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The Gut-Mast Cell Connection: SIBO, Digestion, and Supporting Gut Health

Updated: Nov 1, 2023





If you’re one of the many people with histamine intolerance or mast cell activation syndrome (MCAS), it is likely that you also struggle with gut issues - you are not alone, a large majority of people I work with who experience histamine or mast cell issues also present with some type of digestive problem.


The gut and mast cells have an intricate, two-way relationship. Inflammation in the digestive system can trigger mast cell degranulation and histamine release. At the same time, mast cell mediators circulating in the bloodstream can damage the intestinal lining, causing further gut issues. It’s a vicious cycle however, calming mast cells and histamine responses while supporting gut health helps to stabilise things.


In this post, we’ll cover the following topics:

  • Structural Causes of SIBO and Other Gut Problems

  • Poor Motility and Nerve Function

  • Other Causes of SIBO and Gut Problems

  • The Importance of Stomach Acid and Enzymes for Digestion

  • Butyrate and its nourishing effects on the gut lining.

  • How intestinal hyperpermeability can trigger mast cells.

  • My back-to-basics approach

  • Supporting the most sensitive of clients


Let’s get started!


Structural Causes of SIBO and Other Gut Problems

When dealing with chronic gut issues, it’s important to first rule out any anatomical or structural factors that could be contributing. For example, a hiatus hernia, prolapse, adhesions, a tilted pelvis or even surgical procedures such as a hysterectomy can all mechanically alter the shape and function of the digestive tract. Nerve damage, dysautonomia or irritation in the abdominal region can also impair proper motility and flow.


First and foremost it is important to consult with a medical professional prior to seeking holistic support because if there is something structurally out of balance or something needs medical intervention then this needs to be addressed as a priority.


Poor Motility and Nerve Function

Assuming no major anatomical abnormalities are found, the next thing to explore is gut motility, which is simply defined as the movement and flow of food through the digestive tract. Mast cells release histamine that alters gut contractions, so calming mast cells may restore motility and gastrointestinal function.


There are also a few interrelated factors that impact motility:

  • Stomach acid production

  • Digestive enzyme levels and bile flow

  • Vagal tone

  • Migrating motor complex (MMC) function

Inefficient stomach acid production is incredibly common in my clinical practice. This condition is otherwise known as hypochloridria, it hampers digestion and contributes to changes in the gut microbiome. Stomach acid production naturally declines with age, which is one reason why many people find meat hard to digest as they get older because stomach acid helps with the breakdown of protein. Inefficient stomach acid also occurs when you lack vital nutrients such as chloride, zinc and vitamin B1, however infections, food poisoning, or medication use can also contribute to this. One of the most inappropriately used medications in the world are called proton pump inhibitors (PPI’s), such as omeprazole or lansoprazole. Very often people are left on these medications for far too long. Continuous suppression of stomach acid contributes to nutritional deficiencies and negatively affects the health of the gut microbiome and increases the risk of colonisation of pathogenic microbes, including Clostridium difficile and salmonella. Research has found that people on long term PPI have a higher prevalence of oral cavity bacteria translocating to the gastrointestinal microbiome. If you have been on long term PPI medication, please discuss these risks with your GP.

Low digestive enzyme levels and poor bile flow can also impair the break down of foods, undigested food can feed opportunistic bacteria and yeasts that contribute to SIBO type symptoms, which includes excessive burping, gas, indigestions and painful bloating.. Bile is equally important, not only with helping to digest and absorb fats and vitamins A, D, E and K, but bile helps to produce and environment where pathogenic microbes do not have the opportunity to overgrow and proliferate.

The vagus nerve serves as a highway that sends signals promoting motility. Vagus nerve damage or imbalance has a profound effect on digestion. This manifests as either constipation or chronic diarrhoea, but the vagus nerve also regulates the opening and closing of the sphincters of the stomach, the contraction of the gallbladder and the release of pancreatic juices. In my most sensitive of cases, dietary and supplementation interventions do not work until nervous system imbalances have been addressed and I refer these people on the DNRS programme or to a polyvagal expert.

The migrating motor complex (MMC) are responsible for sweeping debris out of the small intestine between meals. To work properly, it requires a period of “down time” of around 3-4 hours after eating. Frequent snacking inhibits the action of MMC. Bacterial-produced metabolites can directly influence gut motility, leading to a cascade of effects and feedback mechanisms impacting the production of the metabolite itself. Gut bacteria replicate and produce their metabolites based on the availability of nutrients. Metabolites impact gut motility, which, in turn, modifies the fluid flow.

The takeaway from all of this is that supporting motility requires a multi-pronged approach some of those approaches may include:

  • Supplement to support stomach acid and digestive enzyme production

  • Support for healthy bile flow

  • Vagus nerve exercises

  • Allowing 3-4 hours between meals for MMC activation

  • Identify any food intolerances of other causes listed below


Other Causes of SIBO and Gut Problems:

Aside from anatomical and motility factors, there are a few other potential causes of SIBO and gut issues to rule out:

  • Previous history of food poisoning

  • Medications like PPIs or antibiotics

  • High stress levels

  • Nutrient deficiencies

  • Underlying infections and pathogens

  • Spike protein persistence

  • Mould toxicity

  • Blood sugar imbalances

  • Thyroid dysfunction


Of relevance for those with mast cell activation is mould toxicity which is almost certainly a common trigger for both digestive symptoms and histamine intolerance and this is something that I see time and time again in my practice.


High cortisol from chronic stress also negatively impacts digestion, immunity, and the microbiomes, so stress management becomes an important factor in supporting gastrointestinal health.


The Importance of Stomach Acid and Enzymes for Digestion

I've hinted a few times to the importance of stomach acid (HCl), digestive enzymes, and optimal bile flow for effective digestion on several occasions. Let's delve deeper into these crucial aspects.


Insufficient HCl can hinder the efficient breakdown of food particles. This not only places extra demands on digestive enzymes and bile but also leads to bacterial fermentation further up in the small intestine. This is a contributing factor to the development of SIBO, as low stomach acid allows for its progression. HCl also plays a pivotal role in activating the enzyme pepsin, necessary for protein digestion, and intrinsic factor, which aids in B12 metabolism. Moreover, ferric iron, the primary form of iron in plant foods, requires an acidic environment with a pH of 3 or lower to maintain stability for optimal absorption. This explains why individuals with SIBO may encounter nutritional deficiencies.


Pancreatic enzymes, released from the pancreas into the small intestine, rely on the presence of an acidic chyme from the stomach to function effectively. In the absence of this acidity, their impact is compromised. Furthermore, low stomach acid interferes with the initiation of the migrating motor complex, as previously discussed. In summary, low stomach acid sets the stage for incomplete digestion, bacterial overgrowth, and impaired motility—a perfect combination contributing to SIBO.


While Betaine HCL, digestive enzymes, and bile acids are frequently used interventions, I prefer to explore more natural approaches. These include incorporating bitter foods, supporting the nervous system, and naturally elevating stomach acid levels through optimising saliva production and thorough chewing.


Butyrates role in the digestive tract

  • Butyrate and other short chain fatty acids (SCFAs) play several important roles in gut health:

  • Serve as fuel for enterocytes (intestinal cells).

  • Modulate gene expression and inflammation.

  • Improve gut barrier integrity.

  • Increase absorption of vitamins and minerals.

  • Butyrate is also an HDAC inhibitor and anti-inflammatory that helps calm mast cells. It’s been shown in studies to reduce allergic reactions.

The primary issue I often observe in most SIBO intervention protocols is the exclusion of foods that promote a healthy microbiome, along with the use of potent anti-fungals followed by the introduction of probiotics. and excessive amounts of butyrate supplementation. I believe this approach may further exacerbate the dysregulation of the gut microbiome. I'll delve deeper into the shortcomings of current SIBO protocols and the issue of probiotic and butyrate contamination in a separate post.

Returning to the topic of butyrate, this short-chain fatty acid is produced through the fermentation of resistant starches. Research consistently demonstrates that resistant starches play a pivotal role in shaping the gut microbiome and producing not only butyrate but also other essential short-chain fatty acids. While butyrate is available in supplement form, it's essential to recognise that butyrate production involves a complex interplay between dietary components and gut microbes. Flooding the gut with an end-stage metabolite like butyrate may potentially exacerbate existing imbalances. Incorporating resistant starches into your diet can be easily achieved by consuming overnight oats, cooked and cooled potatoes, and rice.


Intestinal permeability or leaky gut:

Another crucial aspect to consider is intestinal hyper-permeability, commonly referred to as "Leaky Gut." Mast cell activation syndrome is known to increase intestinal paracellular permeability, in simple terms, widening the gaps between the cells lining the gut. This permits the passage of intestinal metabolites into the systemic circulation, triggering an immune response. This sets in motion a vicious cycle of mast cell activation, originating from the initial source and now compounded by the leaky gut mechanism.

I maintain that the best place to start is with the basics:

My 4 step process provides a guide in clinical practice on how to start to tackle these complex cases. Even though a clinical roadmap has been suggested here is is important to monitor symptoms and adjust according to individual needs and responses.

"Don’t assume supplements alone can 'fix' chronic symptoms"

Step 1: Begin by mitigating inflammation using precise dietary adjustments and incorporating natural antihistamines and histamine binders, such as Toxaprevent, Vedicinals 9, and quercetin. It's advisable to conduct tests for lipid peroxide production, as elevated levels may signal a need for further antioxidant support and lipid replacement therapy through the introduction of omega 3/6 fatty acids, arachidonic acid, specialised pro-resolving mediators (SPMs), and phospholipids.


Step 2: Next, focus on optimising digestive function by targeting the gut-brain axis. The approach will vary depending on the severity of symptoms. B1 and zinc can support stomach acid production and enhance communication between the gut and brain. Additionally, assess bile flow and pancreatic enzymes for efficient nutritional breakdown. Implement mindfulness practices during meals, ensure relaxation, and emphasise thorough chewing. In cases of substantial gut stagnation, options like CellCore Bowel Mover, high-dose vitamin C, or magnesium oxide can provide relief. It's worth noting that initiating anti-microbials or anti-fungals as a first-line intervention, particularly in chronic illnesses, should be approached cautiously due to the increased risk of experiencing herxheimer reactions.


Step 3: As digestion improves, move on to identifying and rectifying any remaining nutrient deficiencies or insufficiencies through targeted supplementation and dietary enhancements. Develop a personalised nutrition plan to maximise nutrient absorption based on individual requirements and digestive capacity. This may entail adjusting macronutrient ratios and micronutrient density. It is also important to support liver function with essential nutrients, such as methyl donors and gentle drainage techniques, and maintain kidney function by ensuring adequate hydration and electrolyte balance. By first addressing digestion, you pave the way for supplements and dietary changes to be better absorbed and utilised.


Step 4: Improvement in the microbiome often becomes apparent after implementing the initial three steps. However, specific support may be required for the oral, nasal, and gut microbiomes, especially in cases of mycotoxin exposure or gum disease. Consider products like XClear or CitriDrops nasal spray, Dentura Med toothpaste, or Biocidin's mouthcare range, in conjunction with personalized interventions to further fortify the gut. Recent research suggests that prebiotics and nutritional interventions, rather than probiotics alone, exert the most significant influence on the gut microbiome. Valuable prebiotics include Myota's gut booster or Microbiome Labs MegaPre.


In conclusion, while I've suggested various interventions within this discussion, it is crucial that individuals collaborate with a knowledgeable practitioner well-versed in histamine-related issues to uncover any underlying factors contributing to leaky gut and SIBO, such as infections or digestive dysfunction. Keep in mind that supplements can interact with medications, so it's imperative to conduct a comprehensive assessment of drug-nutrient interactions before incorporating supplements. Additionally, if you have structural issues within your digestive tract, hernias, gallstones, cysts, adhesions, a predisposition to bowel blockages, kidney disease, or cancer, DO NOT self-prescribe supplements. Always seek the guidance of a qualified professional.


With patience and an integrated approach, you can break the cycle of gut issues provoking mast cell activation and vice versa.


There is hope! If you would like to work with us.


Download our histamine guide by heading to this section of your website https://www.benourished.co.uk/mcas-histamine-intolerance


References


B Y. De Winter,. R M. van den Wijngaard., (2012) Intestinal mast cells in gut inflammation and motility disturbances, Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease,

Volume 1822 (1) pp. 66-73


L B. Afrin., A Khoruts,. (2015) Mast Cell Activation Disease and Microbiotic Interactions. Clinical Therapeutics. Volume 8 (2), pp. 1-13,


G Traina. (2021) The role of mast cells in the gut and brain. J. Integr. Neurosci. 20(1), 185–196


S Buhner, M Schemann, (2012) Mast cell–nerve axis with a focus on the human gut, Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease,

Volume 1822 (1), pp. 85-92,


Deloose, E., Janssen, P., Depoortere, I. et al. The migrating motor complex: control mechanisms and its role in health and disease. Nat Rev Gastroenterol Hepatol 9, 271–285 (2012). https://doi.org/10.1038/nrgastro.2012.57


B Waclawikova., A Codutti et al (2021) Gut microbiota-motility interregulation: insights from in vivo, ex vivo and in silico studies. Nature. Article: 1997296


T Ghosh., A Valdes. (2023) Evidence for clinical interventions targeting the gut microbiome in cardiometabolic disease. BMJ; 383:e075180


Garczyk, A.; Mardas, M.; Stelmach-Mardas, M. Microbiome Composition in Microscopic Colitis: A Systematic Review. Int. J. Mol. Sci. 2023, 24, 7026. https://doi.org/10.3390/ijms24087026


Zhang, J., Zhang, C., Zhang, Q. et al. (2023) Meta-analysis of the effects of proton pump inhibitors on the human gut microbiota. BMC Microbiol 23, 171 https://doi.org/10.1186/s12866-023-02895-w

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