Home > Overview > Framework Matters: Study Links for Safe & Effective Crohn’s Strategies

Framework Matters: Study Links for Safe & Effective Crohn’s Strategies

This post is really a reference guide that includes an outline and framework for thinking about Crohn’s strategies in a differnent way, along with links to a series of studies that go into depth about each area. This is a good place to start research, and a good resource to share with your doctor.

Nothing in biology (nutrition or medicine) makes sense except in the light of evolution. Dr. Loren Cordain

Intestinal Barrier Function & Leaky Gut:

These studies provide the framework for all the rest. Essentially all modern diseases of inflammation can be linked to a series of mismatches between our genes and environmental factors. The origin of this inflammation starts in the gut with a breakdown in intestinal barrier function.

  • The Western diet and lifestyle and diseases of civilization: Cordain, Research Reports in Clinical Cardiology: 2011 March
  • Mechanisms of disease: the role of intestinal barrier function in the pathogenesis of gastrointestinal autoimmune diseases. Fasano Nat Clin Pract Gastroenterol Hepatol. 2005 Sep
    Zonulin and Its Regulation of Intestinal Barrier Function: The Biological Door to Inflammation, Autoimmunity, and Cancer Alessio Fasano Physiol Rev 2011 Jan
  • Leaky Gut and Autoimmune Diseases Fasano Clinic Rev Allerg Immunol 2011 Nov


Below is a simple chart that list the stressors/environmental factors that either increase intestinal permeability directly or damage the balance of the gut flora, all leading to inflammation.

Increasing Intestestinal Permeability





Lectins & Saponins

Low Vitamin D


Sleep Deprivation

Omega 6 Fats



Endurance Exercise






Below is a simple chart that list the environmental factors that either decrease intestinal permeability directly or improve the balance of the gut flora, all leading to reduced inflammation and healing.

Improving Intestestinal Permeability

IBD Diet

Krill Oil

Probiotics & Fermented Food


Proline (Broth & Gelatin)

Curcumin — BCM95

Mutaflor, VSL#3, Lactobacillus paracasei


CLA (Bones & Butter)

Boswellia — 5Loxin

S. Boulardii,  B. Coagulans

Cannaboids (CBD)

D3 & K2

L. Glutamine & Arginine

Sleep, Meditation/Yoga, Acupuncture

IF & HIIT = Growth Hormone



 Fat Balance:

  • Linoleic Acid, a Dietary N-6 Polyunsaturated Fatty Acid, and the Aetiology of Ulcerative Colitis – A European Prospective Cohort Study. Gut 2009 July
  • The Type of Dietary Fat Modulates Intestinal Tight Junction Integrity, Gut Permeability, and Hepatic Toll-Like Receptor Expression. Alcohol Clin Exp Res. 2011
  • Conjugated linoleic acid modulates immune responses in patients with Mild to Moderately active Crohn’s disease. Clinical Nutrition 2012 March.
  • Lipid based therapy for ulcerative colitis-modulation of intestinal mucus membrane phospholipids as a tool to influence inflammation. Int J Mol Sci. 2010 Oct
  • Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers. J Nutr. 2009


Microbiota & Probiotics:

  • Gut Microbiota and Pediatric Disease Dig Dis 2011
  • Association between the use of antibiotics and new diagnoses of Crohn’s disease and ulcerative colitis. Am J Gastroenterol. 2011 Dec
  • Association of Repeated Exposure to Antibiotics With the Development of Pediatric Crohn’s Disease–A Nationwide, Register-based Finnish Case-Control Study. Am J Epidemiol. 2012 Apr
  • Influence of Saccharomyces boulardii (Florastor) on the intestinal permeability of patients with Crohn’s disease in remission. Scand J Gastroenterol. 2008
  • Anti-inflammatory effects of Saccharomyces boulardii mediated by myeloid dendritic cells from patients with Crohn’s disease and ulcerative colitis. Am J Physiol Gastrointest Liver Physiol. 2011 Dec
  • The probiotic Escherichia coli Nissle 1917 (Mutaflor) reduces pathogen invasion and modulates cytokine expression in Caco-2 cells infected with Crohn’s disease-associated E. coli LF82. Trop Med Int Health. 2011 May
  • Probiotic Bacteria Produce Conjugated Linoleic Acid Locally in the Gut That Targets Macrophage PPAR γ to Suppress Colitis. PLoS One. 2012
  • Lactocepin Secreted By Lactobacillus Exerts Anti-Inflammatory Effects By Selectively Degrading Proinflammatory Chemokines Cell Host & Microbe 2012 April
  • Helminthic therapy: improving mucosal barrier function. Trends Parasitol. 2012 Mar 


  • Vitamin D and gastrointestinal diseases: inflammatory bowel disease and colorectal cancer.Therap Adv Gastroenterol. 2011 Jan 
  • Curcumin Ameliorates Hydrogen Peroxide-Induced Epithelial Barrier Disruption. Dig Dis Sci. 2012 March.
  • Therapy of active Crohn disease with Boswellia. Z Gastroenterol. 2001 Jan
  • Dietary supplementation of krill oil attenuates inflammation and oxidative stress in experimental ulcerative colitis. Scand J Gastroenterol. 2012 Jan
  • Glutamine and Whey Protein Improve Intestinal Permeability and Morphology in Patients with Crohn’s Disease: A Randomized Controlled Trial. Dig Dis Sci. 2011 Oct
  • Combined Glutamine and Arginine Decrease Proinflammatory Cytokine Production by Biopsies from Crohn’s Patients J Nutrition 2008
  • Zinc supplementation tightens “leaky gut” in Crohn’s. Inflamm Bowel Dis. 2001 May
  • Intestinal immune system influenced by cocoa-enriched diet. J Nutr Biochem. 2008 Aug 


  • Therapy with the opioid antagonist naltrexone promotes mucosal healing in active Crohn’s disease: a randomized placebo-controlled trial. Dig Dis Sci. Smith & Zagon 2011 Jul 


  • Rifaximin-extended intestinal release induces remission in patients with moderately active Crohn’s disease. Gastroenterology. 2012 May
  • Cannabinoid-induced apoptosis in immune cells as a pathway to immunosuppression. Immunobiology. 2010 Aug
  • Cannabinoids mediate opposing effects on inflammation-induced intestinal permeability British Journal of Pharmacology 2011
  • Linaclotide in the management of gastrointestinal tract disorders. Drugs Today (Barc). 2012 Mar
  • 5-aminosalicylate is not chemoprophylactic for colorectal cancer in IBD: a population based study. Am J Gastroenterol. 2011 Apr
  • Efficacy of 5-aminosalicylates in Crohn’s disease: systematic review and meta-analysis. Am J Gastroenterol. 2011 Apr
  1. Carolyn Micek
    June 5, 2012 at 8:02 pm

    hi Alan,
    this is a great article! thank you so much for your efforts in spreading the word about safe and effective treatments for Crohn’s disease.

    I follow these recommendations and am proof of their efficacy. Your work has been an important part of my healing and I am so grateful!

  2. steve
    June 6, 2012 at 1:59 pm

    great review! as a pharmD and fellow crohnie, I can more than attest to the huge deficiencies in the conventional wisdom of treating IBD. this would be a great resource for all IBDers to print out and bring with them to their next GI appt.

  3. Juliette
    June 6, 2012 at 1:59 pm

    This is great and I am passing it along to my daughter’s GI who is threatening to not see her as a patient any longer unless we comply with 6 MP drug therapy. I am also sending her the contact info for Jill Smith about LDN- my daughter’s been on it for 3 weeks so far but GI says it’s not appropriate crohn’s treatment. I am surprised that even at OHSU in this progressive city of Portland OR, a GI of 25 years doesn’t want to consider “new” alternatives to the traditional drugs and didn’t even mention vitamin D or probiotics as essential supplements for my daughter. She says, “well, what you are doing with diet and supplementation is great for your daughter’s overall health and nutrition, but it won’t heal the perianal crohn’s disease.” I am bothered by the fact that specialists focus in one part of the body instead of looking at the whole system. This article clearly lays out the facts and research and I imagine it will be enlightening to many- let’s hope it gets into the hands of some doctors!

    • June 6, 2012 at 3:15 pm

      Juliette, Part of the challenge is that few doctors are even aware that this research exists. Don’t be surprised if it is met with resistance.

  4. June 28, 2012 at 3:28 am

    Hi Alan,

    What’s your take on http://shop.gapsdiet.com/product.sc?productId=2&categoryId=6

    Thanks again for all the advice you’ve given me!

    • June 28, 2012 at 10:29 am

      I’m very much a fan of GAPS and Dr. Natasha so I wouldn’t doubt that the biokult probiotic is beneficial. However if I were in the UK or anywhere in Europe, I would be looking at Mutaflor first. Mutaflor has shown to be effective for UC and more recently for Crohn’s. Mutaflor is available in Germany and I believe that they will ship anywhere in the UK or Europe. It is also available in Canada and I believe in New Zeland. Mutalfor is a bit expensive, but Dr. Sarah Myhill in the UK has some interesting tips on how to use it as a culture starter for yogurt.

      Other great probiotics are s. boulardii and fermenting your own vegetables – with Kefir which is more likely to colonize the gut.

  5. July 2, 2012 at 10:31 pm


    First of all, I’m so grateful for all the help you’ve given me so far!

    I’ve been doing SCD for three months now and have seen some gains, but not the full recovery that I wanted. One aspect of the healing I haven’t incorporated yet is the probiotics/fermented foods – except for l. acidophiles.

    I hope that’s the missing piece and will be starting the GAPS diet from scratch in two days. I will also start your recommended supplements.

    I was wondering what brand and where you bought the following:

    Vitamin D3
    Krill Oil
    B. Coagulans
    S. Boulardii

    Hopefully they can all be purchased SCD legal?

    My plan is to gradually incorporate these together with Bio-Kult (GAPS probiotics) and fermented foods.

    -I’ve also been thinking about intermittent fasting (IF) – basically eating all my food within an 8 hour window (10am – 6pm) – giving my gut lining some rest. I didn’t find any studies on this though.

    -Another thing I’ve been reading about is the possible relation between Crohn’s and MAP. I’m wondering if the leaky-gut/intestinal permeability/diet-approach would possibly be a good treatment for solving the MAP issue as well?

    • July 3, 2012 at 6:27 pm

      Glad to see that you are improving. On the supplements front, obviously I got mine from US online sources, so I won’t be much help. For the curcumin, if you can’t find bcm95, meriva form is also pretty good. If you can find it as nanocurcumin, that would be even better. You’ll find that many of them are not SCD legal. I honestly wouldn’t worry too much about that.

      IF is a great idea. Doing so one or two times a week should help by increasing your bodies production of growth hormone – naturally – which should reduce inflammation. And on the MAP front – if that is a real factor – this overall treatment protocol reduces TNF and “starves” MAP of its primary fuel. One strategy for MAP is to include antimicrobial supplements that directly kill/weaken it like oil of oregano, coconut oil/lauricidin, betaine hcl and garlic. You could look at an initial course of Rifaximin to jumpstart the process.

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