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Experimenting with a Gut Cleanse – By Richard Sprague

Guest post by Richard Sprague

Your gut microbiome changes constantly in response to everything from diet to exercise, so when looking at multiple uBiome test results side-by-side it can be complicated to figure out what caused a particular change. What if you could radically alter your microbiome with a cleanse and just track that, along with precisely what you eat afterwards? What could you learn?

I recently tried exactly that, using a colon cleanse – the kind you do before a colonoscopy screening. By flushing most of the bacteria from my system and carefully watching them grow back with side-by-side uBiome tests, I learned a few things that might interest you as well:

My gut microbiome recovers pretty quickly. Unlike antibiotics, which are known to cause long-term (and possibly permanent) changes, losing bacteria this way seems only to affect the total numbers, but they sprout right back just like a haircut. In two weeks I was as good as new.

This is an overall view of how my gut biome changed:


Amounts and ratios changed, but not the specific organisms. Of course I lost a bunch of bacteria – that was the point – but surprisingly I didn’t seem to gain anything really new, even after an aggressive attempt at re-seeding. I didn’t gain or lose a single phyla. Other than amounts and ratios, I had to dig down to the Class level of the biological hierarchy to find anything that was permanently lost, and even at the very fine-grained Genus level, only two taxa that had been regularly present beforehand were now extinct. (Holdemania and Methanomassiliicoccus).

There is more change when you look at this functional view, but even then watch how quickly it bounces back:


A couple of weird ones, at small amounts, made a brief appearance. I was especially intrigued by five new taxa that showed up just once, the day after the cleanse, and then disappeared. Maybe I found some that ordinarily get lost in the noise of the microbiome and only show up when the rest of the forest has been cleared. These are some hardy guys and I’m glad I know their names and can watch for them again: Abiotrophia, Bacillus, Catonella, Christensenella, Parvimonas.

It’s pretty hard to make a significant change. These days a little googling will find plenty of web sites, books, diets, and supplements that claim to “fix” or “change” your microbiome. I’m a healthy, reasonably fit adult, so maybe I didn’t try as hard as somebody might with a specific health problem, but I thought simply popping probiotics and eating a variety of new and fermented foods would have a big effect. Nope. There are exceptions – my past experience with sleep hacking demonstrated conclusively to me that I can temporarily change my bifidobacterium levels for example – but those examples are harder to find than I had hoped.

Here’s another important ratio that microbiologists have found useful to see how the gut biome changes:

See much change? Me neither. There’s a short spike during the cleanse, but then it just pops back to normal.

Follow me on Twitter, or check my personal web site for more details of my experiment, and please let me know if you did or are thinking of something similar!


62 Thoughts on “Experimenting with a Gut Cleanse – By Richard Sprague”

  • I have good diversity except in the category for obesity. I am short most of those bacteria and have a weight problem. I eat plant based with modest amounts of wild caught fish, grass fed meat. everything is organic and take probiotics etc. I was thinking to do a colonic and do some major changes. Might it make sense to do a fecal implant of a naturally think person with ample amounts of missing bacteria. I was also found very short of lactobaccilus-and stopped eating dairy. Do you think adding back dairy say, Kefir might help? I am a health coach and want so much to help my clients. (I always experiment on myself first.)

  • Rita says:

    This is all so fascinating!! I’ve been asking my doctor if she would recommend a FMT and she chuckles. My history is constipation since my early 20’s and I am now 57. Diagnosis since 2006: Gastric paresis, 2007: Lyme 2008: Chronic Fatique, Fibromyalgia, Gut Dysbiosis. I was on every antibiotic and parasitic medication imaginable for 2.5 years; oral antibiotics for a bit over 18 months and IV antibiotics for 9 months. I finally gave in and Miralax has been my best friend for 4 years or I would be the poster child for being full of $#!@. I am MTHFR C677T; a genetic issue where Folate is not metabolized and one has a difficult time detoxifying. Supposedly due to this I will never fully rid myself of Lyme which doctors have said is the root of all issues for me.

    I have been eating only organically for 20 years, no soda, no junk food. I do know this – there has got to be a way to get my microbiome in better shape so Miralax can exit my life. Maybe I’ll have to go to another country for FMT! I apologize for unloading but I’ve been trying to find answers/help for far too long.

  • Jim Bitner says:

    Thanks for this…..a couple questions….what is your history of antibiotic use, if any, and what was your intake, post cleanse? “Popping a few probiotics……….” doesn’t give much info., i.e. what type, how many per day, #CFU’s, etc. As you likely know, varieties of probiotics, their quality, etc. appear to vary widely. Thanks

  • Dear Richard,

    I was happy to read the results of your experience. I have done colonic irrigation for 21 years and teach fasting with a self-administered colonic irrigation I call Yogalonics.

    Your findings confirm what I have always thought, and teach to my fasters; that as soon as the last of the colonic is eliminated the body will immediately resume producing the bacteria it needs.

    In addition, I do believe that depending on a person’s genes, dietary influences of their past and present, the microbiome of the soil the food comes from,exposure to vaccines, other drugs, chemicals, their environment including the people, animals, their moods and who they are (maybe even the planets that influence them) all influence their microbiome.

    Thanks so much! I look forward to more articles.

    Hillary Adrian

  • Wendy says:

    This is especially interesting to me as I’ve had 5 colonoscopies over the last 18 months (and will have another next week) and have always felt “wiped out” for quite a while after – as in, fatigued, I guess. I’m not sure how much of that as to do with lingering effects of the sedation, or the loss of some bacteria. My GP has always said that the colon prep shouldn’t have too much of an effect on the body. But I’m now also seeing a naturopath who said doing the colon prep can affect the gut flora in a similar way to taking antibiotics, so she’s given me a couple of different types of probiotics to take. It’s tricky to know who to believe! But I’ll get to see next week if taking the probiotics will help me to recover faster!

    • Janette says:

      Wendy and others might be interested to know that in the US, Danbury Hospital uses an alternative to the drinkable prep for colonoscopy. They do colon hydrotherapy in the hospital for patients who don’t tolerate the usual prep. Apparently the elderly can be at risk of kidney failure taking the oral prep even! I am a nurse in Canada using colon hydrotherapy for correcting and improving function of the lower bowel. What I find clinically is that healthy bowel habits depend on healthy gut flora balance and daily replenishment of good bacteria in the diet along with the fiber and FOS containing foods that feed them and keep them happy. The muscular wave-like contractions of the bowel improve with both added fiber and probiotics. So even if they are just passing through as they would in the contents of foods we eat, they are vital to having health bowel habits. If bowels are backed up with fecal matter this too can affect the micro biome in a negative way.

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