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

  1. It shouldn’t be surprising that the proportions bounce back. Even if the ‘cleanse’ removes 99.9% of each species of bacteria, this still leaves many millions ready to repopulate once the food starts coming again.

  2. Priscila


    I’m a MD from Brasil and I think that your experience so much interesting!!
    I will love to receive newsletter about it.

  3. Ben-Jamin

    I am not sure how thorough a colon cleanse is at the bacterial level. I would assume that it knocks down the numbers of most bacteria. But I wouldn’t expect it to kill all of them off at all.

    And form what I understand, this is exactly the purpose of the appendix: to store gut bacteria for re-population after emptying from exposure to toxins/parasites/bacteria. Antibiotics, unfortunately, kill the stored bacteria.

    1. Richard Lin

      Hi Benjamin,

      Can you provide a study that antibiotics kills the stored bacteria in the appendix?

  4. Fascinating look at a trend I have always wondered about. Looks like you flushed out the transient ones (ones just floating around in your gut) with the prep, but as I would of expected, had little lasting effect on the ones anchored in the biofilm whose job it is to repopulate.

    This experiment would differ considerably from an exposure to antibiotics where you’re actually killing the bacteria and not simply flushing them out. Would love to discuss this with you and learn more if you’re game.

  5. Vardmer

    Fascinating. Do you have similar graphs available for viewing for before and after FMT?

    It would also be interesting to see a longer time series to see what the normal fluctuations are. Without that, its hard to say what “normal variation” is, compared to variation due to any specific treatment, dietary change, etc.

    Thanks for sharing!

  6. Marissa

    I feel as thought you might have more dramatic differences if you tried a diet change, rather than a colon cleanse. Are you planning on experimenting with alternative variables?

      1. Luis

        Hi Richard, I was wondering what fasting would do to the micro biome?. I recently completed a 13 day water fast and that is one of the things I puzzle about.The main reason I fasted in the first place was to attain a deep cleanse and better over all health. One of the many positives of the fast was, I never started coffee and artificial sweeteners again with so far with no ill effects.
        So I wonder if fasting has the same or similar result as your chemical cleanse? or how it may have affected my micro biome?

      2. Steve

        Hi Richard. Without any dietary changes, just a simple change in probiotic species changed one of our patient’s percentage of bacteroidetes to firmicutes dramatically. It was a hunch we tried as the patient had adult-onset acne. He had an overabundance of bateroidetes and when we altered his probiotic regimen, his acne all but went away. What is your website by the way?

    1. Hi, Marissa [and Tim]

      You have a point re: *diet change*
      How about if your diet also included simple to implement measures, i.e. including foods that feed your gut flora – thus maximizing on the food front, or even toasting fennel seeds and then brewing for tea, adding fresh ginger root too?

  7. Billy

    Odd that no one mentions fecal transplanting, which I was most hoping would be discussed in this article, since it seems to be the only way to significantly change one’s gut biome.

  8. Kelly

    Yes, I would strongly request data on FMT before and after data. Can you follow up with this. It would be very helpful.

  9. My husband and I are in the alternative health profession (he’s a chiropractor and I’m a naturopath and acupuncturist), and he’s spent decades doing lab tests on the gut microbiota. He discovered in his practice that diet and probiotics were not causing changes in the lab values. He finally worked with the pathologist at the lab to design a clinical protocol that does make positive changes and we have continued with this protocol and seen fantastic results (we do begin with patients who have gut dysbiosis, not generally healthy people). Also, we have 3 layers of mucus in our gut in which these bacteria live, and it is unlikely that all layers would be completely evacuated in the type of cleanse you did. So, in short, based on physiology and clinical experience, your experience is what I would expect to see. If you’re interested in some ideas of other experiments you could do that might have more of an effect, please email me. I’d be happy to discuss some of the things we see making changes in our patients.

    1. Dave

      Hi there. I have Gut issues and am VERY interested in your Protocol, can you give us a general idea of what it is? Can I email you for info or call? Thank you

    2. James

      Hello Megan/Richard
      I have had a few colon cleanses but my major problem is constipation. Do you have any natural remedies that you would recommend? Your help/advice would be much appreciated.
      Kind regards

      1. Cheryl

        Hi James, I suggest you drink up to 2 litres of water as soon as you get up in the morning. This has worked wonders for me, it really moves everything.

    3. Link

      I would love to hear some of these ideas, how can I contact you? Or maybe you could post them here as a reply so everyone can benefit…

    4. Justine

      I was interested in some of the other things you are doing that are making a difference. Can you please share? Many thanks!

    5. Christian

      Hi megan,

      That is awesome! I am a chiropractor who practices AK muscle testing supplements and my mentors used to say probiotics are a fad. I honestly only find probiotics to test in maybe 5% of my patients. They help symptomatically and acutely but haven’t seen anything worth spending money on in the longterm.

      I’ve got some interesting stuff more based on the terrain of the gut that has worked better.

      Would you email me and we can ping ideas off eachother? Cmcarroll2@gmail.com

    6. Fascinating! I would be very interested in seeing the before/after results of your tests. My experience is that many patients feel better after some of these protocols, but without actual uBiome-like tests, it’s hard to say if that’s due to a shift in microbiome, or to something else. It would be great if you could publish the uBiome results if you have them.

      1. Richard,
        The research that I mentioned was done in my husband’s clinic using DiagnosTech’s GI Health Panel. There were significant changes in the gut biome from before and after treatment. I don’t currently have access to the laboratory results as we are on a 3-month international trip (we teach around the world), but I’d be interested in communicating with you further. I am only just now learning about uBiome, I’d be very interested in doing some testing with the 5-Site Kit as we have been looking also at the vaginal biome recently (another huge issue).

    7. Mary


      Please add me to the list of people who are interested in this. Where can we contact you?

      I’m not seeing anything on your website about this.



    8. Wow,
      I didn’t realize I would get this much of a response. There are so many of you who are interested in improving your health through your gut biome and that is fantastic. I’m left in a quandary. If I were a lay person who had experienced this protocol I suspect I would put it up on a website for anyone to read without a 2nd thought. As a physician, there are legal issues regarding me providing “treatment” protocols without having seen you as a patient. I’ve never seen any adverse effects from this treatment, but if one of you were to react poorly, or even have an unrelated adverse event occur, I could be liable. So I have to cover my ass. I’d prefer to share this information as widely as possible, but I’m going to have to examine potential ramifications before I do this.

      For now, what I can offer you right now is the source of this information. If you see a Total Body Modification (TBM) practitioner, and if they have taken a seminar recently, they learned the protocol of which I am speaking. On our website, http://www.tbmseminars.com, we have a “find a practitioner” link where you can search for a practitioner in your area. You can call a prospective practitioner and ask if they know the “Acidophilus Surge Protocol”. If they don’t, the practitioner is welcome to email TBM and ask for that information. So in this way, each of you can find a doctor/practitioner who can prescribe this protocol for you.

      I hope this helps.

  10. I’m not personally convinced by anything I’ve really read that simply ingesting probiotics, or even fermented foods, will make much of a difference if you are missing many species. It does seem, like you said, you can make temporary changes, but I’ve had a hard time finding any real references that show a person can improve things dramatically with the current approaches. I was given clindamycin in 2005 which immediately caused a c. diff infection – my recent uBiome results show reduced diversity and many missing phyla, even 10 years later. Granted I don’t know what it looked like before, but given the digestive issues I’ve had since that time (IBS), I suspect it’s all related.

  11. Sheridan Jackson

    This morning, in that free-associating, sometimes creative state between dawning consciousness and actually arising, I was thinking about whether the biomes of fecal implant donors and recipients are assayed, before and after, and how the resulting data might lead to development of a battery of specific cultures that could be prescribed to remedy a wide array of illnesses. Then I read your disillusioning gut-cleanse story. It doesn’t seem to square with the glowing media reports appearing lately about the burgeoning field of biome-based therapies.
    I was puzzled by the graphs…it appears to show that the greatest rate of change was in the period preceding the cleanse, when I would expect a rather static baseline.

    1. Thanks for your comments. The graphs are line graphs, so what you see are interpolations between discrete points. The cleanse happened on the afternoon of the 19th, after the sample that day was taken. What you see on the 20th, then, is the first test result after the cleanse.

    2. Jim

      You miss the point.
      FMT requires 2 weeks of antibiotics prior to the transplant. The recipient has basically no gut bacteria at that point.
      This test with a “cleanse” did not kill of the gut bacteria. It is in no way comparable with FMT.

  12. Dave

    Hello and thank you for this great experiment, very excited really to see more data and experiments you will do going forward.

    I have some comments about this particular experiment:

    – Colon Cleanse – This is vague, what exactly did you do? Its hard to put in context the whole experiment without knowing exactly how you flushed them. Are we talking Colon Hydrotherapy, taking Supplements to help Flush the Colon, both, something else?

    – It would be also interesting to know which Probiotics were taken, how much, and anything else done in detail to repopulate the Gut (like which foods, how much, how long, etc)

    Thank you for doing this and any additional information. I have Gut issues, and feel the Probiotics I have tried to date (several) are not making a difference. I am VERY concerned my Microbiome has permanent damage from a lifetime of taking toxic Antibiotics (NO ONE should take Cipro, EVER!) and I really need to figure out how to correct this.

    I hope you find some volunteers and do some small studies, even if it 5 people, one with no Appendix like yourself, 1 with, etc and hopefully you will find one person who is ABOUT to take Antibiotics, take a Gut picture before and after. THIS would be awesome information, and especially helpful if it DOES end up with a lot of Biome damage, how long it might last, and if it can be corrected at all. I don’t think I have to mention that Antibiotic use is at utterly retarded levels here, so this kind of research would be CRITICAL to the health of many people!!!! Thank you again!

    1. Dave

      I should mention too, that it would be nice to see 3 people who take Antibiotics, Gut before and After pictures with NO supplementation after. And then another 3 people, take SAME Antibiotics, and then after take the SAME probiotics, Gut pics before and after. I mean if these Probiotics are not really having any effect, what a waste of time, money and health!

      1. Drew

        Dave what’s your email as I would like to open dialogue with you as I have similar issues I am trying to address thanks

  13. calle

    What do you take then from Dr. David Perlmutter MD’s book “Brain Maker”, and his use of probiotics with patients?
    Our son has used probiotics rectually and has noticed a difference mentally!
    Megan please email me or share with the group your protocol, as many of us are medical professionals and we are so in need of good practical information.
    So many long to be well, to be healthier and willing to make positive changes in their lives.
    The fact that one does not seem to be able to change the gut is discouraging.
    As a family we have changed our lifestyle including eating habits drastically over the last 15 yrs.
    We have ordered the 5 pac test and will be doing it in the next few weeks.
    Our journey is to heal a family member.
    A FMT is out of our cost range.

    Healing the basic body is important, but if I am reading that ferments, organic, good fats, and healthy sugars are not making a bit of difference in the gut , then those of us in nutrition are deceiving our patients.

    Humm, so sad!

    1. I love the Perlmutter book and refer to it regularly. If you know of anybody who has actual uBiome results showing a difference before/after, please let me know. I’d love to see examples. I’m trying to do this myself, so I’m very curious.

  14. Very interesting. I would be very curious to see the effect of Citricidal (grapefruit seed extract) on the microbiome. This version of GSE is always the most effective natural agent against all manner of yeast and ‘abnormal’ flora (klebsiella, citrobacter, strep species) on the thousands of stool tests I have run.

    The director of a very successful fecal transplant center in the UK is convinced that all probiotics are simply ‘passing through” and never colonize due to the fact that they are cultured in vats of steel and glass, to which they have adapted due to their very short and rapid life cycle. They are ‘lost’ as it were when they find themselves in a human GI tract. Makes sense. FMT is the only real way to dramatically alter the microbiome long term.

    1. It would be awesome if you could do the test yourself and let us know the results. I think you’d want to be careful to measure the day before and again a week or two later, not just a day after. Many probiotics just pass through, making people feel like they worked but really the effect is short-lived.

  15. Claudette

    Just a quick thanks for the science fix. Read about your experiment from Tim Ferriss. If you want some more subjects, I’m game! Can’t wait to read more!
    Thanks and have a wonderful day!

  16. Wendy

    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!

    1. 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.

  17. 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

  18. 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

  19. Rita

    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.

  20. 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.)

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