Bacteria & Food Intolerance

What do bacteria have to do with your gut health?

Did you know that we have 10 times more bacteria in and on our body than we do human cells! These bacteria are referred to collectively as our ‘microbiome‘. We are going to discover today what our gut microbiome has to do with our overall digestive health. When it comes to food intolerances, important research shows us that alterations in the microbiome have a really significant role in whether or not a food intolerance or allergy will develop. We become much more predisposed to these conditions when our gut bacteria is out of balance; however, we are also learning that restoring the microbiome to its optimal function goes a long way towards correcting food intolerances.

Firstly though, let’s take a look at how our gut functions, so we can then see where gut bacteria fit into the picture.

Digestion 101

When we speak of the ‘gut’. We are talking about the whole digestive tract, from your mouth right through to your toosh. Mouth, stomach, small intestine, large intestines and colon make up the passageway through which our food travels. Our digestive tract also includes accessory organs which are the salivary glands, liver, gall bladder, appendix and pancreas.

The digestive process starts before we even put food in our mouths. Our brains cause a physical response at the thought of food, causing saliva and digestive enzymes to begin flowing in preparation for the food that’s to come. Pretty impressive isn’t it!

Digestive Process

Once you take a bite of food, then digestion begins to occur in the mouth in both mechanical and chemical ways. Mechanical digestion is chewing, which allows us to break down the food into smaller particles. This, in turn, creates a larger surface area for chemical digestion to work on, which involves enzymes which break down the food further. When food is swallowed and enters the stomach, further digestion occurs through stomach acids and enzymes and the muscular contractions of the stomach itself. 

When this food is broken down sufficiently, it leaves the stomach and enters the small intestine. This mixture of food and stomach acids is called ‘chyme’, and it needs to be quite acidic as it enters into the small intestines. The acidity triggers the pancreas to release acid buffers and digestive enzymes. It’s also essential at this point that there are enough healthy fat and protein in the food that’s been consumed because this triggers another hormone called cholecystokinin to signal the gall bladder to release bile. This bile helps to emulsify fat molecules, which makes them much easier to digest and break down.

This is important because the release of pancreatic enzymes and bile digests the food enough so that our small intestine can absorb the nutrients for energy and health creation. The large surface area of the small intestine provides a massive capacity for nutrient absorption. Once it has absorbed all that it can from your food, what is left of the meal passes into the large intestine. This is when your microbiome gets to work!

Elimination diet basics.

In a nutshell, an elimination diet is one that removes particular foods from your diet. These foods are either foods that are known to cause you issues or foods that your practitioner recommends you remove due to your specific symptoms. For example, you may need to remove high FODMAP foods, or high histamine foods etc. If you react to many things and aren’t sure where the issue lies, then the most beneficial approach is to remove a wide range of foods (which are reintroduced later). 

Alternative you can take our hair intolerance test. It will give you a list of foods that your body reacts to. You can use this list as the basis of your elimination diet. This stage of removing foods lasts up to 4 weeks, or until all symptoms are gone. The foods are then reintroduced, one at a time and any reactions carefully recorded. This process can take up to 6 weeks, or longer if your case is complex.

Gut Bacteria & Digestion

The remaining foodstuff that passes into the large intestine is not digestible by humansand is usually made up of fibrous plant matter and the like. Our gut bacteria/microbiome get to work on this fibre, breaking it down to produce a range of nutrients and vitamins that are vital for our health. Short-chain fatty acids, amino acids and Vitamins such as Vitamin K and specific B vitamins are all produced as by-products of our microbiome digesting the fibrous parts of our meal.

These amazing bacteria also perform other vital functions for us, including regulating our immune function, producing neurotransmitters for healthy moods, metabolising cholesterol and other hormones so that we maintain hormonal balance and so much more. They really are paramount to our nutrition and health status.

So you can imagine how important it is to keep our microbiome healthy. In fact, when we have an imbalance in the gut microbiome, many things can go wrong with our health. Notably, an imbalanced microbiome causes our immune system to malfunction. Which can pave a pathway towards allergic reactions or sensitivities to food particles. Studies are showing us that imbalances in specific strains of bacteria are linked to the development of things like egg and milk allergies in children, and also possibly to the development of intolerances to FODMAPS, gluten and histamines found in foods.

Symptoms of gut Becteria 

Theoverall imbalance in our gut bacteria is called Dysbiosis. There is ever increasing evidence suggesting that this imbalance is implicated in a broad range of other disease states including:

  • Thyroid disorders
  • Autoimmunity
  • Anxiety & depression
  • Inflammatory bowel disease
  • Chron’s disease & ulcerative colitis
  • Alzheimer’s & dementia
  • Brain Fog
  • Eczema, psoriasis, rosacea
  • Migraines
  • Diabetes

And many more. Notable many of the above conditions are common symptoms of food intolerance sufferers.

Taking care of your gut bacteria can help you avoid these unpleasant situations. So let’s look at some simple ways to keep your microbiome healthy.


Looking after your microbiome

Keeping your microbiome healthy has a lot to do with the diet and lifestyle that you choose to lead. The good news here is that you have a lot of control over thisand can effectively nurture your gut bacteria with good food choices and lifestyle factors. Here are some daily habits and foods that will help you improve your overall gut & microbiome health:

Fermented foods

When the balance of good versus bad bacteria gets out of balance in your gut. It’s important to replenish the strains of good bacteria. You can do this by consuming small amounts of probiotic-rich fermented foods every day. A spoonful of properly fermented sauerkraut of kimchi with your dinner is a great way to start.  If your stomach is very sensitive, it may react to this with gas and bloating after eating. Just start slowly with a ½ teaspoon per day. Gradually working up to a tablespoon over the next week or so. If you find that you still can’t tolerate it, speaking to your naturopath about this is a good idea.

Probiotic supplementation

This is something that you should do under the guidance of your holistic health practitioner because all probiotic strains are different and are used for specific conditions. However, it is noted here because probiotic usage has had some excellent results in alleviating food intolerance and allergy symptoms.

More specifically, we’ve seen probiotics help prevent the development of food and atopic allergies in children with a family history of allergy when particular strains of probiotic are ingested by the mother during pregnancy; and infants with cows milk allergy were able to become tolerant to cows milk proteins with the supplementation of a specific probiotic strain. These studies were conducted in children, but there are also promising adult studies too.

For example, when supplemented with a multi-strain probiotic consisting of Lactobacilli, Bacillus coagulans, and Saccharomyces boulardii patients with non-celiac gluten sensitivity and intolerance saw a significant reduction in their symptoms.

More research needs to be conducted in this area; however so far, the results have been very promising.



Chew your food thoroughly, until it’s almost liquid in your mouth. This small change can really improve your digestive symptoms. It’s important also to pay attention to your food. Make sure your phone and computer are switched off and not part of your mealtime.


Make time for quiet in your daily life. Even 10 minutes every day to sit, relax and be still can have lasting benefits on your health. This is really important for digestion because our gut can’t function properly unless we are in a relaxed state. Stress hormones negatively affect our microbiome too, so making time for peace and stillness is super important. 

Bone Broth

This is such a powerful tool in creating a healthy gut. It stimulates digestion and has many gut-healing properties and nutrients, making it fantastic for healing the gut lining. Make sure you add apple cider vinegar to your broth to get all of the nutrients out of the bones.

Plant foods

Ensuring that you have a wide variety of plant foods in your diet daily is one of the best things that you can do to both feed your microbiome and maintain a healthy gut. Vegetables, beans, lentils, whole grains and fruits are full of vitamins and minerals, as well as the essential bacteria loving fibre.

In closing, we’ve discovered how important our microbiome is to our overall digestive health and also learnt that when it gets out of balance, we are then predisposed to developing food intolerances and allergies. A healthy microbiome is a powerhouse of nutrient creation and plays a vital role in our immune health, hormone regulation, nervous system health, and so much more. Nourishing this bacterial colony is essential if we want to have long-lasting and vibrant health, and also a recovery from food intolerance symptoms. We can look after our microbiome through simple diet and lifestyle practices such as consuming fermented foods& bone broths, practising relaxation, chewing our food properly and ensuring we have a wide array of plant foods in our diet.


As humans, we carry around ten times more bacteria than we do human cells, which makes us basically a walking sack teeming with bacteria. The bacteria that colonise our intestinal tract is collectively called our ‘digestive microbiome’. It has a major part to play in our health. It does vital tasks for us such as produce vitamin K and short chain fatty acids, as well as keep our immune, hormonal and nervous systems healthy. When our microbiome gets out of balance, we are predisposed to many health issues, including the development of food intolerances and allergies!

We discuss in the article how you can keep your microbiome healthy with simple daily practices. So that you can have true and long-lasting health and wellness. Looking after your microbiome can also help you to heal from food intolerances. We look at the main ways you can do this in your daily life.

If you are suspecting that you have bacterial imbalances in your gut alongside possible food intolerances. We highly recommend that you take one of our food intolerance hair tests. Having confirmation of your food intolerances will really speed the process of healing your gut and microbiome.

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