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.



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

  1. Pingback: The Great Gut Experiment – uBiome – What Is My Current State? | Sustenance Kaizen

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

  3. Pingback: Diving Deeper in my Gut! Mapping with Viome. | Sustenance Kaizen

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