Diving Deeper in my Gut! Mapping with Viome.

Although I think my results with UBiome have been very interesting, I still think there is a lot more to be learned from my gut! Especially as I dive deeper into the research, more and more parrallels are drawn between gut health and ilnesses of the modern era!

After learning about Viome at the Bulletproof Biohacking Conference of 2017, I thought this might be a tool to tell me if there are any nasties hanging out in my gut, or if there is a particular deficiency that I can work on.


Viome also boasts many other features such as the metabolic activitiy of your critters in your gut, and will even provide recommendations about foods that your particular gut critters prefer! To continue my Pokemon analogy from my Ubiome posts, Ubiome only provided me the names of the Pokemon in my gut, but told me little about thier strengths and weaknesses, abilities, or how to use them best in my team. Viome promises to tell me more along those lines!

The day before my Viome test was a pretty typical diet day for me. I had coffee with half and half in the morning. Lunch was a large salad with eggs and Kerrygolds cheddar cheese drizzled in olive oil and salt. Dinner was liver and onions, potatoes, cauliflour, and bacon – covered in Kerrygolds butter. My before-bedtime snack was Gold Nugget Ghee’s Chocolate Honey Ghee, yum! I took a few supplements including magnesium, l-theanine, lions mane, and trace minerals.The only slightly gut-disrupting thing I ate yesterday might be the bacon. I last had antibiotics about 5 months ago, so the effects of that should be subsided.

Collection is simple and similar to that of UBiome. You catch your normal stool in a convient toilet bag that is provided in the kit, then take a small scoop with the spoon and put it in the tube also all provided. Shake for a small period, then you are done! You ship it back to them in the pre-addressed package and wait for results.


The second part of the testing is the Metabolic health kit that comes. The main part is a blood sugar test and challenge. They provide a blood-glucose meter and a pouch of pure glucose/sugar for the test. The idea is to take a baseline reading of blood glucose, drink this powder of pure sugar, then re-measure blood-glucose at defined time periods afterwards.


Viome provides some overall scores for health, which are nice, but do not really dive into much details. I would even argue against my “good” scores for gut health and metabolic health, as we will see I need to follow a diet restricted of carbohydrates (which I have been doing), so that tells me I don’t have metabolic or gut flexibility.

Viome Gut ScoreMetabolic Score

I am going to skip over the individual bacteria for this post, and jump right into the diet recommendations. As I mentioned, the diet recommendations are the extra sauce that Viome offers over UBiome, and the recommendations are based on my metabolic measurements and gut analysis.

Macronutrient Ratios

We can see that my macronutrient ratio is very low-carb, moderate protein, and even Bulletproof! The only carbohydrates that they reccomend are non-starchy vegetables or very-fiberous complex carbohydrates like Wild Rice.

As I have been following the low-carb Bulletproof diet for several years now, this is a very reinforcing result that I have been following the correct diet! I think the biggest tweak I will make is to add in more proteins to my diet. Viome recommends that most animal protiens are ideal for me, with my “indulge” proteins being white chicken meat and game meat.

Viome offers more specific food breakdowns and categorize them in terms of “Indulge”, “Enjoy”, and “Minimize”. These are straighforward categories and make for a very easy shopping list if someone is looking to follow thier diet recommendations. They take some of the top “indulge” foods and will list them separatly as your  “superfoods”, but there are more as you dig through the full lists!

Super Foods

Most of these “Superfoods” I have not yet incorporated into my daily diet. It will be interesting to see the health effects once I implement more of these superfoods that are tailored to me.

Important Highlights for me:

  1. No starchy carbs whatsover! Limited complex-carbs.
  2. Zero sweeteners allowed.
  3. No fruits other than blueberries (indulge) and mulberries (indulge).
  4. A variety of non-starchy vegetables including cucumber and leafy greens are recommended.
  5. More protein, particularly from high quality animal sources.
  6. High-fat diet including animal fats, nuts&seeds, butter, ghee, and olive oil.
  7. Plenty of spices including cumin, cardamom, and fennel seed.
  8. Less alcohol and caffeine. I already know from my body that I am a poor metabolizer of both. Luckily Bulletproof coffee is lower in caffeine and seems to agree with me (especially blending in the butter and MCT).
  9. Less fermented foods and kombucha – interesting! I’ve already cut out kombucha from my diet due to the alcohol content.

These highlights sound like the basic outline of the Bulletproof Diet! I am very pleased that for the past 3 years I have followed this diet and have had amazing results. Based on these recommendations I am very reinforced continue my low-carb Bulletproof Diet with some of these great adjustments from Viome! I think Dave Asprey would be pleased too.

I see many Bulletproof and Keto folks being surprised that thier Viome recommendations include MORE carbohydrates. I would offer my opinion that they should be thankful that thier guts allow them the metabolic flexibility to choose different energy sources. I seem to be restricted in this sense. Luckily we are not locked-in to these recommendations for life, as our gut microbiomes can change rapidly with diet changes and over time. This is why Viome recommends a yearly test to get new results.

However, I do see an interesting opportunity here. Perhaps if I could market my gut bacteria in the form of FMT, I could offer people more microbes that love fat and protein and hate carbs! What do you think?

Thanks for reading!


How to Yo-Yo Diet! Part 2: Gaining the Weight Back and Then Some.

As we start the new year and set goals for our health, wealth, and family I want to finish the cautionary tale of my Yo-Yo dieting throughout the past 6 years. The success story is that I am now in the best shape of my life! However, along the way I had many ups and downs and this blog post focuses on the downs (up in terms of weight gain). As we traverse into the new year, I encourage everyone to set attainable and sustainable goals.

As previously shared, in December 2014 I was obese, had terrible energy levels, and was likely pre-diabetic. The important caveat here is: I rarely ever ate sugar! Since some sugar-lovers will say they rarely eat sugar too, let me clarify.

  1. I rarely drank soft drinks (at most once/month). My beverage of choice was water and if I craved something bubbly, I opted for seltzer.
  2. I never ate dessert after meals. I preferred filling up on a real meal rather than “saving room for dessert”.
  3. I never put sugar in my coffee, just cream or milk.
  4. I never snacked on candy or treats. My snacks were typically granola bars, bananas, oranges, or nuts.
  5. I never ate donuts/danish/muffins for breakfast. My typical breakfast was an egg&cheese sandwich and coffee.

Even though sugar is a common enemy in our obesity epidemic, it clearly was not the case for me. So, how did I gain so much weight with a reasonably healthy aversion to sugar?

In a previous post I discussed my first ever diet that I underwent in 2011. Dropping a clothing size was a big success for me! However, as with most diets, over time I went back to my familiar eating habits. This included egg sandwiches in the morning, sandwiches or pasta for lunch, and pasta, pizza, and french fries for dinner. A pretty standard American approach that seemed harmless to me.

During this time frame, I met my future wife and we shared a love for obtaining deals on food. We created accounts with numerous restaurant deal sites including Groupon, LivingSocial, SaveNowCT, LocalFlavor, DealChicken, and Restaurant.com.  In fact, for a short time I even wrote about some of our food-adventures in my first blog. At the time, it was so exciting to get an abundance of food really cheap. Unfortunately, the major downfalls to my health were:

  1. Going out for dinner 4-5 times per week.
  2. Large portion sizes at restaurants.
  3. Minimum purchase value on Groupons/coupons, so we were ordering more food than we normally would have.
  4. Low nutritional value foods and an improper balance of macronutrients.
  5. Leftovers to eat the next day.

What really put the nail in the coffin for me was the 8 months that I worked in Perth Amboy, NJ. I was living out of a hotel room for those 8 months and only had access to restaurant food at the time. That, combined with the loneliness of the situation, I could really feel my energy being sapped. I had low energy and barely got by with coffee and frequent snacking each day.


From 2009 to 2012, I slimmed down to a fitted large shirt. Then in 2014, I was back in an  XL shirt.

After leaving that job, I was relieved to be back home, but was still struggling with energy levels. Eventually, even coffee betrayed me as I started feeling jittery and anxious. I ended up giving up coffee completely for awhile. I always kept snacks of oranges, bananas, and granola bars nearby for whenever my energy dipped. I even went in to see an eye doctor because my vision was blurring and thought that I might need glasses. The doctor said that my vision was fine and it would be a bad idea to get glasses. I have since found out that blurred vision is a symptom of pre-diabetes…

Without having a clue what to do with my health, my wife had this zany idea to go to a Raw Vegan retreat. I was on the fence about it for awhile, but finally caved and agreed to go. I estimate that I was about 250 pounds at the time. I never expected the amazing results I got or just how much my overall health has improved!


To leave off on a good note – I’m back into slim fit large shirts or regular medium shirts!

Thanks for reading!


Gotta Catch ‘Em All… In my Gut – UBiome- The Great Gut Experiment Part 3

In earlier posts I’ve talked about my baseline gut profile and my gut profile after fasting. In my final post on gut microbiome, I dive into how to rebuild my gut flora into a more robust profile. It felt like attaining new bacteria was similar to tracking and catching Pokemon. While scrolling through my Pokedex (Ubiome results) and comparing them to the Pokedex of other people I realized I am deficient in quite a bit of bacteria! So the only way to stay in the game is to try to Catch Em’ All! So the plan is to lure them with their favorite treats and trap them in Pokeballs (my gut).


Actual names of gut bacteria… could be good stand-in names for Pokemon!

As I mentioned in my last post, we know we want to improve our ratio of Firmitcuties to Bacteroidities. The other bit of information we generally agree on about our gut bacteria is that we want more diversity. The better the diversity, the more robust our guts will be when they encounter times of hardship.


So we can see my baseline diversity in the 19th percentile is lagging behind the rest of the population. Typical of my experience in Pokemon games, I find myself jealous of all those cool bacteria that other people have that I am deficient in. Just look at all these different family’s of bacteria that I am low in!


Especially knowing those missing bacteria could give me access to cool powers like an improved immune system, brain function, and body composition. In Pokemon this would be a real issue, because not filling out your Pokedex can be a barrier to progress in the game! Also to really fuel my competitive side, UBiome proudly displays my “most rare” bacteria that few other people have. I only have 3 unique types, while it seems that other people may have much more!


So how do we promote diversity in our gut? How do I increase my amount of rare bacteria? After reviewing this article and the book Brain Maker, I did the following:

  1. Prebiotics – Inulin Fiber, Acai Fiber, Aloe Vera Gel
  2. Resistant Starches – Raw Potato Starch
  3. Probiotic Food: Homemade Saurkraut made with Mercola’s fermentation starter.
  4. Probiotic Supplement: I chose Primal Defense Ultra
  5. Probiotic “Greens”: Athletic Greens

It took a few days for me to get into a rhythm with my new routine. I found that doing a morning “shake” with my prebiotics, resistant starch, and Athletic Greens worked best. Then ate probiotic foods at lunch and dinner, and take my probiotic supplement at night. I did that for about a month. I will say that month I had the most gas I’ve ever had in my life, luckily it wasn’t smelly (to my knowledge). I also found that the raw potato starch gave me super solid poo’s, unfortunately as I read deeper into the literature it tends to cause gut dysbiosis, so I stopped using it after a few days. It is still a handy thickener to cook with.

I also noticed that I tended to feel full most of the day, and delayed my lunchtime till around 2pm, compared to my normal lunch at noon. So this program was a powerful appetite suppressant, and I found I shed a few pounds through the process. Pretty nice!

Unfortunately, the UBiome results themselves indicate a significant loss in diversity! I believe this is an error in how I took the sample, and not a good representative of my entire gut profile. So the lesson learned here, without getting too graphic, is to do well to homogenize the sample before swabbing for UBiome. Yuk!


That ends my trilogy of searching for all of the gut bugs in my body. Even though this part of the study was inconclusive due to poor data, I still plan on continuing to do probiotic supplements and foods, as well as occasionally adding prebiotic supplements to my regimen. Hopefully as the science develops I will be able to return to this data and learn more, or do more testing in the future (if there is another sale on the UBiome store)!

Happy hunting for your own gut monsters!

Thanks for Reading!


How to Yo-Yo diet! Part 1: Losing the Weight

So here is the story about the first time I’ve gone on a diet. After reading an article recently in the New York Times recently about how most Biggest Loser contestants have regained weight, it makes me concerned about the effects of extreme and yo-yo dieting. The article talks about a lowering of metabolism that follows weigh loss, along with painful urges to eat more and massive lethargy. Have they failed? Are these people weak-willed because they stopped working out 9 hours a week? Certainly not, it boils down to an issue of biology. Basically it revolves around the theory that we have a biological set-point for weight.As we attempt to lose weight, our bodies compensate by increasing hunger and decreasing activity/metabolism. Sheer force of will is often not enough to overcome this basic biological drive. I too have yo-yo dieted, and ended up weighing much more than I started. Here is my story.

You may know that over a year ago I was 250 lbs, obese, tired, and foggy. But for most of my life I feel I maintained my weight well around 230 lbs, likely starting back in high school after I was cut from the soccer team (mostly because I was too slow and lacked coordination). Nonetheless my weight and energy levels maintained well through high school and even college, although I’ve rarely weighed myself through the years. I’ve always eaten foods that taste good to me and eaten till full or satiated. I’ve never had a taste for sweets or chocolate, but do love my carbs of bagels, french fries, fettuccine alfredo, and rice. However, when it came time to get started in the dating world in 2011, I figured it might give me a leg up to slim down.


Me at my typical weight in 2009-2010, I’m sporting Extra-Large Ralph Lauren T-Shirts in both pictures that I am filling out quite nicely.

I did, in 2011, manage to lose a bunch of weight by following the Flat Belly Diet For Men. This diet touted the science of the Monounsaturated Fatty Acids (MUFAs) found in high concentrations in olives, olive oil, avocados, nuts&seeds, and dark chocolate (see the pattern here? I like diets that allow me to eat fat.). These foods were somehow naturally slimming for your waistline. And by following the meal plan of 5 small meals a day highlighting these foods can help you lose weight! At the same time I had also transferred to a Manufacturing engineering position that had me on my feet more often, and I was starting school for a Masters in Chemical Engineering. I was counting calories at the time, and even looked up low-calorie alcohols to consume while out with my college buddies. I eventually settled on bourbon-on-the-rocks, and my friends would even start to ask me “how is your bourbon diet going”?  And it was going well! I started to fit in my old high-school clothes, went down a size in shirts and pants, and started getting compliments from my co-workers!

When I think back to that diet knowing what I know now, here are the things that worked in my favor.

  1. Lower in carbs – By focusing on getting more “good fats” from olives, avocados, and nuts I was able to crowd out a lot of the carbohydrates typically in my diet, as well as being lower in potentially inflammatory fats like dairy or vegetable oils.
  2. Portion control – I did learn portion control by counting out my nuts into tiny prepared baggies, preparing wraps with feta, spinach, hummus, and turkey, and measuring the volume of my vegetables. While I think calorie counting isn’t the key to success in dieting, it is still good to understand the meaning of portion sizes and relative calories in foods.
  3. Skipping meals – Who has time to eat 5 small meals a day?! When I was busy in my Manufacturing Job and juggling school, I often skipped one or two of my 5 meals a day.
  4. More activity – As I mentioned I was on my feet much more for work during this time. I wasn’t doing any rigorous exercise but staying active at work and some occasional walks around the block seemed to help.
  5. Substitute beer for hard alcohol – Bourbon on-the-rocks is a much more fat-burning drink than beer. Hard alcohol is much lower in carbs, more concentrated so you drink less for the same buzz, and if filtered well avoids toxins that can come from beer or wine. Even now this is my drink of choice.
  6. Avoid the scale – For this diet I did not own or check in on a scale at all. As I mentioned I was doing this to look more trim and attract ladies. So for this purpose I didn’t need a scale, I could feel it when my clothes start to get baggy. When people asked me how much weight I had lost, I mostly just shrugged, truly not knowing.



Pictures of me in 2011 and early 2012, In the left I am wearing a Large Tommy Hilfiger T-shirt, showing I dropped a size through my new diet and activities.

Unfortunately, at that time I had no idea the reasons why I had been successful for weight loss. I only knew that blindly following the diet and counting calories seemed to be helping me. Eventually I would get bored of counting and measuring my food, start eating out more and slip back to old habits. Part two of this series I will dive into how I gained back more weight than I started with!

Thanks for reading!



Dorking out in Aruba

My wife and I visited Aruba a few weeks ago, the One Happy Little Island! It is an amazing place to visit, the beaches were gorgeous, food was great, and totally relaxing. In preparing for the trip, I also planned a few biohacks I would want to do before and during the trip. The term biohacking is part of an art of controlling your surroundings to improve your performance. While travelling you can expect whole new environments to try to work in your favor. Knowing we would be getting extra sun exposure was a key area of focus, aside from my normal focus on nutrition.


Obligatory thoughtful pose looking out over the water.

Sun protection is key due to skin cancer concerns, however, this advice is often conflicted by the fact that Vitamin D is so darn important. So I set out to try to understand how to improve the quality of my sun exposure. A supplement I stumbled across is Astaxanthin, which is an antioxidant member of the carotenoid family (think carrots and tomatoes). Astaxanthin is a naturally occurring substance responsible for the red color in salmon and krill. This supplement is reported to be protective from sunlight and extend the amount of time you can spend in the sun without turning red. So, for the weeks prior to our trip to Aruba, my wife and I started a daily supplement of this substance.

I definitely didn’t want to rely on Astaxanthin as my only protection, so I went to the EWG’s list of approved sunblocks to stock up on ones that avoid many of the risky chemicals in conventional sunblock. I ordered a few different brands, because we had used the Badger brand before and it didn’t spread well.

Finally, if we were outside not intentionally absorbing sunlight, I made sure I was always wearing a wide-brimmed hat to protect my face and neck from exposure, which are the most common places people get sunburn. I didn’t care if I looked like a dorky tourist, I definitely didn’t want to get a burn on my moneymaker (face).

When we arrived on the island, I really geeked out when I found out the island had an amazing supply of Gouda cheese! Not only is Gouda a delicious type of cheese, but it contains the highest Vitamin K2 content than all other cheeses. Why is this important? Well, K2 has been shown to be synergistic with the effects of Vitamin D, and having the right balance of K2 and D will help prevent Vitamin D toxicity. So as you are basking in the sunlight, enjoying some gouda cheese will be synergistic. Also, the fat from the cheese will help the body absorb both of these fat-soluble nutrients.


So much Gouda!

I put my Astaxanthin to the test one day by intentionally laying out in direct sun for 25 minutes without sunscreen. Afterwards I retreated to the shade, and allowed my newly produced Vitamin D soak in for 20 minutes. Then I applied sunscreen and we went in the water for a little while. I did get mottled redness around my shoulders, collarbone, and one forearm, but overall I did really good. I think the combination of being in the sun without sunscreen and being in the water losing some sunscreen caused my mild burn. So the Astaxanathin proved not to be a miracle skin protector, but I would like to think it helped avoid more severe sunburns.

Afterwards, I was able to apply some Aruba Aloe to my burns by using the free samples from the storefronts peppered across the island.

I found it quite easy to stick to my diet on the island. Most of our meals we prepared ourselves in the condo, having stopped at the grocery store on the first day to stock up for the week. The grocery store had a great name!


Super Food grocery store, with a Dragon Ball icon above it?

When we did go out to dinner, I also had an easy time sticking to my diet. I typically ordered the French Onion soup, and pulled all the bread out and ate everything else. The bread really looks nasty when it is dissociated from the rest of the soup. My meals were usually the fresh catch fish from the island, vegetables, and I always substituted the starch for extra vegetables! As a bonus, I asked for extra butter with my meals, and they came out with a server full of pre-melted butter! It was great!


Delicious Red Snapper with double veggies!

Aruba turned out to be an amazing trip. The beaches, sunlight, and scenery were beautiful. On top of that, I felt great by maximizing the benefits of the sunlight and nutrition sources on the island.

Thanks for reading!



What Happens to the Microbiome after a Fast and Cleanse? – uBiome – The Great Gut Experiment

The study of the human microbiome with relationship to health is a very exciting new field. Not wanting to fall behind the curve on this new health trend, I am jumping in head-first wanting to take full control of the bugs that live in my gut. I’ve enlisted uBiome to take a baseline sample of my microbiome, and have completed my first phase of the experiment to do a full gut cleanse! My cleanse included 4 days of fasting, some antimicrobial supplements, and top it off with colon hydrotherapy!

Knowing that gut bacteria generally survive by fermenting the foods from my diet, especially fiber, I wanted to see what would happened if I essentially “starved” them for several days. I came up with a liquid meal plan that would give me what I needed to thrive for several days but also deprive my gut as much as possible. Here was my overall plan:

Breakfast” – Water with Himalayan Salt & Bulletproof Coffee
Lunch” – Lemon Juice and Ginger Tea blend, & 32 Oz Green Juice from Cucumber, Celery, and Cabbage.
Afternoon Snack” – Dandelion Tea
Dinner” – Bone Broth w/ Butter & Garlic
Nightcap” – Heaping Tablespoon of Raw Honey before bed

I think this meal plan worked out phenomenally well. The timing of the fluids were around the normal mealtimes keeping my body nourished at the times it expects foods. The bone broth for dinner is very satisfying in the evening, and taking a tablespoon of raw honey is a clever biohack to promote sleep and calm the brain before bed. Foods like lemon, ginger, cabbage, and raw honey are all naturally anti-microbial which also help me in my effort to decimate any “bad” bugs down there. Recent buzz around bone broth as a means of healing the gut is another big reason why it is included in my diet.

As I mentioned I also wanted to take this opportunity to clear out any “bad” bacteria. There are many reports of foods that are naturally antimicrobial, antibacterial, and antiviral that can be used to boost immunity. The issue is that these alternative supplements and therapies are difficult to find effective doses and brands. However, in the spirit of this experiment, I went ahead and did as many as I could get my hands on. Here is the list of supplements I was taking during my fast:

  1. Coconut oil
  2. Oregano essential oil (mixed in the coconut oil and ingested)
  3. Honey
  4. Cinnamon (in the honey and tea)
  5. Garlic
  6. Echinacia & Goldenseal
  7. Oil Pulling (with the Coconut Oil)

Showing my collection of fabulous anti-microbial and immune boosting supplements.

Throwing all of these into my fast was hopefully making an impact on my gut. I do understand that supplements like these aren’t to be taken recklessly, as the same issues with developing resistant bacteria can occur with these supplements as they can with traditional antibiotics.

Finally, on the 3rd day of my fast I did colon hydrotherapy. This is a session lasting about 45 minutes where your colon is continuously flushed out with water. Without getting into too much details, I will say with this being the 3rd day of the fast, there really wasn’t much to come out. This is ideal, because now I am really getting down to clearing out the mucus and altering the lining of my gut. All hopefully in a positive way.

My experience during the fast was generally positive. I had plenty of energy, was going to work normally, and never really felt “hungry.” It is very interesting to separate the difference between feelings of hunger versus feelings of having an empty stomach. I had a few times in the afternoon when I felt some brain fog and fatigue, but really it wasn’t worse than the normal afternoon snooze feelings I usually have. After my colon hydrotherapy I felt light as a feather, and continued with my fast feeling energized and great. On the morning of the 4th day I went to a yoga class! Yes, I had no issue after 4 days of fasting to do some gentle exercise. After yoga I dreaded breaking the fast. I knew that if I started to eat it would trigger a cascade of food cravings. I drank a smoothie of avocado, cucumber, and celery, then waited for my next movement to collect a sample for uBiome.

Over the course of the fast I lost a total of 5 lbs. Pretty good! 5lbs in 4 days! However, my 4th day was also Christmas Eve, and by the time I came to my Christmas parties the food cravings had taken over. By December 30th I had gained back 7 lbs, uh oh! So take this as a cautionary tale, that fasting may not get lasting results, especially if you do it just before the holidays. I’m sure if I broke the fast and went back to my Bulletproof diet I could have retained some of the results, but unfortunately it did not work well.

So lets take a look at the uBiome results!

Fast Compare Bacteroides

My Before and After (Before in Grey, After in Blue) gut biome results from fasting. Definitely a dramatic shift in Firmicutes down and Bacteroidetes up in positive directions.

The first thing I will mention is the Bacteroides to Firmicutes ratio has greatly improved! As I mentioned in my previous post we generally see high Firmicutes associated with obesity and the Western diet. So it is good I am able to drive my results further to the Bacteroidetes spectrum. My results are consistent with the results found in this American Gut Project study. In fact, like the study I too found a beneficial shift in my Akkermansia, increasing that particular genus by 40% with my protocol (read more in the link to learn about Akkermansia’s role in the gut)! It is exciting to see that I am able to reproduce the same results as that study with my own data!

I did not see a particularly compelling loss of diversity, my diversity measure only dropped by 1 percentile. I was expecting to have a much bigger impact on the diversity having only lost 8 species of bacteria total. Oddly enough, those missing microbes were replaced by 7 new species, including proliferation of a beneficial Bacteroides species. This finding is consistent with Richard Sprague’s finding of new bugs after his gut cleanse experiment. So, while many species of bacteria did show significant shifts in their counts, only a few were completely wiped out. This is perhaps a good finding that our microbiomes are relatively robust even when subjugated to short term extremes. It does raise many more questions about where the new bacteria came from, and if the additional supplements of my 4-day diet affected the results at all. However, I am happy to have made a measurable difference at least in the relative ratios so far.

The two references in the previous paragraphs show that after a fast and/or a gut cleanse, the microbial communities quickly return to their original state (assuming you resume your same pre-cleanse diet). My next phase of my experiment is to settle back into my usual diet, however now supplementing prebiotics, probiotics, and more probiotic foods. This I hope to sustain some of the good shifts, while introducing and promoting even more good bacteria into my system. My results so far show that I am deficient in many of the Lactobacilli bacteria that are contained in popular probiotic supplements. So I am interested in seeing if those bacteria appear in my next sample.

Update – see the final posting of my UBiome trilogy here!

Thanks for reading! Let me know if you have any questions on the diet or outcome! I feel like I can slice the data in many different ways to analyze it, but want to keep what I am reporting relevant and concise.


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!