CONFIRMED: Crohn’s Disease is a FUBARed Microbiome

Posted on Posted in Science & Research

The headline is a mix of truth and lie. I’ll get to the lie later, but now let’s talk about the truth. The March 12 issue of the Cell Press journal Cell Host & Microbe has a study conducted by twenty-eight gastroenterology centers across North America, the largest of its kind. They studied a total of 1,742 samples from pediatric and adult patients with either new-onset or established Crohn’s disease.

ScienceDaily says, “The team found that microbial balance was disrupted in patients with Crohn’s disease, with beneficial microbes missing and pathological ones flourishing. Having more of the disease-associated organisms correlated with increasing clinical disease activity.” (1)

Dr. Ramnik Xavier of Massachusetts General Hospital and the Broad Institute of MIT and Harvard said the study will help develop new diagnostic tools so that if a doctor sees a similar composition of gut microbes in a patient, they can diagnose them as having inflammatory bowel disease, without the need for a colonoscopy. That alone is a great benefit because the prep for colonoscopies can be dangerous for patients by further upsetting the microbial imbalance.

The study found that antibiotic use in children with Crohn’s disease caused an increase in pathogenic microbes (likely causing more inflammation) because the good microbes were killed off. This confirms that antibiotics are a dangerous treatment option for patients with Crohn’s disease. You don’t want to make a condition of imbalanced gut microbes worse!

Dr. Ramnik also said, “More importantly, our study identified specific organisms that are abnormally increased or decreased in disease, which forms a blueprint to develop microbial therapeutics.”

What he means by this is identifying and creating products of the chemicals released by the beneficial microbes which help reduce inflammation, and kill pathogenic inflammation causing microbes. (2) This ideally would mitigate the dangers from the imbalance.

I do not believe this would ensure success in patients who don’t change their lifestyle to cultivate a healthy, balanced microbiome. It would simply be another way to mask the symptoms, and sell another drug or supplement. If they don’t develop a healthstyle, they’ll sustain the status quo that created the imbalance in the first place, which is likely eating lots of sugar and grains.

Dr. Ramnik is on the right path, but he’s not wearing the right shoes for it. What research needs to establish next is how patients can use food and other healthstyle changes to rebuild their gut microbiome to a healthy, balanced state. This will help either manage or cure their inflammatory bowel disease.

For decades patients have been telling their Gastroenterologists that the foods they ate mattered in controlling their disease activity, but Gastroenerologists say no. Whether they know it or not, Gastroenerologists have lost credibility in the alternative treatment communities for their inability to even simply acknowledge that there might be something to all the anecdotal reports.

Twenty years ago, in 1994 Elaine Gottschall wrote Breaking the Vicious Cycle – Intestinal Health Through Diet. Today on it has over 415 five star ratings, plus another 71 four star ratings. The next three ratings of 3, 2, 1 combine for 57 reviews.

Her work outlines that inflammatory bowel diseases, both Crohn’s and ulcerative colitis stem from intestinal dysbiosis, the imbalance of microbes towards inflammatory types rather than anti-inflammatory types.

I have had doctors say that food plays no roll in the disease process, but research by the Human Food Project (3) and others over the years (4) have proven that we know for a fact, food is one of the most effective ways to modify the gut microbiome composition. You can either change the composition towards disease or health, depending on what you eat.

Back to the study, some online discussions have wondered which comes first, Crohn’s disease or the dysbiosis? But this is not a chicken or the egg situation. The observance of an imbalanced microbiome IS the very definition of Crohn’s disease.

Crohn’s disease and ulcerative colitis are not some tangible thing you acquire like the H1N1 flu virus. They are a state of being inside your body. They are temporary conditions of symptoms that manifest from the composition of specific microbes. Those microbes can be removed or added, at will.

Let that sink in for a few seconds.

Ready? I said above that the headline was partly a lie. The lie is that our microbiome is not Fucked Up Beyond All Repair. It changes very easily with the use of drugs (antibiotics), stress, food, and supplements.

The 5-R Framework gives you a holistic approach and alternative treatment options to help you rebuild your gut microbiome so that over time you have more beneficial microbes vs. pathogenic ones.

I have used the 5-R Framework since discovering the Specific Carbohydrate Diet, and many of the patients I have interviewed for the documentary, who were doing very well managing their IBD have done the same.

Every patient I meet who manages their disease to the point of not needing any medications, uses this approach whether they know it or not. The 5-R Framework is a description, an observation of what I saw the successful, empowered patients doing. I have broken down what it was they and I do, and with the framework, you too can have success.

The study I discussed above confirms what I and many others have experienced over the years. It’s unfortunate that most gastroenterologists and national research and patient advocacy organizations haven’t gotten the message.

What do you think about the research? Does it ring true for you? Are you interested in trying the 5-R Framework for the first time? How do you feel about doctors and national Crohn’s & colitis organizations who seem to ignore this research? Let me know in the comments!


  • Yessss! Reid I’m so psyched to have found your blog.

    I was diagnosed with Crohn’s in 2000 and have been med-free since fall of 2001 after rejecting western medicine. I eliminated sugar and inflammatory foods, cured a systemic candida overgrowth, treated for parasites and repopulated my gut with huge doses of probiotics. I haven’t had a flareup worse than 10 seconds of gas pains in over a decade.

    It was almost impossible to get anyone to take my story seriously until this research started being confirmed. I want to talk to you about your Crohn’s experiences, healing, and your documentary. Please get in touch! Sincerely, Liz Butler

    • Hey Liz, sounds awesome. I’d enjoy talking w/ you. Can you please shoot me an email at We can set something up for early May bc I’m going on a trip next week.

      • Done! Check your inbox. Thanks Reid!

  • A Critelli

    Read about Dr. Thomas Borody’s treatments. He’s genius! In my opinion, he’s one of the only doctors in this field who understands IBD and has made a dent in the area of real medication. Real treatments gets to the root issue, not just mute the symptoms for a little while. The man gets it and has saved lives from the treatments he has developed. Maybe you’ve heard of him or some of the treatments that he’s innovated. He came up with FMT’s to treat C-diff patients who would probably otherwise die. Ha… too bad our country can’t even come up with a billing code for the procedure. Dr. Borody is in Australia.

  • ebertch

    Reid- So, so pleased to have found this. Just beginning the journey away from Western medicine after being tired of being told TNF-blockers were my only option despite the enormous amount of research on the microbiome. Have begun SCD but don’t know how to navigate it to personalize it for my situation nor the right supplements to include. Any tips for finding a doctor? Naturopath/nutritionist? What do you recommend? THANKS FOR THIS WORK!

    • Hi Elizabeth,

      Thanks for the comment. I’m excited for you. You ask a few questions that could take a long time to answer, but instead I’ll try to give quick answers that can get you started.

      The healing journey is a process, it’s not a race, go slow, find ways to enjoy it and grow over months, years even.

      To personalize SCD, try new things slowly, in small amounts if you are unsure they are safe for you. Continually experiment. If you can’t tolerate something, try again in a few months. Definitely follow the CAN’T eat list strictly, but if you find you can’t tolerate something that is “legal” i.e. allowed, then don’t eat it. Once symptoms decrease and your health is stable, you can try things again, even illegal items once in a while, a few times a year. At this point, I don’t ever want to go back to my previous diet. BTW: I eat more closely to GAPS, which is an evolution of SCD. But SCD is a good place to start.

      I’m not a huge fan of supplements, but some are helpful. Liquid vitamin D drops, from Carlson. Cod Liver Oil from Carlson, or Fermented Cod Liver /High Vitamin Butter Oil from Green L-Glutamine for crohn’s, Butyrate for UC.

      For Naturopaths, see if your insurance co has a list. If not ask your health conscious friends who they recommend in your town.

      Nutritionists usually don’t understand SCD and often recommend illegal foods that harm people with IBD, so I stay away from them.

      Hope this helps. -Reid

      • ebertch

        Thank you so much! In terms of naturopath vs. functional medicine or the like do you see much difference? I attempted SCD before and after a month didn’t see much progress but know I went too quickly through the stages. I think having a little guidance would be helpful for me to not feel like all the choices were so random or that I was totally alone in my attempts. Do you ascribe to GAPS because of its more elimination-type approach? Just curious. Also, where can I contribute to your cause?! I would be so happy to support this.

        • I don’t have any experience w/ functional medicine to compare with Naturopaths. I do know Naturopaths don’t make a lot of money, so they try to sell you diagnostic tests, and supplements, that may or may not need. Have you considered hiring a health coach who has experience helping patients with your goals? If you just want to do dietary changes, an IBD focused health coach may be helpful. Some will also recommend tests you may not really need. But a good one should def. want to help you in achieving your goals, make you accountable, and help you create actions steps.

          I prefer GAPS because it encourages a greater holistic approach, get rid of toxic cleansers in the home, detox body, and fermented food. Overall it’s an evolution over SCD. The two are very similar. Starting out on SCD may be a good idea, GAPS can be intimidating. But don’t get stuck on SCD if healing seems to peak and not go anywhere further after a year or two.

          Thanks for asking if you can contribute to my efforts. I appreciate that! Here are several options,

  • gandia77

    I would like to hear about the biotic regime. I have been med free for a year (UC) and always want more info on proB. Many thanks Cyrus

  • Nicole Martin

    I am there with Liz Butler – my doctor called me the Magical Unicorn last month because my disease is not only gone, but no scarring whatsoever – brand new colon! She was very happy to put me in the small percentile where the disease just goes into remission. I of course said, “well it didn’t go away on it’s own, but I know we aren’t allowed to talk about that!!”. Very sad and so many are suffering daily with no where to turn but their doctors…Also happy to be of help in any way…Nicole