Bowel Disease, Part IV: Restoring Healthful Gut Flora

A healthy gut is a multi-species society: it is the cooperative product of the human body with trillions of bacterial cells from a thousand or more species.

An unhealthy gut is, more often than not, the product of a breakdown in this collaboration. Often, it is triggered by displacement of cooperative, commensal species of bacteria by pathogenic bacteria, fungi, viruses, and protozoa. This is why a long course of antibiotics, killing commensal bacteria, is often the prelude to bowel ailments.

It is difficult for the immune system to defeat gut infections without the help of commensal bacteria. Think about what the immune system has to deal with. The ulcers in ulcerative colitis are essentially the equivalent of infected skin abscesses, but in the colon. Here is a description of a bowel lesion in Crohn’s disease:

Ileal lesions in Crohn’s disease (CD) patients are colonized by pathogenic adherent-invasive Escherichia coli (AIEC) able to invade and to replicate within intestinal epithelial cells. [1]

Now imagine an infected skin abscess, but with feces spread over it three times a day, or stomach acid and digestive enzymes.  How quickly would you expect it to heal?

Commensal “probiotic” bacteria are like a mercenary army fighting on behalf of the digestive tract.  By occupying the interior lining of the digestive tract, they deprive pathogens of a “home base” that is sheltered from immune attack. If commensal bacteria dominate the gut, the immune system can usually quickly defeat infections.

This suggests that introduction of probiotic bacteria to the gut should be therapeutic for bowel disease.

Probiotic Supplements Are Inadequate

Most supermarket probiotics contain Lactobacillus or Bifidobacterium species. These species are specialized for digesting milk; they populate the guts of infants as they start breastfeeding, and are used by the dairy industry to ferment cheeses and yogurt.

These supplements are very effective at fighting acute diarrhea from most food-borne infections.  A fistful of probiotic capsules taken every hour will usually quickly supplant the pathogens and end diarrhea.

However, against more severe bowel diseases caused by chronic infections and featuring damaged intestinal mucosa, these species are usually not helpful.  One issue is that they provide only a tiny part of a healthful adult microbiome.  A recent study surveyed the bacterial species in the human gut, and found these species to be most abundant [2]:

Figure: Abundant gut bacterial species

As this figure shows, Bacteroides spp. are the most common commensal bacteria, with Bacteroides uniformis alone providing almost 10% of all bacterial genes in the gut. Lactobacillus and Bifidobacterium do not appear among the 57 most abundant species.

This study showed, by the way, that patients with irritable bowel syndrome have 25% fewer types of bacterial gene in their gut than healthy people, and that the composition of bacterial genes in feces clearly distinguishes ulcerative colitis, Crohn’s disease, and healthy patients.  In other words, in the bowel diseases a few pathogenic species have colonized the gut and entirely denuded it of about 25% of the commensal species that normally populate the gut. This finding supports the idea that restoring those missing species might be therapeutic for IBS.

Bacterial Replacement Therapies Work

So if IBS patients are missing 25% of the thousand or so species that should populate the gut, or 250 species, and if common probiotics provide only 8 or so species and not the ones that are missing, how are the missing species to be restored?

The answer is simple but icky. Recall that half the dry weight of stool consists of bacteria. A healthy person daily provides a sample of billions of bacteria from every one of the thousand species in his gut. They are in his stool.

So a “fecal transplant” of a healthy person’s stool into the gut of another person will replenish the missing species.

Scientists have known for a long time that this was likely to be an effective therapy, but it is only now entering clinical practice. The New York Times recently made a stir by telling this story:

In 2008, Dr. Khoruts, a gastroenterologist at the University of Minnesota, took on a patient suffering from a vicious gut infection of Clostridium difficile. She was crippled by constant diarrhea, which had left her in a wheelchair wearing diapers. Dr. Khoruts treated her with an assortment of antibiotics, but nothing could stop the bacteria. His patient was wasting away, losing 60 pounds over the course of eight months. “She was just dwindling down the drain, and she probably would have died,” Dr. Khoruts said.

Dr. Khoruts decided his patient needed a transplant. But he didn’t give her a piece of someone else’s intestines, or a stomach, or any other organ. Instead, he gave her some of her husband’s bacteria.

Dr. Khoruts mixed a small sample of her husband’s stool with saline solution and delivered it into her colon. Writing in the Journal of Clinical Gastroenterology last month, Dr. Khoruts and his colleagues reported that her diarrhea vanished in a day. Her Clostridium difficile infection disappeared as well and has not returned since.

The procedure — known as bacteriotherapy or fecal transplantation — had been carried out a few times over the past few decades. But Dr. Khoruts and his colleagues were able to do something previous doctors could not: they took a genetic survey of the bacteria in her intestines before and after the transplant.

Before the transplant, they found, her gut flora was in a desperate state. “The normal bacteria just didn’t exist in her,” said Dr. Khoruts. “She was colonized by all sorts of misfits.”

Two weeks after the transplant, the scientists analyzed the microbes again. Her husband’s microbes had taken over. “That community was able to function and cure her disease in a matter of days,” said Janet Jansson, a microbial ecologist at Lawrence Berkeley National Laboratory and a co-author of the paper. “I didn’t expect it to work. The project blew me away.” [3]

Fecal transplants can be done without a doctor’s help:  someone else’s stool can be swallowed or inserted in the rectum. If taking feces orally, swallow a great deal of water afterward to help wash the bacteria through the stomach and its acid barrier.

Dogs and young children sometimes swallow feces.  It is unpleasant to consider, but desperate diseases call for desperate measures. Perhaps one day, healthy stools will be available in pleasant-tasting capsules, and sold on supermarket shelves.  Not yet.

Attacking Pathogenic Biofilms

Most bacterial species will build fortresses for themselves, called biofilms.  These are polysaccharide and protein meshworks that, like bone, become mineralized with calcium and other minerals. These mineralized meshworks are built on bodily surfaces, like the gut lining, and protect bacteria from the immune system, antibiotics, and other bacterial species. 

Pathogenic species known to generate biofilms include Legionella pneumophila, S. aureus, Listeria monocytogenes, Campylobacter spp., E. coli O157:H7, Salmonella typhimurium, Vibrio cholerae, and Helicobacter pylori. [4]

Biofilms favor the species that constructed them. So, once pathogens have constructed biofilms, it is hard for commensal species to displace them.

Therapies that dissolve pathogenic biofilms can improve the likelihood of success of probiotic and fecal transplant therapies. Strategies include enzyme supplements, chelation therapies, and avoidance of biofilm-promoting minerals like calcium.  Specifically:

  • Polysaccharide and protease digesting enzymes. Human digestive enzymes generally do not digest biofilm polysaccharides, but bacterial enzymes that can are available as supplements. Potentially helpful enzymes include hemicellulase, cellulase, glucoamylase, chitosanase, and beta-glucanase. Non-human protease enzymes, such as nattokinase and papain, might also help. [5]
  • Chelation therapy.  Since biofilms collect metals, compounds that “chelate” or bind metals will tend to gather in biofilms. Some chelators – notably EDTA – are toxic to bacteria.  So EDTA supplementation tends to poison the biofilm, driving bacteria out of their fortress-shelter. This prevents them from maintaining it and makes the biofilm more vulnerable to digestion by enzymes and commensal bacteria. It also tends to reduce the population of pathogenic bacteria.
  • Mineral avoidance. The supply of minerals, especially calcium, iron, and magnesium, can be a rate-limiting factor in biofilm formation. Removal of calcium can cause destruction of biofilms. [6] We recommend limiting calcium intake while bowel disease is being fought, since the body can meet its own calcium needs for an extended period by pulling from the reservoir in bone. Upon recovery, bone calcium can be replenished with supplements. Iron is another mineral which promotes biofilms and might be beneficially restricted. We do not recommend restricting magnesium.

Some commercial products are available which can help implement these strategies. For instance, Klaire Labs’ InterFase ( is a popular enzyme supplement which helps digest biofilms, and a version containing EDTA is available (InterFase Plus).

Attacking Biofilms With Berries, Herbs, Spices, Vinegar, and Whey

Plants manufacture a rich array of anti-microbial compounds for defense against bacteria.

There is reason to believe that traditional herbs and spices, which entered the human diet during the Paleolithic and have been passed down through the generations for tens of thousands of years, were selected by our hunter-gatherer ancestors as much for their ability to promote gut health as for their taste. Dr. Art Ayers notes that:

Plants are adept at producing a wide array of chemicals with refined abilities to block bacterial functions. So when researchers sought chemicals to solve the problem of pathogens forming biofilms, it was natural to test plant extracts for inhibiting compounds. In a recent article [7], D.A. Vattem et al. added extracts from dietary berries, herbs and spices to bacterial pathogens, including the toxin producing Escherichia coli (EC) O157:H7, and checked for the ability to produce a chemical that signals the formation of a biofilm. The effective phytochemicals inhibited the bacteria from recognizing a critical density of bacteria, i.e. quorum sensing, and responding with the production of the biofilm-triggering chemical.

Blueberry, raspberry, cranberry, blackberry and strawberry extracts were effective as quorum sensing inhibitors (QSIs). Common herbs such as oregano, basil, rosemary and thyme were also effective. Turmeric, ginger and kale were also tested and found to contain QSIs. [8]

A few other remedies can weaken biofilms:

  • Acetic acid in vinegar can solubilize the calcium, iron, and magnesium in biofilms, removing these minerals and weakening the biofilm; citric acid binds calcium and can disrupt biofilms. [9]
  • Lactoferrin, a molecule in milk whey, binds iron and inhibits biofilm formation and growth. [10]
  • N-acetylcysteine can destroy or inhibit biofilms. [11]


Fecal transplants are the best probiotic. Tactics to disrupt pathogenic biofilms can assist probiotics in bringing about re-colonization of the digestive tract by commensal bacteria.

Along with a non-toxic diet (discussed in Part II) and nutritional support for the immune system and gut (discussed in Part III), these steps to improve gut flora make up a natural program for recovery from bowel disease.

UPDATE: Please read the cautions by two health professionals, annie and Jesse, about potential dangers of self-treatment with fecal transplants and EDTA. It is always better to pursue these therapies with a doctor’s assistance and monitoring.

Related Posts

Other posts in this series:

  1. Bowel Disorders, Part I: About Gut Disease July 14, 2010
  2. Bowel Disease, Part II: Healing the Gut By Eliminating Food Toxins m July 19, 2010
  3. Bowel Disease, Part III: Healing Through Nutrition July 22, 2010


[1] Lapaquette P, Darfeuille-Michaud A. Abnormalities in the Handling of Intracellular Bacteria in Crohn’s Disease. J Clin Gastroenterol. 2010 Jul 7. [Epub ahead of print].

[2] Qin J et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010 Mar 4;464(7285):59-65.

[3] Carl Zimmer, “How Microbes Defend and Define Us,” New York Times, July 12, 2010,

[4] Donlan RM. Biofilms: microbial life on surfaces. Emerg Infect Dis. 2002 Sep;8(9):881-90.

[5] Tets VV et al. [Impact of exogenic proteolytic enzymes on bacteria]. Antibiot Khimioter. 2004;49(12):9-13.

[6] Kierek K, Watnick PI. The Vibrio cholerae O139 O-antigen polysaccharide is essential for Ca2+-dependent biofilm development in sea water. Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):14357-62.  Geesey GG et al. Influence of calcium and other cations on surface adhesion of bacteria and diatoms: a review. Biofouling 2000; 15:195–205.

[7] Vattem DA et al. Dietary phytochemicals as quorum sensing inhibitors. Fitoterapia. 2007 Jun;78(4):302-10.

[8] Art Ayers, “Spices are Antimicrobial and Inhibit Biofilms,” Dec. 7, 2008,

[9] Art Ayers, “Cure for Inflammatory Diseases,” Sept. 2, 2009, Desrosiers M et al. Methods for removing bacterial biofilms: in vitro study using clinical chronic rhinosinusitis specimens. Am J Rhinol. 2007 Sep-Oct;21(5):527-32.

[10] O’May CY et al. Iron-binding compounds impair Pseudomonas aeruginosa biofilm formation, especially under anaerobic conditions. J Med Microbiol. 2009 Jun;58(Pt 6):765-73.

[11] Cammarota G et al. Biofilm demolition and antibiotic treatment to eradicate resistant Helicobacter pylori: A clinical trial. Clin Gastroenterol Hepatol. 2010 May 14. [Epub ahead of print] Zhao T, Liu Y. N-acetylcysteine inhibit biofilms produced by Pseudomonas aeruginosa. BMC Microbiol. 2010 May 12;10:140.

Leave a comment ?


  1. There is a blog called naturaldigestivehealing. com that has some info. on using natural antimicrobials for IBD. Also google info on the Chinese scientist who discovered bowel microbes causing obesity. One of the articles about him talks about his results with berberine reducing pathogenic microbes and increasing beneficial ones in the gut.

  2. One of the things that has been discovered about berberine is that it disrupts bio films by interrupting the microorganisms communication with one another.

  3. erm… why do people get sick when they eat poop if it’s so good for you? 😕 I mean this agony is bad but I don’t think I could do that.

    • LOL Poop is NOT good for you. But fecal bacteria such as e.coli has been used medically to treat some bowel disorders. People get sick because their immune system cannot compete with the particular bacteria / toxins it contains. Actually more correctly we get sick from improper hygiene then handling the food! The fecal bacteria on hands transfers to food and then it multiplies in the moist warm food which has insufficient ‘good’ bacteria to restrict it. The immune system can also be compromised for many reasons such as pregnancy, old age, chronic inflammation, auto immune disease and also in babies who are still forming one. But I would not risk eating ‘any old poop’ and I would caution relying on results from short term studies also.

  4. Hi Paul

    In the case of not having access to fecal transplants, do you think that it might be an option to ingest for example 100 trillion CFU (more or less the content of 110 packets of VSL 3 double strengh – more or less 1kg) or inserting that as a probiotic enema, of half ingested hald enema?

    Thanks a lot. Because I’ve never seen this possibility being considered and I wonder if that would cure me.

    • You might also search probiotics and prebiotics by using those terms with your condition–usually the fewer keywords the better, i.e., “probiotics IBS” “prebiotics IBS” “probiotics crohns” etc., you get the idea.

      Another suggestion is input your condition immediately after “natural remedy for”.

      Best wishes

    • If you haven’t yet tried, take fresh inner leaf gel Aloe vera. You should see improvement immediately.

      “Fresh” meaning fresh cut. Filet the leaf and rinse it off (to avoid the harsh laxative effect that comes from the outer leaf). Eat several ounces. It will gradually lose its effectiveness. (I know that its efficacy on burns is less than three days. I don’t know how long it will stay effective for internal healing.

      If you see any noticeable improvement, keep doing it a couple of times a day extending a bit beyond full recovery and you will have saved yourself a ton of money and have a healthy gut.

      If you want to know a good high quality source of pure, processed Aloe, let me know, but to see if it works find someone with an Aloe vera plant and take an outer leaf.

      Doctors WILL NOT tell you this. It costs them too much financial loss.

      • Thanks a lot!! Great suggestion!

        • You’re welcome!

          Please let me know what solutions worked for you.

          Best Regards

        • I don’t know your condition. That said, if you choose to take probiotics, be aware of the wide variety of strains and the difference in number.

          It’s my understanding that our gut has perhaps a thousand different strains of good bacteria. You can find probiotics of from one or more strains and from about one billion to one product I know that has 66 billion, and so if you’re in great need, several different products and a good dose will show faster benefit.

          Years ago I ate something that was bad and it put bad bacteria in me and I didn’t know it and because I didn’t know anything about probiotics, I suffered unnecessary consequences. When I found out, I didn’t ingest enough and didn’t improve fast enough.

          Eventually, I learned and started taking more and more often along with a great quality Aloe vera. I added FOS (they feed the good bacteria) to the probiotics and things improved.

          The biggest mistake I made was not taking enough Aloe or enough probiotics. I thought following the label was the right thing to do until I realized that one label said “one before meals” and had only three billion bacteria and another label said “one before meals” and had 66 billion bacteria.

          My lightning fast mind [;-)] only took MONTHS to figure out that I needed more than three billion and in reading, I eventually found that buying a variety of different strains was wise.

  5. It’s incredibly bad advice, e.g., E. Coli.

    • If you haven’t yet tried, take fresh inner leaf gel Aloe vera. You should see improvement immediately.

      “Fresh” meaning fresh cut. Filet the leaf and rinse it off (to avoid the harsh laxative effect that comes from the outer leaf). Eat several ounces. It will gradually lose its effectiveness. (I know that its efficacy on burns is less than three days. I don’t know how long it will stay effective for internal healing.

      If you see any noticeable improvement, keep doing it a couple of times a day extending a bit beyond full recovery and you will have saved yourself a ton of money and have a healthy gut.

      If you want to know a good high quality source of pure, processed Aloe, let me know, but to see if it works find someone with an Aloe vera plant and take an outer leaf.

      Doctors WILL NOT tell you this. It costs them too much financial loss.

  6. I don’t know about pleasant-tasting, but Germany’s had Mutaflor for almost a century. I think they are not available in the US, but they seem to be sold in Canada. & for more information.

    • Available in Australia just google Mutaflor. It is sold as cure for CONSTIPATION. I would hesitate taking for other conditions. My own experience was nil ecoli on stool test following 3 months on antibiotic to rid bowel of BH which did not alter. E-coli came up to normal following 30 days treatment of Mutaflor (ecoli ) and certainly changed stool hydration within day.

  7. Hi Paul,

    Do you have any information on the effectiveness of fecal transplants in treating IgE mediated food allergies?

    Since late 2010 I’ve developed over 55 severe IgE mediated food allergies–I stress IgE because it has been proven through skin, blood, and oral introduction testing. My reaction is violent – swelling and feeling of paralysis from throat to gut + extreme nausea/gut reaction, all within minutes of introduction of even a tiny particle of the food. I’m incapacitated for days afterwards.

    Been working with a functional medicine doc and through rigorous testing have found the following additional conditions: eosiniphilic esophagitis, hypothyroidism (which doc didnt believe at first since I’m 5’7, 28 yrs old, 112 pounds), b. hominis & candida infections, low pancreatic enzyme production, mild adrenal fatigue, and cholesterol that keeps rising (but HDL dropping) – over past six months I went from about total cholesterol of 262 to total of 375. LDL are type A at least.

    Treatment has been as follows:
    hypothyroidism 1/2 grain NatureThroid;
    b.hominis and candida – 2 rounds (1000 mg/day) alinia + 30 days of fluconozale (100 mg/day) + removing the little remaining fruit/honey/wine from my diet;
    Enzymes – Take AzeoPangen ExtraStrength with meals
    Also supplementing now with Amino DTox and Adrenatone, SCDophilus probiotics + 24 hr goats milk yogurt, Vitamins C, D, and fish oil (deathly allergic to fish/shellfish), and I’m about to start a glutamine therapy.
    I’ve also been strictly adhering to SCD diet for 15 months (removing all legal foods I’m allergic to, and the remaining sugary foods during candida treatment). What I’m left with is grass-fed ruminant animals, 100% pastured pork, lots of grass-fed butter, olive oil, and the few vegetables I’m not allergic to (avocado, spinach, zucchini, asparagus, lettuce, tomato on occasion, artichoke, rutabagas, cooked carrots and celery). That’s it.

    Despite all these diagnoses and treatments, I still live with oppressive brain fog, fatigue, and constipation. Not to mention my food allergies haven’t budged, and I keep developing more (albeit at a slower pace – 5 this year compared to abut 40 last year).

    My doc and I have been poring through your book for ideas to get me back on track. I’m going to start supplementing with iodine and adding some starch in slowly. Do you think a fecal transplant has any promise here? Assuming the allergies came from a very leaky gut (even though they are allergies not food sensitivies?), would a fecal transplant help to repair the gut barrier and possibly bring some relief to the allergy symptoms?

    Thanks for any suggestions you can offer!

    • HI Ige girl. I have the exact same thing. Really bad leaky gut that has made me allergic to all foods except grass fed beef and cabbage. My stomach swells and my joints and body will retain water as well if I eat other things with on and off diarrhea and constipation. Have you had your ileocecal valve checked? Have you had metamatrix testing done? Do you know where your leaky gut is from? I wondered about fecal tranpsplants to help it. I had the same symtpoms along the exact same labs as you and I am really small and fit and my thyroid is doing the same thing along with colesterol and cortisol. I did the transplant with and without antibiotics prior and it didn’t help.

      • sorry I am at work so I didn’t spell check and wrote replied very fast. I am a nurse so I did the transplant by NJ tube and by enema. No change for me. I am getting my metamatrix tests back soon. I am hoping that will help. stay away from western meds. What is your history? birthcontrol, soy, antibiotics? What caused your candida? man I wish I could fix this! I want to be able to eat things and it is so frustrating. I have a problem with carbs as well which is hard being an athlete

        • Hi Portia,

          Wow I’ve never met anyone with as many allergies as me. I’m sorry to hear about all your trouble and completely sympathize with how frustrating this condition is! I love to travel and spend lots of time outdoors and the allergies have totally killed my ability to do so freely – I take a huge insulated box with my frozen meals in it with me wherever I go, ugh! Not to mention just the decreased enjoyment from not feeling my best (or more accurately, from feeling pretty terrible!)

          I’ve done both the Metametrix and the BioHealth stool tests – that’s how we determined I had candida and B. Hominis, and how we knew for sure my pancreatic enzyme levels were low. The BioHealth test also showed some e. coli but my functional medicine doctor (an m.d.) wasn’t concerned about it. I’m not sure where the candida came from – reading Paul’s book I was wondering if I inadvertently caused the overgrowth while on SCD by not getting enough carbs – particularly from starch. But frankly I’m allergic to most carbs, and I have weird reactions to starch (esp. varieties of yams that I’ve tried) – I get instantly dizzy and fall asleep within 20 minutes, plus get stomach cramps. Not anything like my severe allergies, but its still a bad sign.

          We assume the leaky gut is from a history of overuse of antibiotics since childhood, 10 yrs on the pill, diet full of processed food in childhood and young adulthood, and higher than average stress. Soy is one of my worst allergies! No big surprise why my body started reacting to it! I’ve had a clean diet for more than 2 years (get my meat from a farm, olive oil from a local producer, etc. so I know exactly what I’m getting), have tried removing most toxins from my home (I clean everything with baking soda and vinegar and oil cleanse my face!), do lots of yoga, switched from a high stress job to something more reasonable, get 9-10 hrs of good sleep a night, etc. But the allergies are still there and multiplying (albeit much more slowly), and I feel like I’m getting weaker and weaker. The brain fog in particular is killer.

          It’s disappointing the fecal transplant didn’t work for you. I’ve heard it can be helpful for environmental allergies – I don’t know why food seems to be so different!

          One thought – are you allergic to fish and/or eggs? I am and I’m wondering if my hypothyroidism was induced by an iodine deficiency – since those are the main sources of iodine, and they are completely absent from my diet. Maybe you are in the same boat? I also don’t eat any dairy except for grass-fed butter and 24 hr goat’s milk yogurt, and don’t use table salt (all sources of iodine). To be fair, the 1/2 grain of nature-throid has my hypothyroidism under control – my levels are in a really good range, and I’m not freezing for the first time in my life! But I’d prefer to treat the root cause whenever possible, and may switch to supplementing with iodine if I can tolerate it.

          On the other stuff, esp. the cholesterol, both my doc and I are scratching our heads. We’re doing lots of research into what could be causing the cholesterol to be not only so high, but constantly rising. Happy to keep you posted if there’s a good way to keep in touch.

          • U have covered all bases thoroughly and still present main problem. Check out role of Vit D and K2 in disease processes. It is eye-opening! see e books by jeff t bowles and mercola interviews with Kate Rheaume-Bleue

            Sunlight and fermented veges are maybe what u need too – or more supplements lol….

          • re high cholesterol. There is much info out there now that explains the role of cholesterol and it is NOT what w have been told for decades. Cholesterol is a marker for chronic inflammation it is not a cause. see Ravsnikov Book Description from amazon here::
            “Publication Date: Jan 26 2009
            Did you know? …that cholesterol is not a deadly poison, but a substance vital to the cells of all mammals? …that your body produces three to four times more cho¬leste¬rol than you eat? …that the internal production increases when you eat only small amounts of cholesterol and decreases when you eat large amounts? …that heart patients haven’t eaten more saturated fat than other people? …that stroke patients have eaten less? …that people with low cholesterol become just as athero¬sclerotic as people with high? …that high cholesterol is not a risk factor for women? …that high cholesterol is not a risk factor for old people although by far most heart attacks occur after age 65? …that many of the cholesterol-lowering drugs are dan¬gerous to your health and may shorten your life? …that the cholesterol campaign creates immense pros¬perity for resear¬chers, doctors, medical journals, drug producers and the food industry?” The GAPS diet and books by J Van Eps have useful info. What i have learned from the roundabout of living with my hypersensitive body is that all those reactions are “normal” (ie what the body must do given the circumstances prevented to it) and that it is we who are reading their signs incorrectly. Ie cholesterol is rising BECAUSE the body needs it! However heavy marketing of the anti-chol. msg has made us fearful of it. Same with eating fats..

          • Have you ever run a mfthr gene mutation test?
            That is huge in how your body detoxs and absorbs vitamins.
            23andme test is $99. I’m saving up to get my son tested as he has tons and tons of allergies too

    • Although I have no experience re fecal transplants, I think that unless your diet and bowel condition supports the survival of the contents of the transplant I cannot see success from this for you. Re Diet we need calories to provide the needs of the body and unless you are getting sufficient even the best program of supplements and avoidance can be disappointing. At the very least it seems u need to be consuming highly digestible stewed allowed meats and vegetable broths , including fats, which become the building blocks to repair the damage which seems ongoing. (..Although somewhat slowed instanced by presence of new allergies.) “I still live with oppressive brain fog, fatigue, and constipation.” these all look like a body that is closing down – please investigate Vit D level and look to optimise it.

  8. Have you tried a product like Verapol? If you haven’t, you really should. Considering the expenses you’ve already endured, a quality Aloe product is pennies. GOOD Aloe is very healing. I know of nothing better than Verapol and you can get it from for $50 and if you buy two, the shipping is free. I’d encourage you to spend the $100. It will be the best $100 you’ve ever spent. Start with a scoop (1/2 gram) and you’re likely to see some improvement immediately. If nothing else, it will help with the constipation, and might do much more.

    Please try it and let me know your results.

  9. Another consideration is finding a Christian who believes in the healing redemption of the Lord Jesus and ask them to pray for you and lay hands on you.

    An Internet search on “healing in Jesus’ name” (and other keywords) should encourage you in this area. There are many testimonies and examples of people being prayed for on the Internet.

    BTW, regarding Verapol, it is pure freeze-dried Aloe Vera with all the anthraquinones removed.

    Because of the severity of your issues, you might want to try a smaller dose and wait for thirty minutes. If it is as beneficial as I think it will be, I would expect you to feel a soothing within that time and that would encourage you to take a bit more and so on.

    This Aloe product is the most beneficial and effective natural product I’ve ever used in my life. “Effective” meaning that this product, more than any other product I’ve ever used, showed me the greatest significant improvement in my GI tract and overall well-being than anything I’ve ever tried.

    I hope it helps. Because of the severity of your symptoms, you might request overnight shipping.

  10. Hello Paul,

    Could you tell us what to think about this study ? That sounds like a radical argue, and so, one could believe healthy food has nothing to do with restoring health and good shape..? I was wondering what kind of food or diet could be in case in M. Smithii status ? As we cannot really know which bacteria has grown in dairy products, or fermented beverages like kombucha, could this mean that it’s “dangerous” in some way, to supplement with “extra” fermented products ? Thanks for your advice, Best , July

    • My observation is that such news report of a study becomes a diversion away from common sense. Media often present a story for a viewpoint that was never intended. Eg giving the implication that “healthy food has nothing to do with restoring health and good shape”!! The prime motive for media is to sell their product, not to educate or inform in a non-biased way. There may well be some merit to this study or the story, but not if it makes us distrust our basic instincts with respect to food. Even if the theory has valid worth it does not overturn knowledge that foods themselves are responsible for the eco-environments that suit these bacteria and that which we have a large measure of control over. We know that the overeating of highly processed, non nourishing foods, create toxic ,inflammatory weakened, body states including obesity. Science is in danger of making us food-faddists and afraid of ingesting wholesome foods such as ferments. Fermented foods have been part of traditional diets over many centuries – tried and true. Fermented foods are balanced ecosystems and only “dangerous” if consumed in non-traditional ways such as being heated for processing.

  11. I’ve been drinking bone broth, because I frequently read that it remineralizes your body and heals your gut; and also apple cider vinegar, hoping it also helps gut disbiosys. But if the point of vinegar is that it depletes you of calcium (which, at least in the short run, is a good thing) shouldn’t bone broth be a bad move for those who have leaky gut syndrome, as it’s also putting back the calcium that one should try to get rid of?

    • It is questionable that ACV “depletes you of calcium”. Why would you be trying to get rid of calcium? Current theory holds that calcium is removed from bones and cartilage where it should be, and deposited in arteries and joints as a result of inflammatory processes. That would not be a reason to try to ‘deplete body of calcium’. Rather the calcium needs to be re-routed and theory is it requires Vit K2 to organise that. K2 is now thought to be deficient in our diets due to reduced consumption of meats and products like butter cream and even eggs, as well as the other source – some fermented foods. Meaty broths are therefore very useful as healing agent as well they are part of traditional diets. ACV is an ‘alkaliser’ of body chemistry after it is digested and would contribute to normalising inflammatory responses. Gut dysbiosis starts with healing the gut as well as change the inflammatory factors such as gluten, and sugar and others until the leaky gut heals. Calcium is very important to the body structure and many functions so continuing to have the broth is both healing and nourishing.

      • “Removal of calcium can cause destruction of biofilms. [6] We recommend limiting calcium intake while bowel disease is being fought, since the body can meet its own calcium needs for an extended period by pulling from the reservoir in bone.”

        Therefore, according to the text (not written by me or expressing my opinion) bone broth would have to be removed, as it contains minerals, including calcium.

        And, if (again, according to the text) vinegar “binds calcium and can disrupt biofilms”, and that is the reason why it is beneficial, that would confirm my interpretation of the text that taking calcium is bad for people with gut problems.

        My question is if this is true.

        • thx M , 😳 now i see what you mean… I came here via a link to a specific comment and did not read the lead article to which you referred. Its advice seems ambiguous, but if they mean all calcium sources i would totally disagree with:
          “We recommend limiting calcium intake while bowel disease is being fought, since the body can meet its own calcium needs for an extended period by pulling from the reservoir in bone.” Reason: because bowel disease is not short term, and skeletal calcium is not an insignificant storage bank of calcium. It can deplete rapidly and is not easy to rebuild bone after childhood either. …My take on “Mineral avoidance” is to mean not take in extra minerals as supplements during the treatment advised.[I also dont know if that is valid either.] All foods including bone broths contain minerals but they are also packaged in a way that the body knows how to break them down for use and or to safely eliminate them… To me the argument of: if the pathogenic bacteria are so clever in preventing their demise thru use of biofilms for which we have to not consume minerals in order to beat them back then is, that is not the effective way. Reason: we put ourselves further into a weakened state which may create even worse outcomes. To me the bowel problem is to address the leaky aspect by use of repair suitable diet.
          re: “if the point of vinegar is that it depletes ‘you’ of calcium..” i believe to be an incorrect interpretation. I think that it was referring to: that acids reduce (deplete] a the raw material- calcium- for both making and maintaining the ‘biofilm’ of the bacteria…Also it is my understanding that ACV becomes alkaline not acidic by the time it reaches the gut and so there should be negligible effect on the biofilm anyway…
          SO this is why i think that 1 ACV is not useful in the recommended treatment as stated and that bone broth should not be discontinued because of its mineral content. I believe it is not conclusive to find that taking calcium is bad from the evidence stated, but if the calcium has found its way to the bowel ie eliminated from being needed or usable that alone says something !
          In all, I would also caution the leaps made in the article about minerals, biofilm and QSI as these statements do not appear to have been evaluated in research for human bowel disorders and therefore may be entirely inappropriate. The Gaps diet has been subject of positive research results however!
          I also think you were on the money spotting ambiguities in the article. I hope I have been of some assistance here.

          • Yes, I tend to agree with you on this one. As much as I respect Paul Jaminet’s views I have found that the information available on the internet re: vinegar is extremely confusing and contradictory and full of holes. I do see that there appears to be anectodal evidence that some experience improved digestion and lower glucose spikes (for whatever reason) but I am going to discontinue the use of vinegar until such time as I can find any article that can explain to me on no uncertain terms exactly what it’s made of, what its effects are, to which conditions it provides benefits, and most importantly, why it’s beneficial. And I will of course continue to drink bone broth, as there is plenty of evidence that it’s medicine for those who suffer from leaky gut syndrome.

      • Calcium is needed for proper muscle function as well, as low calcium levels can lead to tetany. Taking K2 would move it to the bones, but what about the need for calcium in muscles?

        • Yes, calcium is needed, but supplementation can easily give too much which is also harmful. PHD recommends frequent bone broths/stocks, spinach/green leafy vegetables, and dairy, so calcium deficiencies are unlikely. We calculate that the bone stocks/soups/stews put you about at the optimum for calcium.

  12. I have ulcerative colitis mainly affecting my sigmoid colon and wanted to know what can I do to heal myself without medication. ❓

    • The gut is like an eco system. It is therefore necessary to restore it to balanced function. There is not Good or Bad bacteria- only inappropriate conditions causing overgrowth of these strains that then result in poor health. Overgrowth is a conditional state not absolute and many factors contribute. Overgrowth will easily recur unless all contributors are moderated.
      Strains of bacteria are missing because those that are passing through normally, cannot survive in your gut. This must be tackled too. You can flush out all the ‘bad’ and introduce all the good -missing strains and still have only low or short term benefit simply because the gut ‘garden’ you are providing cannot support their growth.
      I think it is too simplistic to picture that the gut is like a hose that must be unblocked and flushed so clean water can pass thru it.
      The treatments that you have outlined seems very disruptive and harsh and doesn’t account for the adaptive process that must take place in order to restore health and function to your gut.
      Healthy diet is also full of contention.
      It seems important to look to at least normal Vit D test; bone and meaty broths every meal.
      I would caution the treatment you outlined, without overall health plan as it is likely to result in a period of even poorer health as the gut tries to recover from the trauma- even from laxatives.
      1. cease allergens/ irritants ( like laxatives, dietary chemical additives, highly processed products and especially sugar and polyunsaturated oil products which are highly inflammatory.
      2. repair the gut – use of pasture-fed animal fats and meats and bones – they supply the building blocks for tissue repair
      3. a variety of non-heated fermented products introduced slowly to restock the gut and to contribute to normal health functions

      4. easily digested diet of live and cooked foods to maximise enzymes or production of in the body- reduce or avoid gluten as associated with inflammation.
      **Caution before doing anything in desperation- research widely. The fecal transplant remains an option but dont be a blind guinea pig PLEASE…

  13. I’ve commented before and have been surprised at how many have ignored by comments about the internal healing ability of aloe vera.

    This is particularly odd considering that everyone has the entire Internet to investigate the many claims regarding aloe’s healing ability.

    Additionally, Manuka honey has been shown to be very effective with many different bowel issues and quite a few people have had their issues resolved by using both these products.

  14. I should have mentioned the fact that the quality and efficacy of aloe varies so greatly that without fear of contradiction, one might have tried an aloe product that was of no value and then assumed that it was representative of aloe products in general. That is a great mistake. Many aloe products have little value and little if no efficacy, partly because not enough people understand that he latex will always have a laxative effect, but the inner leaf get, which has the healing properties is ONLY of value if the aloin has been effectively and thoroughly removed and many process aloe without doing this (either by ignorance or technological limitations) and their aloe products are very inferior.

    The very best aloe product with which I’m familiar is Verapol® and is available on the Internet, as is Manuka Honey.

    • I took aloe once for a whole week, Pukka brand. Seems very natural. This one:
      However, I started having a lot of mucus with and in between bowel movements coming out. It was very worrying. I stopped the aloe vera and the next day no more mucus. I wonder why this is?

      • I missed your remark because I quit monitoring the group because it seems no one cared for a simple, easy, effective remedy for digestive issues.

        Now, to your point. What’s the problem with mucous? I would consider a mucosal lining a good thing! Yes, inner leaf aloe is very thick and slimy–that’s part of its characteristics. Why would that alarm or concern you? It’s not a negative, but a positive for someone with IBS especially.

        Now, I don’t know the brand of aloe you were using so I’m speaking positively for the product you used only that your concern about mucous is misplaced.

        I’d encourage you to go back to the aloe–specifically a quality aloe of which you can find only positive reviews that proclaim significant positive benefits because there are far too many aloe manufacturers of questionable character. I personally recommend only Verapol® but I have heard and read many very positive reviews for George’s Aloe. While very different (Verapol® is freeze dried and George’s is a clear tasteless liquid) they are not far off in price per equivalent dose.

        BTW, high quality probiotics are also highly recommended as are fermented foods, kefir and real yogurt.

        • Oops. 😳 I skipped a word. I meant to say, “I’m NOT speaking positively for the product you used…”

          Sorry for the error. I did look up the product you used. The only thing that concerned me is “preserved with 0.1% citric acid.”

          I don’t see a properly manufactured aloe product needing a preservative. From my understanding, which is limited because of the secrecy of the various manufacturers, preservatives are only used because the manufacturers don’t have an effective process for removing the anthraquinones and aloin from the product and add a preservative to lengthen the useful life.

          However, the truth is that alion destroys the healing ability of the inner leaf gel in only three days. I’ve *never* yet seen any study, much less, a reliable one, that addresses how long aloe is efficacious with a preservative but without the aloin and anthraquinones removed.

          If you don’t want to go to the expense of buying Verapol® ($50-$70 for 30 grams freeze dried–half gram is considered a dose), then, though I can’t verify George’s efficacy, the reviews for it are the very best for any liquid aloe about which I’ve ever read and it is absolutely tasteless. It tastes like pure water.

          I know because I used it, BUT I used it WHILE I had ALREADY been using Verapol® and I didn’t see an improvement greater than I was experiencing *but I DIDN’T EXPECT TO* because I felt I was already getting pretty much full benefit. Therefore, though I took the product and though I didn’t see an improvement, I can’t count that against the product because I was already getting as much benefit as I expected. I had been taking Verapol® for months, along with Manuka and probiotics and was very, very pleased with the improvement in my system that had previously been messed up for years. (I hope I’m being clear enough.)

          • (I wish they would add an ‘edit’ option.)

            I’ll say something about my digestive problem. Many years ago, I ate some bad food and didn’t know it and didn’t realize that it slowly, greatly harmed my digestive system so badly that the time came when I was hardly digesting food. Vegetables would pass through me still easily identified and even in whole pieces with their original color. My health, including my mental acuity was suffering.

            First, I started with probiotics and they helped. I took them for a few years, then remembering the benefits of aloe (Man-Aloe®) that I’d experienced almost 15 years previously, I started again on it and found that Mannatech has greatly reduced the amount of Manapol® in each capsule of Man-Aloe® (30mg) and simple math showed it was now absurdly expensive. I also found out that the product’s manufacturing farm and facilities had been sold (through bankruptcy) and I started using their product (which company now supplies Manapol® for Man-Aloe®).

            All this time I was also doing research to try to learn more about aloe and its many benefits and value. It’s a worthwhile endeavor. It’s called “the potted physician” for good reason. The first things I learned about aloe, I learned from Dr. Bill McAnalley, who discovered how to neutralize aloin but Dr. Ivan Danhof is considered the world’s leading authority on aloe vera.

            I have now used Verapol® for about a year every day and have even cut back on probiotics and feel like my system has been practically completely restored for some time, but I have recently added Kefir and enjoy it. I previously mentioned that I had used Manuka honey. I used about three half kilos and it was a good addition and noticeably helped. If I was rolling in money, I’d take it regularly.

            For anyone considering my words, I want to emphasize that I recommend that you DO NOT buy any inner leaf gel aloe product without examining carefully all the reviews you can find ON EACH PRODUCT YOU’RE CONSIDERING because most manufacturers are NOT transparent about their manufacturing procedures. I consider that a silent admission of bad process. Natural Aloe® is an exception! I do know that NO ONE uses the *pharmaceutical grade alcohol bath* that Natural Aloe uses to separate the aloin and anthraquinones from their product, which means IT DOES NOT DETERIORATE! The only caution the manufacturer will give you is to KEEP moisture AWAY from the product because it is pure freeze dried aloe which means it has NO preservatives and it is highly absorptive of moisture. In other words, each time the container is open, it’s exposed to air which has a higher moisture content than the power and air is full of all kinds of airborne bacteria which is why our food goes bad so quickly and why we cover our food even when we leave it on the stove. Now, don’t freak out. That simply means don’t leave the container open and don’t put a wet spoon in it. This is the same care you take (or should) with all products you ingest. Normal, reasonable care and one won’t have a problem.

            I’ve used the Internet for 18 years. I’m regularly and routinely surprised that people do not effectively use and do not appreciate how the wise use of keywords can usually get you to the information you need very quickly. The Internet is your GREATEST ASSET in quickly and easily finding the truth; not your friends, not the TV, not the radio and not the newspaper.

            Because I love the product so much, I now sell it.


        Some good information that most doctors aren’t likely to tell you.

        I noticed the location of the site you gave me was in France, so I’m assuming you’re in Great Britain. If you choose to try Verapol®, I would think you might be able to find a distributor in Great Britain.

        Since aloe can be grown quickly in just about any climate where it’s not freezing, fresh aloe is always a great option though some don’t like the slimy texture.

        If you (or anyone who reads this) decides to use fresh aloe, you’ll know you’re getting a good product. Here are some recommendations if you do:

        Find or make an easy to use fileting tool and/or watch some YouTube videos on fileting.

        The reason I mention this is that when one cuts aloe, one releases the aloin (and the anthraquinones) which is yellow and bitter, that rapidly deteriorates the aloe and causes the laxative effect.

        THEREFORE, if one develops one’s skill in fileting the aloe leaf into one large piece, one can RINSE IT OFF WITH WATER and effectively remove almost all the negative constituents. The more skilled one becomes in fileting into one piece, the less surface area will be exposed to aloin, making it easier to rinse and retain the maximum amount of aloe. Additionally and more importantly, one will remove the bitterness and eliminate the laxative effect.

        Nevertheless, the aloin has already started attacking the aloe so you should consider it very perishable and freeze what you don’t use immediately. As I understand it (yet don’t know with absolute certainty), freezing stops the attack by the aloin on aloe’s efficacy.

        If one asks, “How long does it take for aloin to destroy the efficacy of fresh aloe,” the answer is “sitting in a petri dish at room temperature, three days.”

      • As a gel it provides a medium for your probiotic colonies to thrive – it is not digestible by you so it will be expelled and need to be replenished . You can then become dependant on it for regularity. To much laxative effect is as bad as too little. We should not need laxatives however.

        • earthgirl, you’re confusing Aloe inner leaf gel with an ill-advised combination of inner leaf gel with outer leaf. The outer leaf, while having some benefits, has many liabilities and should always be avoided.

          The outer leaf is NOT part of either product I recommended, nor do I ever recommend any outer leaf product.

          If fact, if someone is using fresh Aloe, they need to develop an effective skill to fillet the leaf AND THEN RINSE IT under running water to remove the anthraquinones or at least rinse it in a tub of fresh water. That will remove the anthraquinones sufficiently so that they won’t demonstrate an effect.

          You’re misinformed. You’re correct that Aloe isn’t digested; but INSTEAD it’s absorbed by the digestive walls and goes into the bloodstream and inner leaf gel DOE NOT create a dependency, nor does it create a laxative effect. You’ve been misled by bad information, which is, as I’ve mentioned before, characteristic of much of the Aloe industry.

          Pure inner leaf gel has no drawbacks and creates NO dependency and does not “just pass through.” All the negatives come ONLY from the aloin and other anthraquinones that are in the outer leaf.

          This is part of the reason why I spent time in the past addressing a lack of integrity in the Aloe industry. It is not regulated and most companies are deceptive and dishonest about how they process their aloe. Separating the anthraquinones is an expensive process and since they have a laxative effect, unscrupulous manufacturers will sell their product including the outer leaf (and far too often touting “whole leaf Aloe” as a good thing which is totally dishonest!) with the inner leaf “for relief of constipation” when inner gel Aloe alone will help relieve constipation without giving the cramping that the comes from the anthraquinones.

          Additionally, too few doctors will tell people that they would stop having problems with constipation if they would simply supplement with magnesium and they would also benefit from Vitamin C.

          • Hi Gary, please provide link / reference re

            “that Aloe isn’t digested; but INSTEAD it’s absorbed by the digestive walls and goes into the bloodstream ” .

            as I cannot understand this statement. What are the ” digestive walls?
            What purpose does AV gel have for the large bowel if it is in the blood stream?

          • Refined “Vit C” is not one formulation, nor the whole vit C complex. Therefore its refined use as a supplement is for therapeutic purposes not dietary. To take ‘Vit C’ for constipation is to misuse this therapy’s protocol, since loose stools is a side effect of the treatment. Such ‘supplemental Vit C’ dosages, that result in loose stools,are not normally found naturally via diet. Loose stools are NOT what is aimed for in a healthy bowel. Diarrhoea is a well known red flag.
            It is incorrect to say a supplement is safe or non toxic at such therapeutic levels when unaware of its pathways in the body. From the other perspective, if high levels are not what our bowels need normally, what is the long term effect of artificially creating loose bowels or put differently constipation has not been demonstrated to result from VIT C deficiency!

            Constipation should not be addressed by the simplistic supplementation of refined VIT C megadoses.

            I would add the same cautions to using supplemental magnesium outside of Professional advice. Traditionally ‘diet ‘ supplies what the the body needs and the body utilises it accordingly. Using megadoses of non natural (refined) substances may well create problems elsewhere in the system and at that the same time their patchwork fix temporarily masks the cause and the proper definition of the real problem, to be addressed.

            Refined substances generally cause problems to the functions of the human systems and should be the last NOT first resorts when problems arise.

  15. Hi Paul,

    Quick question. I’m about to go on Rifaximin for suspected SIBO. Are there any modifications to the PHD I should consider while on anti-biotics?


  16. Hello.
    I have a donor for a fecal transplant and this one is very healthy, never took antibiotics and is full of good bacteria, my question is, since i have IBS and dysbiosis and is missing 25% of good becteria, (as said on this website), the bad bacteria took hold in my gut as i did have alot of pathogens in my stools test and if they make biofilms, will the fecal transplant kill those biofilms and bad bacteria and colonise in their place or will they not get through the biofilms, do i have to try to kill the biofilms then do a fecal enema or can i tackle the biofilms naturally after a fecal enema?

    Thank you. ❓ 🙄

    • Are you doing this under a doctor’s supervision? Normally they give you compounds to induce diarrhea and have you fast before these so that you clear out many of the existing gut microbes before inserting the fecal transplant.

      Assuming you have a doctor, you should follow his advice.

      If you don’t, then I’m not sure what you should do.

      • Thanks, No im not doing it under a doctors supervision because its a family member and has gone for the stools testing i have done, no parasites, no pathogens and normal levels of good bacteria, this person has no allergies or acne or anything like that, so im going to do it myself, the reason is, all the doctors i go to tells me to take probiotics and diet, so i have been on the diet for long and taking probiotics but nothing, so i know im missing lots of strains.
        Yes i will do i liquid diet the day before and take OTC laxatives like dulcolax or senekot the day before to clear out bowel then perform it using an enema and hold it for 6 hours then follow a healthy diet afterwards.
        Thats my plan.

        Thank you.

        • Please give us an update after treatment 🙂

        • The gut is like an eco system. It is therefore necessary to restore it to balanced function. There is not Good or Bad bacteria- only inappropriate conditions causing overgrowth of these strains that then result in poor health. Overgrowth is a conditional state not absolute and many factors contribute. Overgrowth will easily recur unless all contributors are moderated.
          Strains of bacteria are missing because those that are passing through normally, cannot survive in your gut. This must be tackled too. You can flush out all the ‘bad’ and introduce all the good -missing strains and still have only low or short term benefit simply because the gut ‘garden’ you are providing cannot support their growth.
          I think it is too simplistic to picture that the gut is like a hose that must be unblocked and flushed so clean water can pass thru it.
          The treatments that you have outlined seems very disruptive and harsh and doesn’t account for the adaptive process that must take place in order to restore health and function to your gut.
          Healthy diet is also full of contention.
          It seems important to look to at least normal Vit D test; bone and meaty broths every meal.
          I would caution the treatment you outlined, without overall health plan as it is likely to result in a period of even poorer health as the gut tries to recover from the trauma- even from laxatives.
          1. cease allergens/ irritants ( like laxatives, dietary chemical additives, highly processed products and especially sugar and polyunsaturated oil products which are highly inflammatory.
          2. repair the gut – use of pasture-fed animal fats and meats and bones – they supply the building blocks for tissue repair
          3. a variety of non-heated fermented products introduced slowly to restock the gut and to contribute to normal health functions

          4. easily digested diet of live and cooked foods to maximise enzymes or production of in the body- reduce or avoid gluten as associated with inflammation.
          **Caution before doing anything in desperation- research widely. The fecal transplant remains an option but dont be a blind guinea pig PLEASE…

          • Thank you so much for your concern earthgirl, i hear what you are saying, but i have gone for food intolerance testing and cut them out but now im reacting to other foods, i also understand the easy to digest foods and to cut out gluten and sugar for example.
            but still very little progress, i also had this for so long and am tired and desperate for a cure, the donor is a sibling, so it should be similar strains, however, please remember i was not born through vaginal birth and was not breastfed when i was a baby, so it must be missing strains and i understand what you saying that i must use caution, but if this works, ill be so happy, i have to give it a try. im gna try it this week, ill tell you next week how i feel.

            thank you dear. 😥 🙂

        • You have the knowledge of the world with the prudent use of keywords in an Internet search with your favorite search engine.

          Experience almost 20 years ago led me to the internal healing ability of high quality inner leaf aloe vera that amazed me. No natural product had ever had such a dramatic benefit in any way and certainly not in my gut, but I saw dramatic results overnight.

          In the last few years, by searching, I found out about the internal healing properties of Manuka honey and heard about it healing things that nothing else could.

          I also was told of numerous reports where people had used Aloe and Manuka to heal IBS. This is why I chose to contribute on this forum and am still shaking my head that no one will bother to spend the *seconds* it takes to confirm what I’ve said. Does no one know how to use keywords effectively?

          I’ll give you a hint:

          “Manuka IBS” “Manuka & Aloe IBS”

          Additionally, if you have “auto complete” on with your search engine, you’ll see other things that others have entered that might give you more ideas.

          This solution costs less than $100, has no negatives, no side effects and no drug interactions. It’s not gross and it’s not unhealthy. It does not require a doctor and helps many people very quickly and significantly.

          I suppose some of you might not have thought that in the process of healing, you might kill some bad bacteria and some good bacteria might begin to flourish.

          It’s worked for many and your own research will demonstrate that.

          Tunnel vision can sometimes be not a good thing.

  17. Zac Did u try Manuka?
    Did u give the transplant a go?
    Have u had a Vit D test done yet?
    Are u getting daily sun or taking Vit D supplements?
    What vit D dose?
    Did you consider that how tired etc you are feeling are also symptoms from your IBS and not absorbing well.
    Have you taken enzymes -lipase especially for fat absorbtion to improve critical uptake of fat soluble vits. A E K
    Have you tried daily ‘green’ juices – spinach kale etc

    • no, i didnt have manuka, i take 5000ug vitamin d per day starting recently, i have tried juicing but gave up because i dont have time, but i will incorparate that to my future.
      Yes, i have considered strong depression, imsomnia, tiredness, to my leaky gut, however i think the bigger problem is my leaky gut affecting my visual life, thats where most of the depression came from, my lack of living a normal life. the acne, dry skin, black eyes, swelling etc.
      i had this all my teenage years and because of it was isolated.
      Yes i did 2 fecel transplants and still the allergies, however, i will do more and liver flushes and kidney and let you know in a few months.
      Thanks for the support 🙁

  18. From your symptom discription it is highly possible you have SIBO (Small intestine bacterial overgrowth). Fecal transplants are for the large intestine and they do not impact the small intestine. Small intestine issues need to be addressed in a similar way to what earthgirl is suggesting. Bacteria from your large intestine has migrated into the small intestine. Consider diet and probiotics and the other things recommended here to replenish your good bacteria. The Natren line of probiotics is quite good. Megadophilus for small intestine, bifido for large and finally Digesta-lac. No I don’t sell the stuff but it is very powerful in its impact on gut health over time in combination with diet.

    • yes i believe i do have SIBO.
      I am taking glutamine, and eating no sugar, wheat etc, and probiotcs with turmeric anti fungal capsules, i hope it will work, thank you.

      • You mentioned before that you have an allergy to aloe vera. Because of the confusion/deception regarding aloe, that leaves me wondering if the tests were for “whole leaf” aloe or “inner gel” aloe. If it was for whole leaf, the one who did the test doesn’t know their job. You should ONLY consider inner leaf gel and if you’re allergic to that, then I can see why you’ve struggled with depression; you’ve got a serious problem.

        I suggest you research Barberry Bark and research for a qualified herbalist who can tell you other herbs that might work against your intestinal issues.

        You didn’t mention whether you’d ever researched the Manuka honey enough to make the decision to try it.

        In the few years that I’ve been reading and learning about herbs and natural products, I’ve been amazed and appalled–amazed at the natural products that are so effective for so many maladies and appalled at the medical industry for deliberately staying ignorant about these things to the HURT of the public.

  19. Earthgirl he should watch the green juices with dysbiosis because juicing can really feed the bad guys. Yes even green juicing. Ask Dr. Robert Lustig. And over alkalizing can cause the body to produce more acid to compensate. Think it is better to stick with whole foods IMO.

  20. Are you certain that the aloe you have a “high allergy” is *only* the inner leaf gel?

    A very sad fact is that there is a great lack of integrity, honor and standards in the aloe industry and there are no govt. regulations. The variety of efficacy and quality issues run the gamut as an examination of the independent research that is available on the web will show.

    I personally did the research because after finding such an excellent product in the mid-nineties, *no other* aloe product I ever tried was nearly as good, though the manufacturers have no problem claiming their product is the best. Being unable to find any product as good as the one I had originally used raised the question of “why not” and “how are they processes” and I wanted to know the answers.

    If you do the research, you’ll find that *very few* will give answers, claiming “proprietary methods,” which, since their products are poor, simply tell me they don’t want people to see their low standards. (The aloe that I think is the best made a video of their process. Incidentally, their process is the most expensive and it used to be patented. Though the patent expired, it’s still so expensive, no one has yet duplicated it. It’s a pharmaceutical grade alcohol bath that separates the aloin and anthraquinones from the gel before they freeze dry the product. They then sell it in 30 gram containers. It’s called Verapol® and it is the same thing as Manapol®, the trademark name owned by Mannatech®.

    The outer leaf contains anthraquinones and aloin that both give a bitter taste. For economics (primarily) many companies offer “whole leaf” aloe, claiming benefits of whole leaf that the inner gel alone does not have. This is *contrary* to the opinion of the recognized world authority on aloe, Dr. Ivan Danhof.

    In other words, I suspect you have an allergy to aloe at all. I suspect that what you had is a *normal* reaction to the constituents that should have been removed from the aloe because they should be considered inedible (and are by many) and at least one study has shown them to be carcinogenic.

    Although, I have become so fond of high quality aloe that I have become a distributor for what I believe is the best freeze dried aloe in the world, because of the issue of conflict of interest and the possibility that you may indeed have an alergy to the inner leaf gel (something I’ve never heard of in my 60 years of life), I’d encourage you to buy a small container of George’s Aloe. It’s available at a variety of locations and you can purchase it for as little as $7.79 for a quart (an eight day supply)(I know Swansonvitamins has it at that price). It is tasteless (like water) and the reviews and recommendations for it are excellent across the Web. Since it’s a tasteless, clear liquid, you could dilute it as greatly as necessary to ensure that it will not cause you any problems.

    I encourage you, if possible, to examine the complete make-up of the aloe product that was used to determine that you have an allergy.

    It’s expensive to isolate the aloin and anthraquinones (I think there are about 8-12 of them) from aloe products in addition to removing bulk which increases profit since virtually everything is sold by weight or volume. Also, the outer leaf has the constituents that, at moderate levels, do have what seems to be a positive laxative effect and this is part of the reason so many use whole leaf aloe.

    I do hope you can easily confirm that the aloe to which you are “allergic” was whole leaf (or poorly prepared inner gel) and get to try a quality aloe product.

    There are very many benefits to aloe. One thing that many do not know is that because of Dr. Danhof’s frequent work with the FDA, they have approved aloe for research in it’s ability to prevent and heal cancer. I’d encourage you to investigate but remember that because of the lack of standards and integrity, be careful to check credibility and stick with pure inner leaf. Dr. Danhof’s recommendation is freeze dried aloe.

  21. Agree about the aloe, but some people have such a leaky gut and so much inflammation from the LG, and additionally the dysbyosis has migrated to the small intestine and so aloe -even properly prepared (bone broth also!) can just be TOO strong at first. I was on a very trusted aloe supplement and it made my SIBO symptoms worse. Sometimes some gut healing has to happen before these things can be introduced or else they will SPIKE inflammation. This is particularly true with bone broth because of the high gelatin/b-vitamin content. The immune system overracts to it initially. Sometimes meat broth has to be introduced first and then later bone broth. This is why I really don’t understand why people self treat especially when they have advanced gut infections.

    • “This is why I really don’t understand why people self treat especially when they have advanced gut infections.”

      I think it’s two-fold. First, a lack of finances. Some people simply don’t have the money and/or insurance. Secondly, lack of confidence in the medical industry.

      Many people bear with problems hoping something turns up that is simple and economical and sometimes they find such solutions, like I did with conjunctivitis. I’d never had it for over 50 years and suddenly it appeared and started getting worse so I asked the pharmacist what was the remedy and I was told “a doctor’s visit and a prescription.” I thought, “A hundred dollars for a small infection? That’s nonsense.” It angered me; I said, “there’s something simple and easy and cheap. On the way home, I stopped by my neighbor, who had a visitor in his driveway and said, “Do either of you know a remedy for pink eye? My neighbor’s guest said, “A pinch of boric acid in a quart of warm water; if it burns, you have too much.” I had boric acid in my house, mixed a pinch with warm water and washed my eye a couple of times before I went to bed and it was already improved and was completely gone in three days.

      Sometimes the “authorities” are as ignorant as the people they’re helping. There are sound reasons it’s called “practicing” medicine and don’t forget it’s ERRORS that cause 100,000 WRONGFUL DEATHS EVERY YEAR IN AMERICA ALONE.

      Have you never heard the audio, “Dead Doctors Don’t Lie”? Some people self-treat because they don’t want to leave the hospital as a corpse. That 100,000 figure on WRONGFUL DEATHS PER YEAR is NOT a new figure. It’s been that way for years. Malpractice isn’t high because the insurance companies are greedy; it’s because there is so much malpractice. If you don’t know it, then you haven’t researched it.

    • “Dead Doctors Don’t Lie” is easily found on YouTube. You should listen to it. It was made BY A DOCTOR, whose advice is, “If you want to live, stay away from doctors and hospitals.”

      Let me tell you a bit more about him. He grew up on a farm, and, as a boy, saw that his dad had vitamins added to the animals’ feed and asked his dad, “Why don’t you do that for us too,” to which he said his father responded, “Shut up, boy.”

      This intrigued him and through his college education, first for veterinary medicine, then in the application of his work and later his education for his medical degree, he discovered that in EVERY (emphasis his) PREMATURE death by “natural causes” it was ALWAYS a nutritional deficiency.

      Now, my first question to you is, “how many times have you ever heard those words from a doctor?” (Probably NEVER) My second question is, even if that is true only half the time, why is it the vast majority of doctors only offer POISONOUS drugs (ALL of which have an LD50 and USUALLY a frightful list of side effects) or surgery, which should remind one of the saying, “When your only tool is a hammer, all the problems look like nails.”

      Since, by your own admission you “don’t understand” self-treatment, I suggest you give a lot more consideration to just how significant 100,000 WRONGFUL deaths a year are DIRECTLY CAUSED BY “CAREGIVERS” in the country that should have the lowest percentage of deaths in the world.

      If that doesn’t help you appreciate the new paradigm, I then suggest you do research on the Internet with such terms as “ama fraud” “medical murders” “medical scandals” and then, from the results of that research, pick up new keywords and recognize why many are simply afraid of being legally murdered as BOTH my parents were from an evil system that is geared FOR THE BENEFIT OF THE MEDICAL INDUSTRY and not for the health and life of the patient.

      You don’t have the time to read all the more_than_convincing examples, Mimi.

    • Please don’t think I was trying to be contentious, just emphatic. I noticed your reference to “holistic” and I appreciate that you’re not of the ilk which I referenced.

      Because people don’t like to be “negative” (reasonably and understandably so, yet, not without its drawbacks), unfortunately, people find themselves in circumstances unable to extricate themselves because it’s already too late, having been the unwitting ‘guinea pig, or worse yet, ‘fool’ of someone to whom they trusted their health because they wore the label of “professional.”

  22. Mimi,

    thank-you for this very valuable input!!! (i might game say in defence of ‘self-treaters’ that we are forced to do trial and error therapies due to lack of practitioners who care and whom are advanced in their knowledge and how to find those that are 🙁

  23. Earthgirl I agree to an extent but there are functional medicine and holistic doctors around the world that skype now so if you search you can usually find someone that is very knowledgeable

    • hi , hope it is ok to ask here, sorry if not appropriate in this thread, but can someone point me to “someone that is very knowledgeable” as mimi says, who can skype regarding dealing with healing probably upper colon or small intestine issues a dear relative has had for 20 years now .. gas/bloating ,clear mucus, shortening sleep awfullly,
      ( sleep addressing things all useless and many tried)..

  24. Health overpowers – initial research | Fusion Organic - pingback on January 6, 2014 at 3:35 pm
  25. I’ve had ulcer active colitis since 2003(in remission now through diet). For the last five years, I’ve been getting these boils or abscesses on my body, It has dramatically reduced since going 95% raw vegan 6 months ago. But since the start of this new year I had 2 painful sores pop up.
    Please help.

  26. I think cleansing diets like raw and vegan serve a purpose in temporarily alkalinizing the body and helping some in the detoxification. From my experience in treating with a holistic doctor is that the problem with these extreme diets is that they put the body in an alkaline state, and then the body produces more acid to try to balance the PH, thereby creating new/different problems. When the skin is troubled, it is a reflection of the balance or lack of balance in your gut flora. Raw and vegan diets contain certain microbes and also feed certain species of microbes in the gut so I think for many it is not a good long term solution. The perfect healt diet or similar with nice balance of 1/4 carbs, 1/4 protien, 1/2 veggies at each meal, plenty of healthy fats, avoidance of processed sugar and minimal alchohol under the guidance of a good holistic doctor is the way to go. Also consider looking into getting some nutrient dense food back into your diet in the form of grass-fed beef, grass-fed butter, sardines, etc… these are very good for gut balance. When your gut is out of balance it is hard to digest meats. When your gut is more balanced it is much easier. Also look at the Specific Carbohydrate Diet and the SCD Lifestyle website for more information on gut diseases. Consider single strain probiotics from reputable source such as the Natren line. Get a good holistic doctor. Best wishes.

  27. Thanks for the reply I am going to try the protease digesting enzymes and single strain probiotics. Digestive enzymes was what I used to help me get into remission. I can’t recall if I had these sores when I was taking them with every meal. I did try Probiotics before, but maybe it wasn’t a good kind.
    I am on the 80/10/10 raw vegan diet, and when I follow that 100%, my skin is flawless and I feel amazing. I have been off of meat for 6 months and don’t plan on every consuming meat ever again. Its when I cheat a little is when these sores pop up again.

  28. just wondering if any can recommend links to holistic practitioners good and up to date in this area like Mimi talks about who work via skype internationally??? i hope this is ok to ask here but my relative has suffered long enough and needing to find some one good !!
    thank you !!

  29. Sure, i would love to help, but i dont know exactly what you are asking me?

  30. I’ve had chronic constipation since losing 80 pounds 26 years ago. I’m trying now to do something about it. I understand my gut is deranged, and to heal I must ingest some ‘good’ bacteria and also give it resistant starch to feed on. I’ve got the potato starch and psyllium, but am concerned about taking a soil based probiotic as a few sites have recommended. I’m scouring your site for information on this, but so far haven’t seen anything. I already eat plenty of fermented vegetables – and sweet potato and butternut squash. My diet is close to the PHD. I’m still constipated – although there has been improvement. Any thoughts on the SBO probiotics? Thank you!

    • Hi Debbie,

      The SBOs are generally safe, they can create a mild transient opportunistic infection that lasts a few days, but they don’t survive well in the body or the gut. What’s good about them is they are great antifungals and antimicrobials, they are good at killing parasites, fungi, and other things that don’t belong in your gut. I don’t object to taking them when you know you have an unhealthy gut, they can help, but I wouldn’t take them when healthy.

      • Hi Paul- Can you explain why you do not recommend taking SBO if one is reasonably healthy? Consuming RS/SBO has become quite popular in the paleo world and I have been using these supplements with the intent of “covering all my bases”.

    • Debbie,I understand that constipation is an effect from large bowel not small intestines. The SiBO probiotics are not meant for constipation or treatment of the large bowel. I was prescribed e-coli tabs (mutaflor) as a profile of my stool test showed i was extremely low in in this and other normal bacterias following an extended treatment for Blasto.Hominis (BH). This corrected constipation from that day. I only took a single 2 month course after which the constipation tended to return, which i now recognise as due to being dehydrated. I think there is more to it than trying to feed or to replenish the “good bacteria” . i suspect that if otherwise healthy from bowel diseases or food allergy issues affecting the gut, then diet is not moist enough (for your needs). I saw a standardised chart of bowel content consistency which is rated according to moisture level. It was then obvious, that to keep things moving nicely, that diet needed to mimic the body composition of approx. 70% fluid. All life requires water for survival including gut bacteria which therefore also will die off if insufficient moisture is present for them to be able to do their thing! You may need to increase fluids intake via drinks, raw/fresh/long moist cooked /sweet /salty/ wet foods, to balance your existing diet. Or perhaps those things are good but that you have too much drying foods whether fast cooked ones, dried ones or very spicy or pungent ones. Weather affects our moisture content so consider its effect on the diet too. I continue to include natural dietary ferments ( mainly for the small intestine health), and don’t bother using expensive supplements any longer. The final point is that antibiotics and food preservatives also cause temporary gut flora dieback and managing this may mean to give time for the diet to replenish and balance it again. I don’t know that ‘probiotics etc’ can populate it any faster, nor that in the interim that they will deter bad bacteria ‘weeds’ from getting a foothold.

    • To be honest debbie, i have given up on trying to heal my gut with commercial probiotcs, digestive enzymes, anti fungals and fermented foods as a primary source of healing because there are over 500 different strains of bacteria in the gut and most has not been discovered yet, so how can fermened foods and probiotics in the shops heal the gut completely if they only contain less than 10 strains. if u take digestive enzymes, they make you feel so good and help alot, but its unnatural to take it and if your body gets used to it, digestive enzymes could cause you to rely on it and make your body lower its ability to manufacture your own digestive enzymes, its a scary thought, so dont rely on digestive enzymes. i never meant i give up, i meant i give up on those things, i have been trying to heal my gut for 2 years, fiber powder, digestive enzymes, probiotics, glutamine, colostrum, fermented foods and still nothing. my biggest question is, why can other people eat garbage whole day and feel so good, its because their gut is populated by all the native bacteria and we have lost it due to antibiotics etc or we have not gotten it from our mothers because they never breastfed us for 2 years.
      I am not saying dieting is useless, by no means, the correct diet is essential.
      I recommend trying all those things first, like diet, probiotics, anti fungals, fermented foods, glutamine etc for a year or two. and if no progress consider a fecel transplant. although i have no knowledge if that will help you or cause worse side effects, i am considering it as a must for me, not doing it myself, but having it done at a clinic, then from there, a healthy diet with lots of great foods. here is a link to a treatment clinic
      i have come to the conclusion that all those things we do to heal the gut are only for people who have caused minor damage to there guts but still have the native bacteria, so they are easy to heal, but what can we do with our diets if we dont have native bacteria.
      remember all i said was based on my own research and trials and errors, use caution. thank you. 😀

      • Thanks for your advice, Zaq. I honestly don’t know yet “how bad” my gut is. I think since my diet is finally pretty good, it’s time to get tested. But, my constipation has improved since changing my diet to include more protein, more fat, and fermented vegetables. Now I’m adding the PS. I’m just concerned the PS might feed my SIBO… Dr. Jaminet, if you have a chance, could you comment on that? My understanding is RS isn’t digested in the small intestine, but some say it can be… Thank you!

    • Constipation is defined as dry stool. DRY stool. My current working hypothesis is we are 70% water thereabouts. We need to maintain that or become dehydrated. If we were to measure everything that goes into our body and everything that goes out in the course of a day, we would need to maintain that balance. So when we consume dried or cooked or pre-processed foods, then the deficit needs to be made up, over and above even the losses from breath vapour sweat and metabolic processes. If there is a deficit of moisture for our body’s processes then our gut fluids are used top us up. Our probiotic colonies also need adequate moisture, so dehydrated stool almost certainly impacts their viability. It is VERY important that if you are going to increase fibre you must increase your fluids just to maintain status quo, and to INCREASE even further if you were already suffering dry stools. Environment is key to survival for all of life – forget about sending new colonies to their inevitable demise in your gut desert and start adding lots of ‘nitrogenous’ fertiliser to balance and rebuild the gut “compost bin”. I’d start with GREENS- like spinach smoothies with cool sweet fruits like apples pears, watermelon. (LOL i just had a thought.. I used to wonder why i had so much diarrhoea when i was on a somewhat fruit excess diet!) So although it is hydration that is missing don’t look only to water to address this. As just like in nature a sudden downpour simply runs off the land, the body will expel it similarly. Moisture has to be inside your foods to be absorbed beneficially.

  31. Dr. Jaminet,

    Thank you for providing such useful advice. I had dinner with a woman who just got her Ph.D. in microbiology (mine is in neuroscience). I told her I was worried I wasn’t eating well since I spend so much time in the lab, and had bought some kefir at Whole Foods. I asked her that if kefir replenished the gut bacteria, why did one need to keep drinking it every day. I thought once the gut bacteria were repopulated, they’d continue growing on their own.

    Surprisingly, to me, she said to not drink kefir, and that you had to keep drinking it because it overwhelmed and killed off the natural gut bacteria. Her advice, and what I think is your’s, is to eat more vegetables, sauerkraut, and try to coax my gut bacteria back to the normal constellation of those present rather than overwhelm my gut with store-bought probiotics that don’t represent the normal distribution.

    Am I interpreting this correctly?


    • re “they’d continue growing on their own.” they need to be in a culture medium which your gut may/not supply or they will lose vigour and die. They may not necessarily be destroyed by our own gut flora which may may be good or bad mix at any time. Sauerkraut is akin to kefir or yogurt or other ferment foods that supply beneficial nutrients in our gut. Our ‘Natural*” bacterial ‘constellation’ is a response to the good/ bad dietary intake as well as other disturbance- sickness antibiotics etc. Natural is therefore not necessarily same as ‘good’. Sounds like your friend was also implying that manufactured probiotics are unlikely to be representative of the the strain variety in your own gut which is likely true. But this is not the point. Their role is simply to provide some temporary beneficial nutrients that may not be available from your own mix of gut flora. And that is still a good thing. What I question is whether concentrated probiotics in a capsule is a cost effective delivery method for gut health. I think we do far better with natural dietary intake of fresh foods including ferments, such as kefir to keep our gut in a healthy state.
      Finally what does “the normal distribution” represent if not good health. This is the way to judge the effectiveness or not.

  32. Thank you very much Dr. Jaminet and Earthgirl.

  33. So, I’ve read that chronic constipation is an indication of SIBO – especially if bloating is an issue (which it is). However, I wonder if I do need an extraordinary amount of water, since I can never get enough, and I don’t have a blood sugar problem or anything like that. I wonder if in spite of drinking 3 liters at least of water a day, I need even more. My constipation has improved tremendously over the past months eating sweet potatoes and butternut squash, more protein and more fat (mostly coconut oil). So, perhaps constipation isn’t an issue anymore (having a bm about every other day or more). But, I still have the bloating and upper belly area discomfort. I am going to get tested – but I like to have as much info as possible. Based on what Dr. Jaminet said, I’m still unsure about taking the soil based probiotics.

    I really appreciate the feedback!

    • This comment actually went to the wrong reply so I am repeating it here where it was intended!
      Constipation is defined as dry stool. DRY stool. My current working hypothesis is we are 70% water thereabouts. We need to maintain that or become dehydrated. If we were to measure everything that goes into our body and everything that goes out in the course of a day, we would need to maintain that balance. So when we consume dried or cooked or pre-processed foods, then the deficit needs to be made up, over and above even the losses from breath vapour sweat and metabolic processes. If there is a deficit of moisture for our body’s processes then our gut fluids are used top us up. Our probiotic colonies also need adequate moisture, so dehydrated stool almost certainly impacts their viability. It is VERY important that if you are going to increase fibre you must increase your fluids just to maintain status quo, and to INCREASE even further if you were already suffering dry stools. Environment is key to survival for all of life – forget about sending new colonies to their inevitable demise in your gut desert and start adding lots of ‘nitrogenous’ fertiliser to balance and rebuild the gut “compost bin”. I’d start with GREENS- like spinach smoothies with cool sweet fruits like apples pears, watermelon. (LOL i just had a thought.. I used to wonder why i had so much diarrhoea when i was on a somewhat fruit excess diet!) So although it is hydration that is missing don’t look only to water to address this. As just like in nature a sudden downpour simply runs off the land, the body will expel it similarly. Moisture has to be inside your foods to be absorbed beneficially.

    • I’d encourage you to consider your magnesium intake.

      Years ago I read that the majority of America is magnesium deficient and I know that when I learned that magnesium deficiency creates a problem with constipation, I started supplementing with it and constipation “magically” disappeared. I immediately thought ugly things about the medical industry because this information should be heard from them INSTEAD of their promotion of mammographies (which aggravate rather than alleviate problems).

      Because I also eventually adjusted my diet and nutrient intake, whereas I started with 400 to 800 mg a day of magnesium I now take less and sometimes skip a day or two, but usually see the negative effect of my negligence, especially if I repeatedly fail to take magnesium.

      Regarding Vit C, Linus Pauling recommended high doses of Vit C and many know that a sign of saturation or excess is the beginning of diarrhea, or, if one is increasing moderately, say, a gram at a time every hour or so, one might perceive the onset of peristalsis.

      These are two supplements that you can consider that might help individually, and almost certainly collectively, in addition to other benefits they give, which an Internet search will reveal.

      When I found out about the ‘Pauling Therapy’ (you can google it find out this natural solution to heart disease), I soon started it and, eventually found that 4 grams of Lysine, .5-1 gram of Proline and 5 grams of Vit C were effective for me (once or twice a day)–and there are additional benefits of all three supplements that you might want to search) and gradually but very significantly increased the amount of work I could do without getting quickly tired, which was the sign that showed me that arterial plaque indeed had become a problem, and my recovering significant energy while working testified to the effectiveness and legitimacy of the Pauling Therapy, which the medical industry has completely ignored now for over 20 years.

      I mention that because, in the process, I also discovered the truth that I’d also read that high doses of Vit C (‘high’ is a relative term that varies with each individual and toleration increases) can cause diarrhea, which first effect for someone with constipation would be relief from constipation.

      I don’t know whether that information will help you, but it might help someone. 🙂

  34. Dr. Jaminet: Actually I have two questions.

    If one has SIBO, can eating potato starch (with or without psyllium) actually make it worse, or does the PS make it to the large intestine undigested?

    and regarding your protein recommendations, you say 200 calories or protein per day is sufficient, but even 8 ounces of protein would be more calories than that, wouldn’t it? And I’m wondering if 8 ounces of protein is enough – I was eating about that, maybe a little less, for years, and since upping my protein to close to 12 ounces per day feel clearer, more energetic, my bruising and hair loss stopped. BUT, I’m feeling as if I’m now eating too much ! protein, because lately I can’t stand the sight of meat, don’t even want it unless it’s sort of mixed with the vegetables. That’s weird for me, as someone who as a formerly obese woman and compulsive eater, never experienced this.

    I’m eating a lot of coconut oil though, and some of the benefits I cited above could be due to that, and not the additional protein. So, my question is how to determine how much protein one needs? I’m 58 and 5 ‘ 1″. Thank you!!

  35. I just read your post regarding Cod Liver Oil and eating seafood. I eat 7 1/2 ounces of canned Wild Salmon – with bones – every night for dinner, and about a teaspoon of Cod Liver Oil/Butter Oil fermented gel. Oh boy – can I be overdosing on Vitamin A?!

  36. Hello Paul,
    Do fermented cruciferous vegetables (sauerkraut, or kimchi…) are compatible with good iodine absorption ? And are green vegetables concerned with iodine malabsorption ? Thanks a lot Paul !!


  37. What Is The Perfect Health Diet « Recipes for Health - pingback on July 24, 2014 at 4:57 pm
  38. Hi Paul. Please clarify how probiotic bacteria make it through the stomach and small intestine (outside of a pill). Common logic tells me that, as living organisms, probiotic bacteria are basically made up of proteins, fats, and carbohydrates. These are the substances our stomach, pancreas, galll bladder and small intestine are designed to break down and absorb. Do these organs have a mechanism that says, “Hey wait a minute, don’t digest these guys, they are probiotics.”? I don’t understand how it works, and wonder if it works.

    Also, there is a theory that as the body produces or “invites” yeasts and other so-called “bad” bacteria to help with toxic overload, the body also produces “good” bacteria when the conditions require such bacteria.

    Your thoughts please.

  39. I would like to point out that I got severely ill on probiotics and I would like to understand why. All my specialist are very surprised (gastro and dieticians). It’s like they look at me as if I am crazy, but really they should be investigating the ‘why’.

    All I know, I have had IBS symptoms all my life, but was manageable, just mainly lactose intolerant.

    I had a flair up over a year ago, and decided to go to gastroenterolist to see if she could help me with my IBS. She put me on to a dietician, who recommended the FODMAP diet, but something strange happened, my health deteriorated rapidly and I started to become intolerant to almost all foods and became very unwell. I was hardly eating, because I felt so nauseous everyday, and my bones began to ache, I started getting flu like symptoms every second day, terrible brain fog and lethargy, scents were so heightened that I felt ill just walking outside. The aroma of eggs cooked on the stove made me want vomit. I could barely function. My dietician then thought I had a chemical intolerance, so put me on an even stricter diet, I became worse and worse. Foods that were never an issue brought on severe symptoms.

    It just didn’t makes sense, that when I entered the dieticians door 6 months earlier, I was okay, not brilliant but I could function and 6 months later, I was at the point of wanting to end my life. That’s how bad it was. I was very scared.

    And then I looked at my diet, and said it can’t possible be anything food related, it just didn’t makes sense. And so, I looked at the supplements and medication I was taking. All I was taking was Vit D, Pandol, and Probiotics. That’s when it hit me, I knew instantly it was the probiotics, because I had a reaction to them the year before, but not so extreme, just terrible pains in my stomach and diarrhea.

    Now I know it was the probiotics, because over 6 months I was going down hill. I stopped the probiotics straight away, and two weeks later my symptoms dissipated and never have gone back that dreadful time. Now I am just left with chemical intolerances, where I feel nauseous for a number of days if I eat the wrong foods, but all the other symptoms have disappeared and I can function and think clearly at least. In fact I am thinking much more clearly than I ever have, due to the strict diet.

    So what happens in this situation? What do I do to get my healthy flora back?

    • Simone, were the probiotics you took this time exactly the same as the one you took when you had a reaction the past year?

    • I’d recommend a stool test to see what levels of which bacteria you have in your gut. You could have taken what you already had high levels of.

      Also, this will sound silly, but I highly recommend you take a look at a video on youtube entitled “Food Sensitivities” on James Tozer’s channel. The woman had lyme disease, and had increasing food sensitivities throughout her life, until she found the mind-body connection.

      Also helpful is the “Faster EFT” videos on youtube — over 800 free videos to learn more about the mind-body connection.

      I’m not involved with either group, am just at your stage as well, maybe worse, and I’ve found that some of these methods are helping me to realize that I may be unconciously talking myself into these bad reactions.

      • Opps sorry I replied below.

      • My wife has been effectively applying EFT to her GERD problems. When she feels the first hint of indigestion, she goes over potential stressers, and when she finds the culprit, uses EFT tapping. It works 90% of the time, and the other 10% is usually when she hasn’t rooted out the stress. EFT and energy psychology have a “too good to be true” reputation, but they really do work. And science is catching up with them. More case studies and other research work involving veterans and sufferers of PTSD are popping up all the time.

        • I concur that EFT is a very useful adjunct to any treatment, we simply are unaware of the extent of how our beliefs, attitudes, habits etc influence our daily wellness. It can be applied with very little effort and costs are minimal for the return received. There is much info online so you don’t even need to leave your home to access the treatment.

      • Thx Kelly , for being brave enough to consider that “I may be unconciously talking myself into these bad reactions.” Sometimes I think that in the battle to be heard we make our reactions worse. Also we follow advice in desperation that may not be suitable. I am so grateful for likeminded community for its reassurance that we are not crazy, that our symptoms are really real; for sharing individual experience, and for affirming that sometimes the medical world has not caught up with these things. I agree with u however there are certainly psychol. aspects associated BUT if this applies to any ill health it applies to ALL ill health. Doindg EFT is not the sam as thinking that my illness is “all in my head”..So I think where physical reactions are experienced the mind is not “making these up’ but it is quite capable of “making them worse”. EFT can address the stress around the illness and sometimes the illness itself can resolve or ameliorate also, simply because the mind has got out of the way for the body to heal itself naturally. Other times EFT can make you feel more positive so then u have more energy to cope with the illness reactions…

    • Simone have u been tested for celiac disease or gluten sensitivity? Do you have any auto immune disease signs or family history of either? Also see my other comment re dairy probiotics below..

      Also I am interested in your comments about aroma sensitivity / brain fog and lethargy. I have had the same and have diagnosis of environmental illness – chemical hypersensitivity, and the specialist I saw ordered a “functional” liver test (aspirin, paracetamol and caffeine tablets were taken then urine collected for ‘x’ hours and tested).

      This showed my liver detox systems were malfunctioning. Apart from prescribing specific supplements to assist with the detox functions; continuing to avoid the triggers – paint gas perfumes, other allergens/ intolerances including food based, but to also lower GI my diet, as our common food habits were leading to fatty livers and compromising its ability to keep us healthy. ( mine did not get biopsied just considered “suspect”). Since then more info has come to light re the role of fructose and trans fats so I am careful to avoid these too and don’t worry too much re low GI.

      I have been using food based probiotic drinks in 2014: Paasiflora from TVSN and also home made Kombucha and feel some improvement to my health overall. Ive also implemented GAPS broths to support good gut lining/ function.

      What foods cause your chemical intolerances? Are you referring to food chemicals rather than added chemicals to foods? i.e. to salicylates, FODMAPS?

      Re: your healthy flora, I think its best to go for ‘food’ based ferments, but make sure they don’t also contain the other chemicals you are not tolerating at present. Sometimes these foods have been sufficiently degraded by the fermenting colony that the food chemicals can be tolerated e.g. sour dough bread ( i can’t ) yogurt / sauerkraut/kimchi/ kombucha and others. Also remember that the specific flora is always an adaptation to the gut environment created from whatever you ingest – logic is if your foods are healthy for you your flora will be surviving and contributing to your well being too. (don’t forget too that antibiotics devastate health flora.)

  40. I am just getting a stool test…I will have to find out what it is called, because my gastro asked for it to be done. It’s not a run of the mill stool test.

    I have had a few people say Lyme disease, but I don’t think it is that, since I am now functioning fine, apart from food intolerances. I don’t have any rashes and all aches and pains have dissipated, brain fog has gone and my energy levels are good.

    • Kelly, what stool test would you recommend? I am situated in Australia, so it might be a bit harder to get the one you suggest.

    • I am also in Australia and was treated by a doctor from the NIIM clinic in melbourne until his recent retirement. I have had several stool tests done also called CDSA there other variants through the Healthscope Pathology. You want a profile of your bowel flora.

      • A further thought Simone.. you said you were taking Inner Health Plus. I took the ‘dairy free” version. Perhaps you were reacting to the dairy content of your probiotic…..

        • Thanks Earthgirl, yes I saw the introduction of dairy free range and wondered if that could’ve been the issue, but such a huge reaction? I do need to get back on to some probiotics but just a little bit scared to be honest.

          I had a CALPROTECTIN stool test. I don’t know the results but I suspect they are okay otherwise gastro would have asked me to come in sooner, and actually saw the healthscope site the other day, I might ask my gastro about the CDSA and other test on Healthscope. I am not sure what the difference between CALPROTECTIN and CDSA is to be honest?

          • simone LOL u can google anything if u have the energy!!.. i got this from the wikipedia intro: “Measurement of faecal calprotectin is a biochemical test for intestinal inflammation, including inflammatory bowel disease.” this means the gastro doc was not checking your bowel flora but more likely the lining of your bowel. the test that kelly and I did was an assay for bacteria /yeast /parasites/and normality of stool itself- yuk- and advises when there is an imbalance in healthy flora or whether there are suspects like candida or giardia, BH etc.

            I agree sounds amazing to have such a huge reaction, to possible dairy cultured probiotics, but if u had been free from dairy?? also they produce the dairy free version for a reason?? I don’t eat dairy as a rule but first almost instant reaction is a sore throat, and only tiny amounts of dairy /beef / gelatine needed…and i still can’t believe that either. But if you have antibodies they do their job…

            I was low i the bifida and e-coli bacteria and presented with constpation. Mutaflor ( ecoli) tabs changed that instantly and now kombucha or probiotic drink has normalised stool but haven’t been CDSA tested recently . BTW test price was AUD132.00 12 mths ago. Have u looked at GAPS diet to improve gut health yet?

  41. Here in the USA it’s called a Comprehensive Stool Analysis — tests for good and bad bacteria, and parasites. Usually called CDSA, or CDSA + Ova & Parasites…or CSA (instead of CDSA).

    This is the lab my doc has used, but of course there are others, and no doubt some in Australia:

  42. Another stellar article. I believe we are only scratching the tip top surface of what’s to come in this field.

  43. the Ayurvedic treatment panchkarma for treating of the intestinal tract might be an alternative to erradicate, treat and recolonize guts :

    5 days of plain rice (or rice water for constipated people) and kurkuma (and some basic vegs) often do a lot for calming down the fire…

    thereupon intestines could be rinsed out with herbal medicines and oils (it is very old therapy but worth a go if you’re really out of ideas how to heal your gut)

  44. I saw this comment, “simone LOL u can google anything if u have the energy!!” so I know you can use a search engine.

    I’ve got a lot of things to do, so, I suggest that you start your search with “digestive walls” so that perhaps once you get that smirk off your face, you’ll be in a position to learn. If you’re unwilling to do that, you can search for the audio “Ivan Danhof audio mp3” which I decided to search for you so that you wouldn’t have any reason to miss it.

    Dr. Ivan Danhof Ph.D M.D. has long been considered the world’s leading authority on Aloe and has an audio (posted by numerous sources) on the web which you should be able to find easily. It is referenced various places on the web with several different lengths but they are incorrect–they’re all the same file. It was on that audio (it’s been on the net for many years) where I heard him discuss the process of endocytosis and pinocytosis which are the process by which the very large polysaccharides are “engulfed” by the cell walls and are absorbed into the bloodstream and Dr. Danhof goes into a good bit of detail on the audio.

    Additionally, you can google this to learn about it and perhaps get a better grasp of these processes that do not qualify as “digestion” nor does the Aloe simply “pass through” (in elimination).

    Here’s are images of endocytosis and pinocytosis:

    This process works on the very large chain lengths of the large polysaccharides, not on the small mannose molecules.

    Aloe contains over 200 different constituents and the research is nowhere near complete, in part because, being a plant, it can’t be patented so the drug pushers (the medical industry) isn’t really interested in investing money in discovering this amazing plant that, for every benefit it provides, reduces the bottom line for the drug pushers by giving people health instead of dependency.

    Every length I gave you has benefit and will help give you a better picture of how much you don’t know about Aloe. Please listen carefully to Dr. Danhof’s message and consider listening to it numerous times and taking notes on it. The information is worth it. It’s less than 31 minutes but will give you the specifics you asked me and other very beneficial information that should be retained. If you like helping people, learning the information on the audio is a great place to start.

    Here’s one additional link:

    Aloe, as a burn treatment for one’s epidermis also isn’t digested, yet, somehow is the very best treatment against beta radiation burns.

    Do enough research and you’ll find that you have underappreciated this amazing plant and have been very misled in its amazing benefits.

    The references that you might notice about Carrington Labs is old information. Dr. McAnalley, whom you can also find on the web (but usually doesn’t give much useful information) is the doctor who worked for Carrington and discovered how to isolate the anthraquinones which destroyed the efficacy of the inner leaf gel in only three days. That patented process was unique to Carrington Labs, who licensed Mannatech® to use Carrington’s Aloe product named Manpol®.

    Carrington eventually went out of business (after the patent expired–not that that had anything to do with it), sold the trademark Manapol® to Mannatech® and sold the Aloe business to Natural Aloe of Costa Rica, where Carrington’s Aloe farm was.

    Knowing how good the product was, I researched and bought Verapol® from Natural Aloe.

    You can read my review of Verapol® here:

  45. Just ran across this article.. I’ve got low iron/ferritin and just recently picked up some Lauricidin and Interfase Plus… will these hamper my iron supplementation? Should I wait till I’ve got my ferritin back up to normal before using the Lauricidin/Interfase? Or would it be enough just to take the iron several hours away from the Interfase/Lauricidin? I don’t want to stop the iron since I’ve already had scary hair loss and it’s now beginning to grow back and I don’t want to lose any more!!!

  46. I recently rid myself of many seemingly unrelated symptoms with a single product, Neem Tincture by Ferlow Botanicals. I’d had gut issues for years. Leaky gut, chronic fatigue and a lot of others I won’t go into here. It seems that whatever was living in my gut got flushed out and the symptoms left with it. Here’s an important detail; My symptoms either came in or became much worse after a tetanus booster. I had an adverse reaction and my health went downhill. The tincture doesn’t do anything for that. It affects parasites and biofilm. Is it possible that many git issues including those caused by infection, surgery or injury make parasitic infestation easier to occur, and because of the absence of good gut flora, also harder to get rid of, especially as the biofilm almost certainly would buikd up on the site where damage occurred?

    • That is so interesting How long was the course ? Did u follow the tincture guidelines? Did u follow up with probiotics or fermented foods?

    • Yes, very interesting. Did you restrict sugar and honey, or any of the usual recommended restrictions?

      I have tried “everything.” My current thing was precribed by a natural practitioner. Homeopathic anti-candida drops from Des Bio, plus a restriction on sugar and other sweeteners. She says her patients who test as I did, if they take the drops and merely go off sweeteners for 6 weeks–—95% of them recover.

      I am eating fermented vegetables and taking soil-based probiotics as well.

  47. Hi Paul,

    I have to say, it’s a sad day when we cannot repopulate the bowels with probiotics and need to resort to bacterial replacement therapies.
    I have just taken Rifaximin w/ Flagyl for 10 days I also incorporated Nystatin to avoid any yeast overgrowth. For the past 4 days after my antibiotics I’ve been taking Prescript Assist and Probiotic-3. After reading this article I feel like the antibiotics are all for a waste. I don’t have a doctor to give me a fecal transplant and it will take some time to get referred to one.

    What are your thoughts on this? Will I need to take antibiotics again and immediately after use bacterial replacement therapies?

Leave a Comment

NOTE - You can use these HTML tags and attributes:
<a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <s> <strike> <strong>

This site uses Akismet to reduce spam. Learn how your comment data is processed.