How to maintain a healthy gut microbiome while balancing food intolerances

We’re all desperately trying to figure out how to nourish our bodies, feel energised, and maintain our health. But with so much conflicting information from food manufacturing corporations, diet culture, and fluctuating trends in what we deem ‘healthy’ or ‘unhealthy’, it’s difficult to know what to believe.

Enter the issue of food allergies and intolerances (often used interchangeably despite being very different), and it’s tempting to throw in the towel and dive headfirst into a pint of Ben & Jerry’s.

People often talk about the rapid increase in food allergies and intolerances, but the evidence paints a different picture. Even in Australia, which has one of the world’s highest rates of food allergies, surveys find that diagnosed food sensitivities have remained relatively stable over the past few decades, hovering between 20 per cent and 25 per cent of the population.

So why is there a perceived explosion of food intolerances? Perhaps it’s related to accessible, but not always reliable, medical information online, leading people to self-diagnose based on inaccurate health advice from influencers, friends, or family.

People may incorrectly attribute symptoms to food, experience psychosomatic symptoms from eating things they believe are ‘unhealthy’, or simply conflate a dietary preference with a genuine food sensitivity.

The ability to use Doctor Google to diagnose ourselves with food intolerance, alongside the normalisation of catering to dietary requirements at functions and restaurants, creates the illusion of increased food intolerance, regardless of whether this is true.

Does eliminating food groups help or hinder your gut health?

Eliminating or drastically cutting back on a particular food group may make you feel better in the short term. This could simply be due to a perceived sense of control or the feeling that you’re taking positive action for your health.

But how does reducing your dietary variety affect your wellbeing, particularly regarding your gut health and microbiome?

Nina Gelbke, an accredited nutritionist and sports nutritionist, explained the importance of balancing food choices that keep symptoms manageable while still including a wide variety of foods to maintain a healthy and diverse gut microbiome.

“Our gut microbiome is highly adaptable to the types of foods and fibres we eat,” she said.

“When removing foods and the carbohydrates and fibre these contain, we have a down-regulation in the types of bacteria that ‘feed off’ and digest these, which can lead to a less diverse microbiome and even further reduced tolerance (or increased digestive symptoms) with these foods.”

She advocates, where possible, for a balanced approach to triggering foods rather than taking an “all-or-nothing” stance. Where possible, she recommends consuming amounts small enough that symptoms are minimal or non-existent, without completely eliminating them to maintain as diverse a diet as possible. Of course, this advice only applies where a genuine allergy is absent.

Our gut contains trillions of microorganisms vital to immunity, digestion, and nutrient absorption. Factors like poor dietary quality, low diversity, and excessive antibiotic use can all disrupt the balance of this complex ecosystem and worsen symptoms after eating certain foods. 

Nutritional deficiencies when eliminating food groups

Besides the potential impact on the robustness and diversity of your gut microbiome, cutting out entire food groups without professional guidance can put you at risk of underconsuming crucial macronutrients and micronutrients.

“When removing any food groups from your diet, we have to be mindful that we are still able to meet our nutritional requirements for overall energy needs, macronutrients and micronutrients,” said Gelbke.

“This might mean finding alternative sources for these nutrients.”

Gelbke uses an additive or replacement approach when working with clients, highlighting the importance of making smart swaps when eliminating food groups to ensure your body and gut get everything they need to thrive.

Whether you’ve been cutting down on your carbohydrate intake, going gluten-free or dairy-free, or eliminating fructose or other FODMAPs, Gelbke said there are steps you can take to protect your energy, gut health, and overall wellbeing.

How going gluten-free can impact your gut

Those with coeliac disease or a genuine allergy or intolerance will naturally feel much better when they avoid gluten. However, many people now simply assume that a gluten-free diet is healthier, whether or not they personally tolerate it well.

In reality, gluten-free alternatives are not inherently healthier and, in some cases, may be lower in fibre, higher in sugar, and lacking fortification with essential nutrients like folic acid and iron.

Gelbke said the most important thing is to ensure you replace gluten-containing grains with alternatives like rice, quinoa, buckwheat, amaranth and teff to ensure you are consuming sufficient complex carbohydrates for optimal health and energy levels.

“It always takes a bit of time to adjust to a gluten-free diet and find good swaps for staple foods you previously enjoyed,” she said.

“Thankfully, there are so many great options these days that it usually isn’t too difficult. The most challenging aspect is often identifying gluten added to products you probably wouldn’t suspect, like certain sauces or snacks, and finding alternatives.”

Dietary diversity while avoiding dairy

An estimated 68 per cent of people worldwide experience malabsorption of lactose, the sugar found in dairy products. However, milk and its byproducts also contain essential nutrients.

“If someone is moving to a dairy-free diet, we need to ensure that we are replacing dairy or adding other foods that provide the calcium, protein, and energy that the dairy foods provide,” said Gelbke.

“Calcium is really important for our bone mineral density, muscle contractions, and cardiovascular function.”

To ensure you continue to meet your calcium requirements, Gelbke advises seeking alternatives, including calcium-fortified plant-based milk and yoghurts, tofu, leafy green vegetables, white beans, unhulled tahini, sesame seeds, and almonds. She said a good target for most people would be three servings of calcium-rich foods daily.

“Dairy also often provides the protein in certain meals and snacks, so finding an alternative to ensure we are still getting enough protein is important too, such as soy milk or yoghurt to replace a dairy one or a tofu-based filling for spinach and ricotta lasagne to replace the ricotta.”

Many popular dairy alternatives use coconut, cashews or oats, which, while delicious and nutritious, do not contain enough protein or calcium to substitute a dairy product.

Low fructose or low FODMAP diets and gut health

People who experience Irritable Bowel Syndrome (IBS) may avoid FODMAPs, an acronym for Fermentable, Oligosaccharides, Disaccharides, Monosaccharides, and Polyols, which includes fructose.

Gelbke explained that the low FODMAP diet can be a useful temporary tool to identify personal triggers and tolerances of certain foods so they can be reintroduced without exacerbating symptoms. Eliminating this large group of plants permanently could do more harm than good for your nutrition and gut health.

“Consuming enough fibre, protein and overall energy can be a challenge on the low FODMAP diet, as well as maintaining a varied and diverse diet, and not starting to experience stress and anxiety around food – whether that’s due to fear of food triggering symptoms or struggles around having to follow such a restrictive diet.”

Are keto or low-carb diets healthy for your gut?

Cutting out or drastically reducing carbohydrate intake has been a method for losing weight since the 1860s. It has popped up throughout the decades under names like Atkins or the present-day craze of the ketogenic diet, commonly known as ‘keto’.

While everyone’s body and response to certain diets is unique, switching to a high-fat, very low-carbohydrate diet needs to be done with careful planning and nutritional knowledge to avoid deficiencies or gut health issues.

“Low-carb diets often end up being low in fibre and plant diversity due to the removal of whole grains, fruits, legumes, and many vegetables,” said Gelbke.

“This can definitely have a big impact on the health and diversity of the gut microbiome.”

Dietary diversity, specifically of whole plant-based foods, is one of the most critical factors for maintaining a strong and resilient gut microbiome.

Most nutrition and gut health experts recommend consuming at least 30 different types of plants per week, including nuts, seeds, legumes, fruits, and vegetables.

Remember, if you’re avoiding any major food groups for an extended period, it’s always best to seek professional advice to ensure your gut receives all the diversity and nutrition it needs to function optimally and keep you feeling your best.