Microbiome & Food Sensitivities

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Table of Contents
Healthy vs Abnormal Immune Responses
Gluten
The Problem With Highly Restricted Diets
Highly Restricted Diet Alternative
Probiotics
Prebiotics
Diet Against Food Sensitivities
Further Reading And References

Healthy vs Abnormal Immune Responses

Healthy immune systems can recognise the difference between harmless and harmful components that enter our bodies. When immune systems go awry, they can react to harmless foods. (1) Normal immune responses to foods are key to preventing adverse food reactions. Abnormal responses may have a genetic basis, but there also environmental factors. (3)

Bacterial and viral infections suppress appropriate immune responses, triggering inflammation and altering gut permeability, which are implicated in food sensitivities. Animal studies have found administration of strains of Bifidobacterium and Lactobacillus changed immune responses, reducing the severity of these reactions. Further studies are needed to understand whether the same is achieved in humans. (1)

Short-chain fatty acids (SCFAs), such as butyrate, which are by-products of the immune system generated by good bacteria in the gut, help to maintain the intestinal barrier and guard against food sensitivities. Butyrate, specifically, regulates components which improve tolerance to food antigens or allergens. In a mouse study, a high fibre diet, which aids butyrate production (6), activated protective pathways needed for reduced responsiveness to food antigens. (1) (2)

The normal human microbiome consists of a number of species of good (commensal) gut bacteria including Bacteroides, Enterobacteria, Bifidobacteria, and Lactobacilli. These bacteria interact with the intestinal mucus barrier, which is part of the immune system of the gut promoting food tolerance. Differences in gut flora between healthy individuals and those suffering from food intolerances have been observed. A lack of microbiome diversity in the gut may predispose someone to gluten, FODMAP and histamine intolerance. Certain bacterial species help in the breakdown of gluten and lack of these may lead to gluten intolerance. Histamine intolerance can occur when there are too many bacteria which produce histamine or produce enzymes that affect the metabolism of histamine. If histamine is suspected to be an issue, it may be wise to avoid histamine producing strains. Instead, it may be helpful to consider histamine degrading strains. (3)

Bacterial diversity can be achieved by eating a broad range of foods.

Gluten

If gluten is not completely digested, it can activate a T-cell immune response (2). Gluten, which is a protein, can be degraded into small molecules called peptides by particular strains of Lactobacillus or Rothia found in healthy individuals. This process decreases immune reactions to gluten. (1) (2) Lactobacillus can also degrade gluten peptides produced by human or pathogen proteases (enzymes that break down protein). Lactobacillus isn’t always successful in reducing this immune response, since the break down of peptides produced by Pseudomonas aeruginosa, which is a pathogen (bad bacteria), creates shorter peptides that hold onto their immune system provoking components. These components break through the intestinal barrier better than those produced by human digestive proteases, potentially causing an immune response rather than reducing it. (2)

In a study, 94 bacterial strains were able to metabolise gluten, 61 strains showed protein enzyme activity against gluten proteins and several strains showed activity that breaks down immune response producing peptides in patients with coeliac disease. Most of the strains were from the Lactobacillus, Streptococcus, Staphylococcus, Clostridium and Bifidobacterium families of bacteria, in particular sub-strains (phyla), Firmicutes and Actinobacteria. The ability of certain strains of bacteria being able to use gluten proteins and peptides as nutrients, could lead to new treatments for coeliac disease. (4)

Patients with non-celiac gluten sensitivity experienced significantly reduced symptoms from a multi-strain probiotic that included Lactobacilli, Bacillus coagulans, and Saccharomyces boulardii. (3)

The Problem With Highly Restricted Diets

Highly Restricted Diet Alternative

Probiotics

Probiotics can assist with food allergies and intolerances in a number of ways:

Increase the level of good bacteria responsible for interacting with the immune system improving tolerance to foods
Decreasing antigen penetration of the intestinal barrier by reducing intestinal permeability
Encouraging the immune system to favour the Th1 response, a branch of the immune system associated with the resolution of allergic symptoms. Allergic disorders involve increased activity in the Th2 branch of the immune system
Increasing intestinal IgA, an immunoglobulin associated with immune tolerance and a reduced risk of IgE-mediated allergic diseases
Crowding out bad bacteria (pathogens) thus reducing intestinal inflammation
Amelioration of SIBO (small intestine bacterial overgrowth), a condition with similar symptoms to IBS and associated with FODMAP intolerance in some people by specific probiotics Bacillus coagulans and Lactobacillus acidophilus, as has been found in a study

(3)

Prebiotics

Prebiotics aid the action of probiotics by acting as feed for them and promoting their growth in the intestine. Many studies have found that supplementation with prebiotic oligosaccharides reduces the incidence of allergic disease. (3)

Note that some probiotic formulas contain prebiotics. Prebiotics may be best avoided when initially treating IBS, since the bad bugs will still be dominating and will be fed by the prebiotics, potentially worsening symptoms. It is best to take probiotics without prebiotics in the first instance, so the probiotics can help crowd out the bad bugs and make their numbers die down. It is safer to try prebiotics once there has been symptom improvement through probiotics and/or medication.

Diet Against Food Sensitivities

A nutrient dense, whole foods diet including omega-3 fatty acids, vitamins C, E, and A, beta-carotene, and zinc are associated with a decreased incidence of food sensitivities. Whereas a diet high in processed and refined carbohydrates including artificial sweeteners, omega-6 fatty acids, and food additives may increase incidence of food allergies and intolerances. It is also possible that intake of genetically modified foods may also lead to food intolerances due to the altered proteins in these foods. (3)

In a study, it was found that IBS patients with the most severe symptoms of IBS showed a higher consumption of poor quality food staples including processed food items such as sweets, soft drinks and fried potato products. (5) Overall a diet high in saturated fats, fructose, emulsifiers and alcohol with vitamin A deficiency and lower butyrate levels in the gut can impair intestinal barrier function and increase permeability. Prebiotic fibres (especially derived short-chain fatty acids), probiotics, polyphenols, glutamine, methionine, vitamin D and zinc can, in contrast, enhance barrier integrity. In laboratory studies, a probiotic formulation consisting of Lactobacillus rhamnosus, Bifidobacterium lactis and Bifidobacterium longum was shown to preserve the integrity and functioning of the intestinal barrier from the damage caused by inflammatory responses. (8)

There is emerging evidence that ultra processed foods, which contain emulsifiers have the potential to reduce gut bacteria diversity and make the mucus wall of the intestines thinner, affecting the integrity of the intestinal wall, increasing the chances of inflammation, theoretically driving food sensitivities. Emulsifiers include, for example:

lecithin
carrageenan
E471 (Mono- and diglycerides of fatty acids)
acacia gum
carboxymethylcellulose
polysorbate 80
E472e (diacetyl tartaric acid ester of mono- and diglycerides or DATEM)
E481, (sodium stearoyl lactylate or SSL)

(7)

Additionally, a 2024 study of 92,000 adults in France, estimated food additive emulsifier intakes over an average of 6.7 years based on dietary records. Higher intakes of carrageenan and mono- and diglycerides of fatty acids were associated with overall, breast and prostate cancer risk. (9)

Avoiding ultra processed foods and preparing your own food from scratch could go a long way towards helping your gut and overall health.