April 14, 2020

I recently traveled to India for nearly 2 weeks, where (as I go over in the podcast “Biohacking Fitness In Asia & Beyond: How One Small Company Is Changing The Face Of Biomarker Testing, Agriculture, Pollution, Health & More!”) there is an incredibly diverse microbiome—possibly one of the most diverse microbiomes in existence, amongst the indigenous population who still eats a traditional Indian diet with loads of herbs, spices, fibers, prebiotics, and so-called “slow carbs” such as chickpeas and lentils.

As a sort of self-experiment, I decided to use the at-home Onegevity Gutbio stool test both before and after my trip to see how my microbiome changed after living in India for 12 days and eating exactly like the locals (save for the fact that I politely asked for substitution of ghee or olive oil for any vegetable oil used in recipes).

This test sequences your entire community of microbes in the gut with DNA sequencing methods (i.e., shotgun metagenomics), then processes this data quickly and at a relatively low cost, providing you invaluable insights on what is present and in which abundances and ratios. You can find out how diverse and healthy your gut is, what is contributing to your inflammation, which diet plan can improve your healthy gut flora, what dietary supplements are right for your unique gut composition, and get predictions on unique gut metabolite levels for your microbiome’s capability of producing B vitamins, short-chain fatty acids, and lactate.

Podcasts and articles I’ve featured on Onegevity Gutbio testing include:

• How To Fix Your Digestion & Gut With Machine Learning & Artificial Intelligence.
• What Your Gut Can Tell You About Exercise, Diet & Longevity (& The Best Way To Test).
• How To Get 6 Gigabytes Of Data From Your Gut: The Fascinating Future Of Stool, Blood, Saliva & Urine Testing (From The Comfort Of Your Own Home).

Anyways, so, using that information and that test, let’s see what happened to my gut before and after my India trip, shall we? Considering this research article showing changes in the microbiome occur as quickly as 48 hours in response to short-term macronutrient change (in this case, a shift to an animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila, and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides) and this study showing significant seasonal variations in the Hazda hunter-gatherer microbiome in response to seasonal variations in diet, I personally expected to see some significant changes in my own microbiome within 12 days.

Pre & Post India Cuisine Effects On An American Gut Biome

You can view my full pre- and post-trip Onegevity Gutbio test results below. The first PDF you'll see is of my gut microbiome results before my trip, and the second PDF shows my results from after.

A Few Of The Key Highlights From My Gutbio Results

Inflammation

Pre India: Onegevity examined the levels of more than 100 inflammation-associated bacterial species. My test result shows a low Inflammation Potential in my gut.

After India: Inflammation remained rock-bottom low.

Constipation

Pre India: Onegevity calculated Constipation score by examining the pattern of hundreds of bacterial species that are known to positively correlate with constipation. Test results have revealed that I have a low risk for constipation.

After India: constipation risk rose to moderate. See screenshot of changes in bacterial species related to this. Some of this admittedly may have been affected by airline travel, which can induce some dysbiosis.

Diarrhea

Pre India: Onegevity calculated Diarrhea Score by examining the pattern of hundreds of bacterial species that are known to positively correlate with diarrhea. Based on the specific microbial composition of stool, test results reveal a low risk for diarrhea.

After India: Remained low, and actually dropped slightly.

Microbial Diversity

Pre India: Microbial diversity in the 96 percentile, which indicates my gut microbiome is very highly diverse—a good thing!

After India: Stayed at 96th percentile.

B Vitamins

Pre India: Test results indicate that my gut microbial population is not contributing significantly to my daily need of one or more of the B vitamins—particularly Niacin and Vitamin B12.

Vitamin B3 (niacin) like all B vitamins, plays an important role in metabolizing food. It aids nervous system function, participates in hormone production, and improves circulation and cholesterol levels. Symptoms of mild niacin deficiency include depression, fatigue, indigestion, vomiting, and canker sores. In developed countries, the most common causes of deficiency are alcohol consumption and malabsorption disorders in the gut. Vitamin B12 keeps your body's nervous system healthy, as well as playing a role in digesting protein and making DNA and red blood cells.

Malabsorption disorders, such as hypochlorhydria (low stomach acid), celiac disease, and Inflammatory Bowel Disease (IBD) can cause a B12 deficiency. Individuals who don't eat animal-derived foods are also at risk of a B12 deficiency. Certain medications can contribute to vitamin B12 depletion. B12 deficiency can manifest as neurological symptoms such as numbness or tingling in the hands, legs, or feet, difficulty walking, and confusion or difficulty thinking. Other symptoms can include anemia, weakness and fatigue, constipation, and a swollen tongue. B12 deficiency can lead to permanent nerve and brain damage and increases the risk of dementia.

After India: Deficiencies risk did not significantly change (I may benefit from niacin and B12 supplementation, obviously).

Short-Chain Fatty Acids

Pre India: High Short-Chain Fatty Acids (SCFAs) – all optimized and high. In the human body, SCFAs can act as an energy source and help our metabolism by improving blood lipid levels, increasing satiety, and improving sensitivity to insulin, act as a signaling molecule in the nervous system, among other systems, help prevent the absorption of toxic compounds, increase nutrient circulation, inhibit the growth of pathogens, stimulate the growth of beneficial bacteria, maintain a healthy pH, and improve overall gut-immune capacity.

After India: Drop in butyrate, drop in propionate, and drop in valerate. Seems all that fiber actually shifted my SFCAs in the opposite direction of what I would’ve expected. Interesting.

Beneficial Microbes

Pre India: Probiotics – Onegevity analyzed specific beneficial bacteria that are linked with commonly consumed probiotics. My microbiome has optimal levels of key beneficial microbes.

After India: Remained elevated.

Pathogens

Pre India: No known pathogens were found in my sample! Pathogens are bacteria, viruses, and parasites that can cause disease. Most of the bacteria in my gut are not pathogenic—in fact, less than 100 species of identified bacteria are linked to infectious diseases. There are tens of thousands of other bacterial species in the gut that are mostly harmless, or even beneficial!

After India: Still no known pathogens.

Firmicutes to Bacteroides Ratio

Pre India: The Firmicutes to Bacteroides ratio was 17% and 12%. The F:B ratio was at one time assumed to be related to health outcomes. Over the years, as research has continued to deepen our understanding of the microbiome, this ratio has been proven to be less relevant. There is roughly an even split between positive and negative associations with the ratio to any given condition at this time. Additionally, each phylum has several beneficial species, and each also has some potential problematic species.

After India: 16%:7%. Not an incredibly significant change, but interesting because many bacteroides species are significant clinical pathogens and are found in most anaerobic infections, with an associated mortality of more than 19%.

Akkermansia & Proteobacteria Levels

Pre India: Keystone taxa showed moderate Akkermansia/high Proteobacteria. Akkermansia muciniphila (AM) is one of the most interesting and beneficial bacteria in our microbiome. It typically makes up 1-5 percent of the microbiome, and your goal should be to maximize its abundance, which can generally be done with prebiotics and fiber. Proteobacteria is a phylum, which is a broader classification of bacteria than our other listings. It's consistently linked to negative health outcomes in the research. Although not all members of this phylum are “bad,” it does harbor a great many that are characterized as opportunistic pathogens.

After India: Significant drop in Faecalibacterium prausnitzii (a key butyrate producer). Significant rise in proteobacteria. Again, it seems the Indian diet actually reduced my butyrate and short-chain fatty acids in the opposite direction of what I would’ve expected.

A Few Final Thoughts

After getting this data, I went ahead and reached out to Connect Ventures in India, who has been gathering plenty of data on the indigenous biome using their own similar version of Gutbio, and here’s what they had to say:

“To begin with, you already seem to have an ideal gut microbiota (Pre-India Report) and most of the changes in microbial composition, abundance, and diversity (Post-India) seemed to be maintained. One of the main observations regarding Faecalibacterium prausnitzii being reduced in its abundance can be explained with few evidences. Plant-based enteral nutrition is known to reduce Faecalibacterium prausnitzii; on the other hand, saturated fat, found almost exclusively in animal sources, increases Bilophila and Faecalibacterium prausnitzii. This can be one of the main reasons why the abundance of this bacteria dropped. Consumption of egg, kefir, and prebiotic raffinose (RAF) (if consumed) also are known to have a similar impact on Faecalibacterium prausnitzii.

However, the key takeaway message from this exercise should be the following: There is no doubt that the dietary changes/habits influence the composition of the intestinal microbiota, and it is conceivable to anticipate a rise in bacterial diversity, SFCAs, and butyrate based on increased fiber consumption (in India). The key thing is, these dietary changes have a relatively fast impact (within a week) on the microbial composition and consequently on its metabolites, and these effects are modest (and even reversible). Changes of microbiota and other parameters after a 3-month vegetarian diet are significant but do not essentially reflect the degree of change that occurs with a long-term vegetarian diet. Since most of the anticipated observations come from the data that rely on a long-term vegetarian diet, it is an important factor in the duration of your dietary changes.”

References:

• The Effects of Vegetarian and Vegan Diets on Gut Microbiota
• Diet rapidly and reproducibly alters the human gut microbiome.
• Impact of diet on human intestinal microbiota and health.
• Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire.

Summary

Interesting, eh?

While my Gutbio results were not what I would’ve expected (I anticipated a rise in bacterial diversity, SFCAs, and butyrate based on increased fiber consumption compared to my fiber consumption at home), I’m constantly intrigued by how much data we can snag about our bodies from the emerging and rapidly developing world of self-quantification. I'm also curious what would have happened had I been on a longer course (based on the info in the feedback from Connect Ventures above) if I had remained on the diet for longer-term, such as 3+ months. Or perhaps I just have a bit of “colonization resistance” based on my immune system being pretty “happy” and well-established with my current microbiome, a concept you can read more about here.

Anyways, I'm back to my Standard American Diet…Ben-style, which is primarily:

• My anti-aging smoothie for breakfast, always after a 12-16 hour intermittent fast, 20-30 minutes aerobic or easy exercise (such as a walk in the sunshine or sauna session) and 2-5 minute cold soak.
• For a 2pm-ish lunch, a giant cup of bone broth with tons of herbs and spices stirred in, along with a mash-up of fermented vegetables such as kimchi and sauerkraut, along with sprouts, pumpkin mash, macadamia or Baruka nuts, oodles of olive oil, and sardines, mackerel, anchovies, herring or salmon, along with a few choice leftovers from dinner the night before (see my recent “weird-ass lunch” post on Instagram).
  • For an 8pm-ish dinner, some kind of grilled, sous vide, broiled or baked meat such as ribeye or fish, along with an organ meat such as liver, thyroid, sweetbreads, heart or kidney, and 100-200g of carbs from sources such as millet, sweet potato, yam, quinoa, carrots, beets, parsnips, etc., with a glass of red wine or a healthy cocktail and a bit of homemade yogurt with stevia or some homemade appetite-satiating, glycine-rich jello for dessert.

Let me know your thoughts below, and to get your own Gutbio test from Onegevity, you can click here and use code: BEN20 to save $20 on a Gutbio test and easy-to-read report.