Thiamine SIBO, IBS, constipation

SIBO, IBS, and Constipation: Unrecognized Thiamine Deficiency?

In many of my clients, chronic upper constipation and gastroesophageal reflux disease (GERD) are misdiagnosed as bacterial overgrowth. Unfortunately, they are often non-responsive to antimicrobial treatments. Yet, sometimes the issues are fixed within a few days of vitamin B1 repletion. This has shown me that often times, the small intestinal bacterial overgrowth (SIBO) is simply a symptom of an underlying vitamin B1 or thiamine deficiency.

GI Motility and Thiamine

The gastrointestinal (GI) tract is one of the main systems affected by a deficiency of thiamine. Clinically, a severe deficiency in this nutrient can produce a condition called “Gastrointestinal Beriberi”, which in my experience is massively underdiagnosed and often mistaken for SIBO or irritable bowel syndrome with constipation (IBS-C). The symptoms may include GERD, gastroparesis, slow or paralysed GI motility, inability to digest foods, extreme abdominal pain, bloating and gas. People with this condition often experience negligible benefits from gut-focused protocols, probiotics or antimicrobial treatments. They also have a reliance on betaine HCL, digestive enzymes, and prokinetics or laxatives.

To understand how thiamine impacts gut function we have to understand the GI tract. The GI tract possesses its own individual enteric nervous system (ENS), often referred to as the second brain. Although the ENS can perform its job somewhat autonomously, inputs from both the sympathetic and parasympathetic branches of the autonomic nervous system serve to modulate gastrointestinal functions. The upper digestive organs are mainly innervated by the vagus nerve, which exerts a stimulatory effect on digestive secretions, motility, and other functions. Vagal innervation is necessary for dampening inflammatory responses in the gut and maintaining gut barrier integrity.

The lower regions of the brain responsible for coordinating the autonomic nervous system are particularly vulnerable to a deficiency of thiamine. Consequently, the metabolic derangement in these brain regions caused by deficiency produces dysfunctional autonomic outputs and misfiring, which goes on to exert detrimental effects on every bodily system – including the gastrointestinal organs.

However, the severe gut dysfunction in this context is not only caused by faulty central mechanisms in the brain, but also by tissue specific changes which occur when cells lack thiamine. The primary neurotransmitter utilized by the vagus nerve is acetylcholine. Enteric neurons also use acetylcholine to initiate peristaltic contractions necessary for proper gut motility. Thiamine is necessary for the synthesis of acetylcholine and low levels produce an acetylcholine deficit, which leads to reduced vagal tone and impaired motility in the stomach and small intestine.

In the stomach, thiamine deficiency inhibits the release of hydrochloric acid from gastric cells and leads to hypochlorydria (low stomach acid). The rate of gastric motility and emptying also grinds down to a halt, producing delayed emptying, upper GI bloating, GERD/reflux and nausea. This also reduces one’s ability to digest proteins. Due to its low pH, gastric acid is also a potent antimicrobial agent against acid-sensitive microorganisms. Hypochlorydria is considered a key risk factor for the development of bacterial overgrowth.

The pancreas is one of the richest stores of thiamine in the human body, and the metabolic derangement induced by thiamine deficiency causes a major decrease in digestive enzyme secretion. This is one of the reasons why those affected often see undigested food in stools. Another reason likely due to a lack of brush border enzymes located on the intestinal wall, which are responsible for further breaking down food pre-absorption. These enzymes include sucrase, lactase, maltase, leucine aminopeptidase and alkaline phosphatase. Thiamine deficiency was shown to reduce the activity of each of these enzymes by 42-66%.

Understand that intestinal alkaline phosphatase enzymes are responsible for cleaving phosphate from the active forms of vitamins found in foods, which is a necessary step in absorption. Without these enzymes, certain forms of vitamins including B6 (PLP), B2 (R5P), and B1 (TPP) CANNOT be absorbed and will remain in the gut. Another component of the intestinal brush border are microvilli proteins, also necessary for nutrient absorption, were reduced by 20% in the same study. Gallbladder dyskinesia, a motility disorder of the gallbladder which reduces the rate of bile flow, has also been found in thiamine deficiency.

Malnutrition Induced Malnutrition

Together, these factors no doubt contribute to the phenomena of “malnutrition induced malnutrition”, a term coined by researchers to describe how thiamine deficiency can lead to all other nutrient deficiencies across the board. In other words, a chronic thiamine deficiency can indirectly produce an inability to digest and absorb foods, and therefore produce a deficiency in most of the other vitamins and minerals. In fact, this is indeed something I see frequently. And sadly, as thiamine is notoriously difficult to identify through ordinary testing methods, it is mostly missed by doctors and nutritionists. To summarize, B1 is necessary in the gut for:

  • Stomach acid secretion and gastric emptying
  • Pancreatic digestive enzyme secretion
  • Intestinal brush border enzymes
  • Intestinal contractions and motility
  • Vagal nerve function

Based on the above, is it any wonder why thiamine repletion can radically transform digestion? I have seen many cases where thiamine restores gut motility. Individuals who have been diagnosed with SIBO and/or IBS and are unable to pass a bowel movement for weeks at a time, begin having regular bowel movements and no longer require digestive aids after addressing their thiamine deficiency. In fact, the ability of thiamine to address these issues has been known for a long time in Japan.

TTFD and Gut Motility

While there are many formulations of thiamine for supplementation, the form of thiamine shown to be superior in several studies is called thiamine tetrahydrofurfuryl disulfide or TTFD for short. One study investigated the effect of TTFD on the jejunal loop of non-anesthetized and anesthetized dogs. They showed that intravenous administration induced a slight increase in tone and a “remarkable increase” in the amplitude of rhythmic contractions for twenty minutes. Furthermore, TTFD applied topically inside lumen of the intestine also elicited excitation.

Another study performed on isolated guinea pig intestines provided similar results, where the authors concluded that the action of TTFD was specifically through acting on the enteric neurons rather than smooth muscle cells. Along with TTFD, other derivatives have also been shown to influence gut motility. One study in rats showed an increase in intestinal contractions for all forms of thiamine including thiamine hydrochloride (thiamine HCL), S-Benzoyl thiamine disulphide (BTDS -a formulation that is  somewhat similar to benfotiamine), TTFD, and thiamine diphosphate (TPD). A separate study in white rats also found most thiamine derivatives to be effective within minutes.

Most interestingly, in another study, this time using mice, the effects of thiamine derivatives on artificially induced constipation by atropine and papaverine was analyzed. The researchers tested whether several thiamine derivatives could counteract the constipation including thiamine pyrophosphate (TPP), in addition to the HCL, TTFD and BTDS forms. Of all the forms of thiamine tested, TTFD was the ONLY one which could increase gut motility. Furthermore, they ALSO showed that TTFD did not increase motility in the non-treatment group (non-poisoned with atropine). This indicated that TTFD did not increase motility indiscriminately, but only when motility was dysfunctional. Finally, severe constipation and gastroparesis identified in patients with post-gastrectomy thiamine deficiency, was alleviated within a few weeks after a treatment that included three days of IV TTFD at 100mg followed by a daily dose of 75mg oral TTFD. Other symptoms also improved, including lower limb polyneuropathy.

To learn more about how thiamine affects gut health:

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Elliot Overton, DipCNM CFMP

Elliot is a nutritional therapist and functional medicine practitioner based in the UK. He runs a private nutritional practice called EONutrition and consults with people virtually from around the globe.

Elliot originally developed a keen interest in the clinical application of thiamine TTFD after reading "Thiamine Deficiency Disease, Dysautonomia and High Calorie Malnutrition. After applying high doses of this nutrient in clinical practice and witnessing the immense benefits it could provide, he now seeks to raise awareness of its therapeutic potential through educating others.


  1. I have sibo and food sensitivities for over a year now. 3 rounds of xifaxin and it just gets better for a month then comes back. The thing is, is I have soft stool/diarrhea, not constipation. I do have a zinc deficiency and lower iron also from this. Could thiamine work for me? Should I try and get tested first or just take it? Thank you

  2. Wow! Very interesting! I have had constipation predominant SIBO for years and have had no answers that have helped. I will certainly look into this more.

    I was also diagnosed with POTS, an autonomic nerve issue dealing with accelerated heart rate upon transitioning from different postures. I wonder if this could also help with that due to the autonomic problems related to this deficiency?

  3. Speaking from direct experience (I was thiamine deficient and treated with TTFD, magnesium and B complex): If you are deficient in B1, you’re likely very deficient in other B vitamins too. This will impact the rate your gut and liver can detoxify. You may become very sensitive to some foods. For me, it was tomato sauce (especially tomato paste!). This sensitivity went away as I healed.

    • How long did it take to heal? I cannot tolerate any histamines. This went in for over a year until I realized I was deficient. I’m on my own and need the encouragement.

  4. I cannot tell you how much this website has helped me! I have Celiac Disease. I suffered greatly until I found the hormones matter website and high dose thiamine.
    Can you share this information with the website I am active on the forum on, but lots of members poo-poo the information on thiamine deficiency. They prefer to blame everything on gluten, despite Celiac Disease being a malabsorption disease. Scott Adams is the administrator there. He’s always looking for contributors for articles.
    Please help!

  5. Dear Elliot!
    I’m so glad I found you.
    And, finally someone questions labels like SIBO and IBS, and try to find the root cause of these “diagnoses”. I admire your work and look forward to continue to follow you.
    Thank you, Elliot.

  6. Mr Lonsdale, I came across your site while doing my research to heal myself and my 2 daughters. We all show symptoms of B1 deficiency. I started taking B1 Thiamine HCL that is the only one there is in my country. I am feeling improvements in symptoms that I have had for over 23years. However I am giving my daughters half of one tablet. My elder daughter who is 32 is experiencing a lot of pain in her hips and legs muscles she says it is deep in the muscle. Could you possibly advise on this. Thankd

    • There are two/three options:

      Allithiamine/Lipothiamine are products manufactured by Ecological Formulas. Lipo contains a little alpha-lipoic acid with the TTFD at 50mg per pill.

      On the other hand, I manufactured my own brand called Thiamax (the company is Objective Nutrients). This contains 100mg per capsule, and is free from any additives for those people who are sensitive or who wish to avoid consuming fillers/bulk agents.

      Both work the same!

      • Hello Elliot! Thanks so much for this great article! I have been borderline SIBO probably for a long time but with D not C due to high histamine. Also run short on choline (MTHFR double mutation) but take lecithin and TMG which helps. I am very sensitive right now, but just a couple days into Benfo I can see there is help with the B1. Thought my multi was covering things but not enough I guess. Interestingly I tested low in B1 three times on Nutreval few years back (even with my multi) and I have suffered like so many here. Am trying to get the “noise” in my head to stop, which I would describe similar to getting a song stuck in your head but this is just a repetitive “deee, dooo” (hard to describe, LOL) which begins the moment my eyes open each day. I know it is not a good thing, for sure. It also sometimes manifiests as counting while doing repetitive tasks such as filling water buckets on the farm. Anyway, I ordered Allithiamine and it’s on the way but don’t like the fillers so will give Thaimax a go next time.

        The real reason I am here though is to see it you know how I could get some clean version of this B1 for my horses. I have 4 here which I do my own research on for metabolic disease and nutrient repletion has been eye opening for sure. I have FM Doc but even she has not been as helpful as what has transpired here with my beloved boys. They have helped me discover things to improve my own health as well (no placebo effect).They are better, for sure but not fixed. Many MANY horses die of impaction colic. When I mentioned to my vet about one of my guys having some walking issues which appeared neurological and asked her about B1 deficiency I might as well have been peeing in the wind. He holds his stool for hours on end and then finally passes a HUGE pile about mid day… SO not normal. So he and the others are all on the Benfo (have seen some changes already) and I am trying to figure a dose, currently 300mg for two of them and 600 mg for other two. Little is known about what is required but I did research that 1000 would not be too much. Would rather have a different version for them though. Any help is appreciated, and I will let you and Dr Lonsdale know if switching to the Allithiamine helps with my head noise. I am currently taking 50-150 Benfo but is kicking up my stomach acid (as did Taurine) so have to go slow. Many thanks to you and everyone here at Hormones Matter….. feel so blessed that I have found you folks after many many years of suffering needlessly alongside a lot of others. Just as an aside, I have a very good pretty clean diet, omnivore with no processed food and plenty of veggies/fiber. Have had this diet for many years but was not the answer obviously. No diet helps if you don’t digest it, LOL!

  7. Elliot, what a superb post! It reflects a lot of study and I am delighted to read an extremely clear and erudite expression of a subject that is rejected and even scorned by the medical profession as a whole. I truly hope that you will get a lot of comments.

    • Thank YOU very much, as it was only after reading all of your published work that I began to appreciate the significance of thiamine in chronic disease. It never ceases to amaze me when someone with severe gastrointestinal distress, who has previously found no benefit in any other therapy, responds very quickly to thiamine supplementation.

      It would seem that doctors/nutritionists will prescribe *every* other vitamin before giving thiamine. Very unfortunate indeed.

      • Hi Elliot,
        I’ve struggled with SIBO and GI issues for several years. I also have edema in my lower extremities, LPR (after eating), tinitus and eustachian tube dysfunction, I purchased Dr. Lonnsdale’s book and I believe this is all related to a thiamine deficiency. I’m curious what the appropriate dosage of TTFD would be.

        Thanks for the insightful post.

  8. Great article, thank you! I have just started dosing with TTFD in the past week, I am hopeful that Allithiamine/Lipothiamine will cure my SIBO, GERD, narrowed esophagus, fatigue, hair loss. I have added the other Bs at higher doses, as well as magnesium and other vitamins/minerals. I have cleaned up my diet and cut out added sugars. I have noticed improvements in digestion and fatigue already. Who knew a simple B vitamin wasn’t simple at all? I never knew how important thiamine and the other vitamins/minerals were!

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