The Great Gut Experiment – uBiome – What Is My Current State?

This past year has been revolutionary with us being able to measure and relate gut bacteria to everything from brain health and immunity, to physical fitness and weight. I’m constantly being bombarded with articles about the importance of probiotic supplements and probiotic foods like sauerkraut, kimchi, and kefir.  Even the idea of supplementing prebiotics, fiber, and resistant starches to “feed” our gut microbiota (bacteria living in our guts) is now a common theme in health news.

What is more concerning to me is that foods and habits common to the standard Westernized world are often feeding the “bad” bacteria while decimating the “good” bacteria. These are the sugars, refined carbohydrates, anti-nutrients, preservatives, artificial sweeteners, plastics, fluoride, chlorine, antiseptics, and antibiotics so commonly found in the Western society. A good place to start to understand all this is Missing Microbes by Martin Blaser.

However, I have remained relatively skeptical about the relevance of these microbes. Even if we do relate certain microbiome-nourising foods to our health, can we really say that broccoli is healthy because it is feeding my “good” bacteria, or is it because of the nutrients it contains, or that we are avoiding bad foods by eating more good foods,  or some combination of all the above? I think it has to be a combination, and as we have seen in nutrition science it is very hard to separate these into individual variables for actionable advice.

However, there are some remarkable studies utilizing fecal transplants in humans and rat models that show the microbiome is causal to the health benefits related to it. We can take the feces from an obese rat and place it in a skinny rat, and see the skinny rat grow obese with no change in diet! And this can work vice-versa! This is exciting knowledge that fecal transplants could become a revolutionary treatment in the near future!

So how can we know what our individual microbiome looks like and how that affects our health? Enter uBiome, a citizen science project in which anyone can take their own stool samples at home and send it in for analysis. Not only can we answer questions for ourselves, our information can be used in concert with thousands of other citizen scientists to build databases of knowledge.

I bought a 3-pack from the website and with it I wanted to answer a lot of questions for myself. What is my current state microbiome? I have made a drastic dietary change last year, but is it still affected by my 26 years of Western diet and antibiotic use? Am I still fighting those “bad” bugs, or have they left me completely already? Am I missing any important bugs?

So that is what I set out to test. I tried to keep my diet relatively stable for the week of my sample. I did my Bulletproof Intermittent Fasting, large salads at work, veggie stir fry for dinner, beef, seafood, cheese, and occasional sauerkraut. The day before my sample I did eat lunch at a Mexican restaurant which may be particularly gut disrupting, but not out of the norm for me to eat out once a week so it should be an accurate representation. See the results here:

Phylum View Breakdown

This figure depicts the Phylum (Phyla?) of bacteria present in their overall percentages compared to the total count of bacteria in my sample.

The only thing I know to look for here is the relative ratio of Firmicutes and Bacteroidetes, which are the dominant Phyla in human guts. We know that the Western diet promotes more Firmicuties, and with a more natural diet you would see more Bacteroidities. These two phylum play a role in metabolism and the absorption of calories from the diet and higher rates of Firmicuties have correlations to Western diseases. However right now I don’t know of any absolute target ratio of these bacteria to be shooting for other than knowing I want more Bacteroidetes in general. I do know, for example, obese rats have a 0.27 ratio Bacteroides to Firmicutes, and lean rats have about a 0.63 ratio. My sample data shows my ratio is about 0.63 – so I compare well to lean rats! That is a good thing!

uBiome also presents a calculation of the functionality of my microbes, and what my gut bugs can and cannot do compared to the rest of the human gut samples sent in. See the chart below for the different categories and my rates compared to all other Men samples.

Function Analysis

The listing of metabolic functions and their relative strength compared to other samples. The blue bars represent my data, and the grey bars are that of all Men from the uBiome directory.

Interestingly, my caffeine metabolism is absolute garbage! Two of my samples confirmed it so I don’t think it is a measurement error. I must be lacking the bacteria that uBiome associates with that function (they don’t tell me which ones I am missing though). This may explain why coffee can easily make me feel wired and jittery (especially if it isn’t Bulletproof), and I absolutely cannot have caffeine in the afternoon! I did a few scholarly searches and found that they were able to identify strains of microorganisms in a coffee-eating insect that facilitate caffeine detoxification. They isolated Pseudomonas fulva as the primary driver of caffeine digestion in this insect by administering antibiotics to wipe out the bacteria, then reinoculated the insect with just this strain. According to my uBiome result, I am lacking in any of the Pseudomonas bacteria genus (I’m trying to be precise with my taxonomy), and they are normally present in humans in small amounts. My loss of Pseudomonas could be related to prior antibiotic use, just like how they were able to wipe it out in the insects in the study. I definitely will be looking further into this if there are any actionable ways to improve this metric for myself.

uBiome offers some great ways to analyze and compare samples, but it also offers functions to export all of my bacterial data to do my own analysis! I’m sure I will be including more discussion and analysis of my results in future posts.

With my next two uBiome samples, I hope to answer: What if I do ALL THE THINGS that can affect my microbiota? So I broke it into 2 phases. Phase 1 is to be as anti-microbiome as possible, but in a “good” way. So I went on a 4-day liquid fast, with as many naturally anti-microbial supplements as possible, and near the end of the fast having a full colon cleanse with colon hydrotherapy. See the results here in my next post.

Phase 2 will be as pro-microbiome as possible. I will go back to essentially my usual Bulletproof-esq diet, however introducing (for the first time) probiotic supplements, prebiotic fiber supplements, resistant starches, fermented foods, and even probiotic enemas. I figure my gut should be primed from phase 1 to receive all this pro-microbiome goodness.

After all of that and the relevant analysis, I will have hopefully answered for myself if I have full control over the bugs in my gut, or if they are relatively unaffected by my intentional perturbations. We shall see!


5 thoughts on “The Great Gut Experiment – uBiome – What Is My Current State?

  1. Really interesting and hot topic right now!!! So glad you are exploring your own microbiome. Can’t wait to hear how Phase 1 and 2 turn out! I’m pretty sure I remember you mentioning that you brew kombucha at home. If so, I wanted to suggest/ask you to do a “how-to” post on brewing kombucha (a great source of probiotics) with how to get started, what to expect, is it cheaper to brew? (I am guessing it is!), maintenance, etc. Thanks 🙂


    • Hi Carianne! Thanks for the feedback! Yes this is a very exciting time for the microbiome subject and very empowering for disease prevention and treatment.

      For Kombucha, I’ve actually stopped brewing/drinking it in the past few months. I found that it adversely affects my sleep (which will be another blog post), but based on your request I can still do a post on it! I’ve got my SCOBY “on hold” right now if I ever want to go back to it. I am still making sauerkrauts and plan on doing more fermented veggies and foods in the future.


  2. Pingback: What Happens to the Microbiome after a Fast and Cleanse? – uBiome – The Great Gut Experiment | Sustenance Kaizen

  3. Pingback: Gotta Catch ‘Em All… In my Gut – UBiome- The Great Gut Experiment Part 3 | Sustenance Kaizen

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