMAO in the liver and enter the bloodstream. High levels of TMAO are associated with unfavorable metabolic and cardiovascular effects.
Ammonia Production (Average)
This activity can contribute to pro-inflammatory patterns potentially harmful to the gut lining and gut motility. Ammonia produced in the gut significantly contributes to ammonia in the body which can negatively impact neurotransmitter production, cognitive function, and mitochondrial health.
Butyrate (Average)
Butyrate is a short-chain fatty acid known to positively affect many wellness areas from gut lining to insulin sensitivity and satiety (feeling full). Butyrate is the primary energy source for cells lining the colon and provides an anti-inflammatory effect.
LPS Biosynthesis (Average)
LPS is a pro-inflammatory molecule that gut microbes make, which can trigger your immune system response, especially if it passes to the bloodstream through the gut lining.
Methane Gas (Average)
While some production of methane gas is normal, a high production of methane is associated with motility issues in the gut like constipation, as well as pro-inflammatory activities that can negatively affect the intestinal lining.
Sulfide Gas (Average)
It can be made from some proteins that contain sulfur amino acids or from ingested sulfate or sulfite molecules found in foods like dried fruit, preserved meats, and some alcoholic beverages. This kind of activity, when high, contributes to pro-inflammatory patterns potentially harmful to the gut lining.
Flagellar Assembly (Average)
Flagella are tail-like structures that microbes produce to help them move, often in response to a threat or undesirable environment in the gut. Flagella are produced by both commensal and opportunistic bacteria. When pathways signaling the production of flagella are high, this indicates higher-than-usual activity by opportunistic organisms that are known to have these structures.
Putrescine Production (Average)
Putrescine is a molecular byproduct of protein fermentation - a microbial breakdown of protein. If the activities of putrescine production pathways are too high, it can be harmful to the gut environment and the intestinal barrier lining.
Oxalate Metabolism (Average)
Oxalate, also known as oxalic acid, is a naturally occurring compound found in many plant foods. Oxalate can form oxalate salts when they bind with minerals like calcium or magnesium, forming crystals that inhibit the absorption of necessary minerals and contribute to kidney stones. Additionally, a high oxalate load has been shown to contribute to impaired mitochondrial and immune function.
Uric Acid Production (Average)
High levels of uric acid are associated with several adverse health effects including gout, kidney stones, hypertension, and metabolic syndrome.
Salt Stress (Average)
This score assesses the levels of activity of all microbial pathways that signal excessive salt in the gut environment. This kind of signaling activity, when high, suggests that you may need to adjust your salt or sodium intake and/or your hydration levels. Too much salt for your gut microbiome makes your gut environment less favorable for some beneficial or probiotic organisms to thrive.
Biofilm, Chemotaxis, and Virulence (Average)
This score assesses the levels of all activity of all metabolic pathways that suggest a pro-inflammatory or hostile environment in the gut.
Bile Acid Metabolism (Average)
If this activity is relatively high or excessive, possibly due to over-stimulation of bile production by certain foods, a lack of certain fibers in the diet, and/or an unbalanced gut microbiome it may be affecting your ability to break down fat or absorb nutrients properly.
This report gave me peace of mind from the inflammatory point of view. All of the pathways controlling the accumulation or excretion of metabolic waste came back "average". To use their words, my gut doesn't seem to foster a hostile environment.
I was pleased to see my butyrate levels were sufficient. Butyrate is a short chain fatty acid (SCFA) created when bacteria ferment specific dietary fiber. It has been shown to increase GLP-1 production (1,2,3,4). It's unsurprising, then, to see that people with diabetes typically test as low/deficient in butyrate levels and the strains of bacteria necessary to produce it (Faecalibacterium prausnitzii and Roseburia intestinalis). Butyrate as a supplement deserves an article of its own for its documented effects on gut microbiota and diabetes.
Another facet of the pathway testing that caught my eye was my putrescine pathway score. Putrescine is a byproduct of incomplete protein digestion and is harmful to the gut when elevated. I thought it interesting that I scored "Not Optimal" for protein fermentation in the Functional Scores, yet did not test for the byproducts of altered protein fermentation.
I'm not entirely sure what to make of that just yet. I've chalked that up to my gut's ability to neutralize any toxins. If it were a major issue it would affect my other health categories.
Now let's take a look at the specifics of my microbiome. Viome gives you a list of all detected strains within your sample. My sample tallied 128 different strains of bacteria, eukaryotes and viruses. For the sake of brevity, I won't list all here but I've highlighted the most interesting for me.
You'll notice that each listing here carries a ranking associated with it. I used a medically-oriented AI to help me decipher my list of bacterial strains. This was NOT put in place by Viome. QuixosisAI is an AI service designed to help the layman better understand their symptoms, empower people in their visits with health professionals and make suggestions when it comes to courses of action.
You can experiment with Quixosis AI here if you're interested. The beta version is free!
Here's the prompt I used to isolate the major players:
I'm going to give you a list of bacteria from a recent gut microbiome test. Can you give me a ranking for each strain from 1-10 in terms of how influential it is in the development of T1D?
Here are all the strains that scored a 7 or above:
Akkermansia muciniphila
Ranking: 8
Notes: This bacterium is known for its beneficial roles in gut barrier maintenance and metabolic health. Some studies suggest that lower levels of Akkermansia are associated with various metabolic disorders, including T1D. It is considered influential in immune regulation.
Bacteroides dorei CL03T12C01
Ranking: 7
Notes: Bacteroides dorei has been specifically studied in the context of T1D. Lower levels of Bacteroides dorei have been associated with children who develop T1D, suggesting it may play a protective role.
Bacteroides fragilis 638R
Ranking: 8
Notes: Bacteroides fragilis is notable for its immunomodulatory properties. It produces polysaccharide A, which has been shown to help regulate immune responses and may protect against autoimmune diseases, including T1D.
Bacteroides fragilis YCH46
Ranking: 8
Notes: Similar to Bacteroides fragilis 638R, this strain is known for its immunomodulatory properties, including the production of polysaccharide A which can regulate immune responses. It may play a protective role against autoimmune diseases such as T1D.
Bacteroides thetaiotaomicron VPI-5482
Ranking: 7
Notes: This is one of the more studied Bacteroides species, known for its capability to break down complex carbohydrates and its role in maintaining gut barrier function. It has been studied in relation to immune function and inflammation, suggesting a more significant, though indirect, influence on T1D.
Bifidobacterium breve ACS-071-V-Sch8b
Ranking: 7
Notes: Bifidobacterium breve is a beneficial gut bacterium, often found in probiotics, known for its positive effects on gut health and immune modulation. Some studies suggest that higher levels of Bifidobacterium species may help protect against autoimmune diseases, including T1D.
Christensenella minuta
Ranking: 7
Notes: This species is a relatively recent discovery but has been linked to a healthy gut microbiome and metabolic health. It may play a role in reducing inflammation and may have implications for autoimmune conditions such as T1D.
Christensenella sp. Marseille-P3954
Ranking: 7
Notes: Similar to Christensenella minuta, this species is associated with a healthy gut microbiome and metabolic health. Its potential role in modulating inflammation gives it a moderate to strong influence on conditions like T1D.
Faecalibacterium prausnitzii A2-165
Ranking: 8
Notes: Faecalibacterium prausnitzii is known for its anti-inflammatory properties and its role in producing butyrate, a short-chain fatty acid beneficial for gut health. It is one of the most studied gut bacteria with a strong potential influence on inflammatory and autoimmune conditions, including T1D.
Lactobacillus delbrueckii subsp. bulgaricus
Ranking: 7
Notes: Widely used in yogurt and other fermentative processes, Lactobacillus delbrueckii subsp. bulgaricus is beneficial for gut health and has been shown to enhance immune function. Its probiotic properties suggest a moderate to strong influence on autoimmune conditions like T1D.
Lactobacillus delbrueckii subsp. bulgaricus 2038
Ranking: 7
Notes: Similar to the above, this specific strain is used in fermentation and has probiotic benefits. Its role in promoting gut health and potentially modulating immune function indicates a moderate to strong influence on T1D.
Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
Ranking: 7
Notes: This strain is known for its use in yogurt and other fermented dairy products. It has beneficial probiotic properties that support gut health and might play a role in modulating the immune system, indicating a moderate to strong influence on conditions like T1D.
Roseburia hominis A2-183
Ranking: 8
Notes: Roseburia hominis is a beneficial gut bacterium known for producing butyrate, a short-chain fatty acid that contributes to gut health and has strong anti-inflammatory properties. Its significant role in maintaining a healthy gut environment suggests a strong influence on conditions like T1D.
Streptococcus thermophilus ASCC 1275
Ranking: 7
Notes: Streptococcus thermophilus ASCC 1275 is widely used in fermented dairy products. It has several health benefits, including supporting gut health and enhancing immune function. Its role in promoting a healthy microbiota suggests a moderate to strong influence on conditions like T1D.
Streptococcus thermophilus JIM 8232
Ranking: 7
Notes: Similar to other Streptococcus thermophilus strains, JIM 8232 is used in dairy fermentation and has notable probiotic properties. It supports gut health and potentially modulates the immune system, suggesting a moderate to strong influence on T1D.
Streptococcus thermophilus MN-ZLW-002
Ranking: 7
Notes: This strain is also used in the production of fermented dairy products and has beneficial probiotic effects. Its role in gut health and immune support indicates a moderate to strong influence on conditions like T1D.
Streptococcus thermophilus ND03
Ranking: 7
Notes: As with other Streptococcus thermophilus strains, ND03 is used in dairy products for its probiotic benefits. It helps maintain a healthy gut microbiota and supports immune function, suggesting a moderate to strong influence on T1D.
My takeaways:
I thought it interesting that each of the top rated influential strains was a beneficial strain. That was confirmation for me that the interventions I've been implementing are having an effect.
While it feels good to see all of the beneficial strains highlighted, and I really do believe my gut is headed in the right direction, I'm still left to wonder why my functional scores aren't better.That's where reading between the lines was required. It's always important to take everything in the context of balance.
Firstly, there were a number of strains that were associated with inflammatory conditions. Of the 128 strains identified in my sample, 20 of them were explicitly described as pro-inflammatory and linked to adverse health conditions. IE Strains such as Alistipes communis, Enterococcus gallinarum and Finegoldia magna.
Additionally, Bacteroides species are typically described as pro-inflammatory in those with autoimmune conditions. This is despite some of the strains being listed with beneficial effects. This is where the balance aspect comes in. Abundance is a determining factor. In isolation, each of the Bacteroides species can be a part of a healthy flora. Yet, when overgrown and left unchecked they contribute to dysbiosis.
I tested positive for 22 different strains of Bacteroides. So might I just have too many strains?
Even that isn't quite true. The literature suggests that Bacteroides are some of the most abundant genus found within healthy guts as well. Anywhere from 10-30% of the total gut fauna with up to several dozen different Bacteroides strains. 22/128 has me at 17%. (5,6,7)
I'm taking it as a sign to increase the number and density of the good bacteria like lactobacillus (I tested positive for 3) and bifidobacterium (I tested positive for 1 strain).
Aspergillus flavus, a mycotoxin (mold) commonly found in peanut butter was also identified. Not surprising considering how much I love peanut butter. It produces aflatoxin which is a toxin known to affect liver health. My unwillingness to say goodbye to one of my favorite treats had me immediately looking for ways to reduce the impact of aflatoxin (like buying higher quality brands and refrigerating your PB) but I may just have to say goodbye.
I also tested positive for several molds and plant viruses. Specifically for apples, bell pepper, tobacco and wheat.
Apples are one of my favorite fruits. I frequent Granny Smith, Cortland and just about any firm, crisp variant. That being said I know they are some of the more treated plants when it comes to herbicides and pesticides and I'm sure to wash each batch I eat.
Red bell peppers were a staple for my daily meals, mixing in salads, sautes and sauces. Viome suggested taking a 30 day break from them to see if had any effect.
I've been experimenting with the Nicotiano rustica strain of tobacco (smoking, steeping in hot water) over the past couple of months for it's harmine content. I bought loose leaf from an independent tobacco farm but I guess that doesn't preclude it from having a virus.
In the 2 weeks prior to collecting my stool sample, I had been eating 3-4 slices per week of unenriched sourdough bread (toast with breakfast mostly). Turns out thats enough to test for it. It's a rare treat for me so I'm not too concerned about it.
Apples | Apple hammerhead viroid-like circular RNA |
Bell Peppers | Pepper mild mottle virus |
Peanut Butter | Aspergillus flavus (Mold) |
Tobacco | Tobacco mild green mosaic virus |
Wheat | Pyrenophora tritici-repentis (Mold) |
On the positive note, I had what I took to be a large number of butyrate producing bacteria as well. That was encouraging. I had 9 different strains explicitly stated as having a role in butyrate-production. Another 4 were listed as being sources of other SCFAs, such as acetate and propionate.
An additional 9 strains were tied to the breaking down of complex carbohydrates. I thought it was good to see that I still harbored the tools to digest carbs, despite my compromised metabolism.
All in all, I'm incredibly encouraged by what I learned in reviewing my gut microbiome results from Viome. It’s clear that the state of our microbiome plays a crucial role in overall health, especially for managing conditions like diabetes. The results shed light on the balance between beneficial and harmful bacteria in my gut, revealing areas where I need to focus on supporting healthier strains.
With personalized insights into my gut’s unique needs, I now have a better understanding of how certain foods can bolster good bacteria and reduce inflammation. By implementing Viome’s dietary recommendations, I’m able to take proactive steps toward optimizing gut health and, in turn, improving my overall wellness journey. Whether you're managing a chronic condition or simply looking to feel better, understanding your microbiome is a key piece of the puzzle that can lead to lasting, impactful change.
If you're interested in giving Viome a try click here.
Thanks for reading!
Bowie
References and Citations:
Lin, H.V., Frassetto, A., Kowalik, E.J., Jr., Nawrocki, A.R., Lu, M.M., Kosinski, J.R., Pilot-Matias, T., Larsen, S.D., and Beysen, C. (2012). Butyrate and Propionate Protect Against Diet-Induced Obesity and Regulate Gut Hormones via Free Fatty Acid Receptor 3-Independent Mechanisms. PLoS ONE, 7(4), e35240. doi:10.1371/journal.pone.0035240
Tolhurst, G., Heffron, H., Lam, Y.S., Parker, H.E., Habib, A.M., Diakogiannaki, E., Cameron, J., Grosse, J., Reimann, F., and Gribble, F.M. (2012). Short-chain fatty acids stimulate glucagon-like peptide-1 secretion via the G-protein-coupled receptor FFAR2. Diabetes, 61(2), 364-371. doi:10.2337/db11-1019
Psichas, A., Sleeth, M.L., Murphy, K.G., Brooks, L., Bewick, G.A., Hanyaloglu, A.C., Ng, S.Y., Ghatei, M.A., Bloom, S.R., and Frost, G. (2015). The short chain fatty acid propionate stimulates GLP-1 and PYY secretion via free fatty acid receptor 2 in rodents. International Journal of Obesity, 39(3), 424-429. doi:10.1038/ijo.2014.153
Canfora, E.E., Jocken, J.W., and Blaak, E.E. (2015). Short-chain fatty acids in control of body weight and insulin sensitivity. Nature Reviews Endocrinology, 11(10), 577-591. doi:10.1038/nrendo.2015.128
"Structure, function and diversity of the healthy human microbiome." Nature. 2012.
Schwiertz, Andreas, et al. "Microbiota and SCFA in lean and overweight healthy subjects." Obesity. 2009.
Wexler, Hannah M. "Bacteroides: the Good, the Bad, and the Nitty-Gritty." Clin Microbiol Rev. 2007.
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