Gastrointestinal tract and thiamine

Gastrointestinal Disease and Thiamine

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The gastrointestinal (GI) tract, long thought to be specific only to the process of digestion, starts at the mouth and ends at the anus. Modern research has revealed that it has a very complex relationship with the rest of the body, especially the brain, and this post is aimed at giving the reader a glimpse of this research.

The Impact of Medication on the GI Tract

Every year many new medications are approved for clinical use, several of which can cause clinically significant GI tract toxicity. An article in the medical literature describes the drug-induced injury to the fragile lining of the tract. A drug by the name of Flagyl is used for resistant bacterial infections. Its chemical name is metronidazole and occasionally it results in the complication of encephalopathy (brain disease). It has been proposed that the adverse effects of the drug may be due wholly or in part to its conversion to a thiamine analog (the drug has a similar formula to thiamine and acts as an antagonist to the action of the vitamin). It seems that this happens enough that a Metronidazole Toxicity group has been formed online and has a considerable number of people with complaints regarding the use of this drug. Because the encephalopathy is said to be uncommon, it is apparently accepted as an occasional side effect, even though many people have been crippled from its use. The number of people reporting serious symptoms in the Toxicity group tends to negate the conclusions of officialdom that this encephalopathy is “uncommon, if not rare”.

Thiamine Deficiency and Obesity

This is defined by a formula known as the body mass index. Obesity is a growing worldwide epidemic currently affecting one in 10 adults. In the United States the incidences is as high as 40%. A publication claims that the only proven long-term treatment of severe obesity is surgical modification of the gastrointestinal anatomy, termed bariatric surgery. Complications are seen in patients who fail to follow the recommended changes in lifestyle. They include nausea, vomiting, so-called dumping syndrome, acid reflux and nutritional deficiencies. The authors note that “despite caloric density, the diet of patients prior to bariatric surgery is often of poor nutrient quality“. Unfortunately it needs to be pointed out that it is exactly why they became obese in the first place. Bariatric surgery is “shutting the stable door after the horse has gone”. Although obesity has been viewed traditionally as a disease of excess nutrition, the evidence suggests that it may also be a disease of malnutrition. Thiamine deficiency (TD) was found in as many as 29% of obese patients seeking bariatric surgery. They can present with vague signs and symptoms. In many posts on this website it has been pointed out that high calorie malnutrition is a widespread scourge in America and is responsible for the high incidence of obesity. The “vague signs and symptoms” are typical of early TD (beriberi) and are often misdiagnosed as psychosomatic.

Constipation or Diarrhea

The commonest form of bypass surgery for obesity, without going into the details, is known as Roux-en-Y. I do not know the reason for this nomenclature, but for surgeons it defines the technique. A publication in the medical literature described thiamine deficiency after gastric bypass and hypothesized that this is common. Of 151 patients, 27 met the criteria for thiamine deficiency, a prevalence of 18%. Eleven of these patients reported constipation after the surgery and treatment with thiamine improved it.

A 29-year-old patient has been described who had experienced sudden blindness and a disturbance of consciousness after two months of chronic diarrhea and minimal food intake. Amongst other physical signs, hemorrhages were seen in the eye. Leaking of blood from capillaries has long been recognized as a phenomenon that might be found in thiamine deficiency. It is of particular interest that the examination of cerebrospinal fluid revealed it to be normal, but magnetic resonance imaging showed changes that were interpreted as typical of thiamine deficiency. After administration of intravenously administered thiamine, both visual acuity and the visual field rapidly improved with the simultaneous recovery of consciousness. No indication was provided to explain a two-month period of diarrhea, although it was accompanied by “minimal food intake”.

A patient with Crohn’s disease and long-standing diarrhea resulted in combined thiamine and magnesium deficiency. Despite massive doses of thiamine given intravenously the symptoms of the deficiency could not be suppressed until the magnesium deficiency was also corrected. Many posts on Hormones Matter have discussed the relationship of magnesium with thiamine. Both of them work together as cofactors for a number of vitally important enzymes that govern energy metabolism. Obviously, literally any lapse of health can occur if energy is insufficient to meet the demands of living. Therefore, it is possible to understand that fatigue and other disorders related to ulcerative colitis and Crohn’s disease are the manifestation of an intracellular mild thiamine deficiency.

It is important to note that, in spite of finding the levels of thiamine and thiamine pyrophosphate in the blood to be normal, 10 patients out of 12 showed complete regression of fatigue and 2 patients showed partial regression when thiamine was administered. Note the doses of thiamine that were given. They ranged from 600 to 1500 mg/day given by mouth. The thing to understand here is that this was not simple vitamin replacement. These authors were using thiamine as a completely non-toxic drug, revealing genuine pioneering. Other authors have noted that micronutrient deficiencies occur in Crohn’s disease. They reported two patients with Crohn’s disease who complained of sudden-onset eye and brain dysfunction and confusion while receiving prolonged total parenteral nutrition. Magnetic resonance imaging allowed definitive diagnosis of Wernicke encephalopathy, a well-known brain disease occurring as a result of thiamine deficiency.

The Gut – Brain Connection

Within the last decade, the complement of bacteria living in the human bowel, now known as the gut microbiome, has become a focus of attention. The GI tract was once regarded simply as a digestive organ, but recent research has led to finding that the microbiome may have an impact on human health and disease. Surprisingly, it has become a focus of research for those interested in the brain and behavior. Multiple routes of communication between the gut and the brain have been established. Recently the gut microbiota (the complement of bacteria) has been profiled in a variety of conditions, including autism, major depression and Parkinson’s disease. Of course, there is still debate as to whether or not the changes observed are primary in causing the disease or merely a reflection of it. Other authors have raised the question of the importance of the microbiota in the pathology associated with autism, dementia, mood disorders and schizophrenia. It is interesting that the GI microbiome has been regarded as a complex ecosystem that reportedly establishes a symbiotic mutually beneficial relation with the host. It is said to be rather stable in health, but affected by age, drugs, diet, alcohol and smoking. Smoking leads to modifications of the bacterial complement and is linked with absence of a protective effect toward ulcerative colitis, and deleterious for Crohn’s disease.

An interesting slant has been placed on this problem of relationship between the host and the bacteria which make up the microbiome. It is pointed out that thiamine is an essential cofactor for all organisms, including bacteria and the role that gut microbes play in modulating thiamine availability is poorly understood. Little is known about how thiamine impacts the stability of microbial gut communities. In order to study this, a model gut microbe (Bacteroides thetaiotaomicron) was chosen. The study showed that thiamine acquisition mechanisms used by this microorganism not only are critical for its physiology and fitness but also provide the opportunity to model how other gut microbes may respond to the shifting availability of thiamine in the gut. Importance of this means that the variation in the ability of gut microbes to transport, synthesize and compete for thiamine is expected to impact on the structure and stability of the microbiota. The authors conclude that this variation may have both direct and indirect effects on human health.

The Role of Energy Metabolism

The question of whether bacterial changes in the gut are primary or secondary makes us think of which is the “chicken” and which is the “egg”. Bacteria are complex one-celled organisms and they require energy to perform their normal function, just the same as our body cells. Therefore, thiamine is as important to bacteria as it is to us, bringing us back to considering the frontier of medical thinking that energy metabolism is the core issue of health and disease.

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Image by Andrew Martin from Pixabay.

This article was published originally on May 6, 2019. 

Derrick Lonsdale M.D., is a Fellow of the American College of Nutrition (FACN), Fellow of the American College for Advancement in Medicine (FACAM). Though now retired, Dr. Lonsdale was a practitioner in pediatrics at the Cleveland Clinic for 20 years and was Head of the Section of Biochemical Genetics at the Clinic. In 1982, Lonsdale joined the Preventive Medicine Group to specialize in nutrient-based therapy. Dr. Lonsdale has written over 100 published papers and the conclusions support the idea that healing comes from the body itself rather than from external medical interventions.


  1. I know it has been a while since you posed your question to Dr Lonsdale. I am wondering if you have any known issues with sulfur. Allithiamine is thiamine with allium as a co-factor. Allium is derived from (most frequently) garlic; but onions are also rich in organosulfur compounds. If you have issues with garlic and onions, you might be reacting to the allium in the Allithiamine. This would be unfortunate because there are so many health benefits from organosulfur compounds. If it is a sulfur sensitivity, perhaps someone on here might have an alternative for you.

  2. Dr Lonsdale

    My husband has Parkinson’s , diagnosed in 2017. I’ve read the Parkinson’s & B1 book. I do find it confusing. Before starting protocol , is it possibleIs to consult with you over a zoom call. Or is there someone on Canada with your knowledge

  3. Hi Dr. Londsale,

    I have suffered for years now from a various debilitating symptoms, among them:
    anxiety attacks
    SIBO / Candida / gastroparesis/ bloating++
    Amenorhea for 2 years 1/2

    I have been diagnosed with heavy metal toxicity (IV DMSA) , with parasites…

    My hormones where completly out of balance (got back my periods 6 months ago now!)
    All of this started with the gardasil injection 9 years ago. I started to experience the gastro symptoms after that?

    I also found out about oxalates toxicity 3 months ago and my symptoms improved dramaticaly (my 6 months pregnant bloated belly disapeared in 3 weeks and I started to remember my dreams again). I just started to read about B1 deficiency and started to supplement for 1 month before doing the TKA test. The result is normal (1.04 and the boderline marquers starts at 1.15-1.25 / deficiency is above 1.25).
    My question is, do you think I should discard the B1 deficiency? Or the supplementation for 1 month can mess up the results?
    Thank you in advance for your response…
    Best regards, Marguerite

    • You were probably borderline thiamine deficient and the Gardasil precipitated clinical deficiency. Anxiety attacks and bloating are typical. But the whole trouble with this deficiency is that literally ANY symptom can develop. Physicians, not recognizing their true nature, try to explain the symptoms by diagnosing disease A, B or C and you find yourself labelled with 3 different conditions, none of which respond to treatment. This is because thiamine deficiency produces energy deficiency, particularly in the brain and the entire brain/body union breaks down. The American diet is high in calories and the thiamine level is good for a relatively low calorie intake. That is why the Mayo Clinic measures the thiamine level in the blood and because they find it in the normal range, they dismiss thiamine deficiency as the underlying cause of (say) 3 diseases. There are also relatively common minor genetic characteristics that do not cause symptoms unless there is nutritional failure. You should persist with thiamine supplementation and add a daily dose of 125-250 mg of magnesium taurate. I am appalled at the frequency of this story of undiagnosed illness that has such a simple treatment.

  4. I wonder if you often see people getting sick when supplementing thiamine? I have tried for 18 months now to supplement allithiamine but get severe nausea. Could this be due to lack of some cofactor (I do take Mg and B2, P5P) or is it rather oxalate dumping? Is this a reaction youve familiar with?

  5. Dr. Lonsdale,

    Last question. When I take 100mg of b6 as pyridoxine (which I’m told crosses the BBB easier than p5p) while on allithiamine I get wild quick bursts of energy mixed with depression and anxiety. I was wondering if that meant my brain was waking up from a possible b6 deficiency too or just to avoid b6 in any amount more than in a multi.

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