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What's the Best Diet for a Healthy Gut?

Updated: Feb 12

If you struggle with Irritable Bowel Syndrome (IBS) or other digestive problems, you might be wondering what is the best type of diet for a healthy gut?

There is a lot of conflicting advice regarding nutrition and diet so it’s not difficult to get confused as to which is the right diet for optimal health and for keeping your digestive system healthy.

Genetic Individuality – Personalised Nutrition

In truth, there is no one diet that is right for everyone. That is because we are all genetically individual with different health needs, and different health and dietary history. Our lifestyle and environmental factors also play a large role in our nutritional needs, both current and historical.

We now know that there is no one diet that is right for everyone, as what works for one person won’t necessarily work for the next. Personalised nutrition is a system that is being used to help people achieve lasting dietary behaviour changes that are beneficial for their long-term health (1).

Personalised dietary approaches that are tailored to the individual may be more acceptable and more effective in the long-term. Studies are showing that personalised nutrition interventions had greater, sustained changes in eating behaviour.

Precision nutrition, nutrigenomics, nutrigenetics, and nutritional genomics are other terms being used to describe personalised nutrition, and these concepts are used to help people with specific diseases, or with special dietary needs during life changes such as pregnancy or old age, or for athletes, and also for improved public health outcomes (2).

The Gut Microbiome

The gut microbiome harbours between 10 and 100 trillion microorganisms, and these microorganisms are responsible for vital nutritional, metabolic, and immune functions within the body.

Extensive recent research has highlighted the importance of the gut microbiome for positive health outcomes. A large body of clinical evidence is showing us that what goes on in the gut also has a huge impact on the brain, due to bi-directional gut-brain interactions. Simple lifestyle changes and improved stress management also affects the gut microbiome through modulation of the hypothalamic-pituitary-adrenal (HPA) axis (3).

The gut microbiome and intestinal tract within the body.

Dietary patterns have a huge impact on the health of an individual microbiota, and studies have shown that a typical “Western Diet” based on processed food which is typically low in fibre from fresh plant-based foods, but high in refined carbohydrates and unhealthy trans fats found in refined cooking oils, corresponds with the emergence of metabolic, cardiovascular, respiratory, and other disease processes (3).

Excessive antibiotic use, a lack of contact with natural biodiversity, and other lifestyle factors such as poor sleep and lack of exercise also have negative consequences on the health of the gut microbiome, which may lead to an imbalanced microbial population.

An overgrowth of pathogenic bacteria can result in increased lipopolysaccharides (LPS), which can promote inflammatory cytokines, leading to an imbalance (or dysbiosis) of gut bacteria, very often seen in Irritable Bowel Syndrome (IBS), Inflammatory Bowel Disease (IBD), and other systemic inflammatory conditions such as mood disturbances, weight gain, skin conditions, and joint problems.

Microbial diversity is key for healthy outcomes, and studies show us that we can support the gut microbiota by following a Mediterranean-type diet which includes a wide variety of plant-based fibre, with plenty of anti-inflammatory healthy fats as found in extra virgin olive oil, nuts and seeds, avocados, and oily fish (4).

The impact of different diets on the health of the gut.

Fermented Foods

Fermented foods have been used traditionally by almost every culture in the world as a culinary addition to the diet, and recent years have seen the adoption of fermented foods and drinks surge in popularity within many Western cultures. This has been as a result of increased interest in gut health and the proposed health benefits of fermented foods. The mechanisms by which they are thought to exert beneficial impacts on health include that they contain potentially probiotic microorganisms, such as lactic acid bacteria. Consuming a wide variety of these foods has the potential to exert a physiological benefit to the gut by competing with pathogenic bacteria, producing immune-regulating and nervous system fermentation by-products (5).

Some examples include kefir, sauerkraut, kimchi, natto, yoghurt, miso, tempeh, kombucha, and sourdough bread.

Importance of Prebiotics

Prebiotics are non-digestible fibres that get fermented in the gut, and which may exert a beneficial influence on gut health and mood. Food sources of prebiotics include onions, garlic, leeks, artichokes, asparagus, chicory, oats, green bananas, and apples, may support your gut flora. Many of these foods are high in FODMAPs, which can be poorly tolerated by many people with IBS or other digestive problems. As these specific prebiotics are so important for our gut health, it is recommended to only ever follow a low FODMAP diet for a maximum of 6 or 8 weeks, so as to avoid removing important food sources for our microbiota.

Supplementary sources of prebiotics include galacto-oligosachharides (GOS), fructo-oligosachharides (FOS), partially hydrolysed guar gum (PHGG), and polyphenol-rich ingredients such as citrus bioflavonoids, blackcurrant, grapeseed, cocoa, pomegranate and green tea. A slow introduction may be necessary to prime the gut microbes for tolerance.


Dietary polyphenols include catechins, flavonols, flavones, anthocyanins, proanthocyanidins and phenolic acids, and are commonly found in fruits (especially berries and citrus), seeds, vegetables, tea, cocoa products, and wine. Consumption of polyphenols has been shown to enrich bacterial microbes such as Bifidobacterium and Lactobacillus. Relative abundance of Bacteroides has also been reported to increase in subjects consuming red wine polyphenols (6).


FODMAP (Fermentable Oligo-, Di-, Mono-saccharides and Polyols) carbohydrates are specific carbohydrates and fibres found in certain grains, fruits, vegetables, legumes, milk products, and processed foods. They include lactose, fructose, fructans, polyols, and galactans. FODMAP foods can be poorly tolerated and not absorbed as they should be, in some people. Therefore, they pass through the small intestine and into the large intestine, where they feed the gut bacteria, causing fermentation and resulting gas, constipation or diarrhoea, or both.

Simply put, FODMAP’s are sugars commonly found in everyday foods.

Whilst a low FODMAP diet may be recommended as a short-term strategy for people with IBS, it is not recommended for long-term use. You should only ever follow the initial stage of the low FODMAP diet for a maximum of 6 weeks, so as not to risk damaging the health of the microbiota.

The Mediterranean Diet

The following image by Rininella et al (2019), shows the impact that different diets such as vegan, vegetarian, gluten-free, ketogenic, low FODMAP, a Western diet, and a Mediterranean diet, can have on the gut flora, the mucus layer, immune cells, and the intestinal lining (4). As shown, the low FODMAP diet resulted in a decrease in total bacterial abundance.

The most beneficial dietary pattern was a healthy Mediterranean diet, which resulted in an increase in microbial diversity and stability.

The dietary impact of various diets on the gut barrier and bacterial balance.

A typical inflammatory ‘Western Diet’ which is low in fibre and high in refined carbohydrates, sugar, trans fats, and processed foods, is associated with an imbalance of microbial gut bacteria, as well as obesity and metabolic diseases.

Whereas the traditional Mediterranean diet, is anti-inflammatory and centres around fruit, vegetables, olive oil, nuts, seeds, legumes, and whole grains. It is based on monounsaturated fatty acids, polyunsaturated fatty acids, polyphenols and other antioxidants, prebiotic fibres, low glycaemic carbohydrates, and with more of an emphasis on plant-based proteins than animal proteins (4).

Stomach full of healthy food and stomach full of processed foods.

Eat a Rainbow

As a summary, the more varied the diet is, the more diverse the gut microbiota is likely to be. Eating a rainbow of bright-coloured fresh foods that are high in fibre, on a daily basis, has been shown to beneficially manipulate the microbial diversity in the gut (3). Rather than aiming for 5-a-day, research is showing us that individuals who ate more than 30 different types of plant-based foods in a week had a more diverse mix of gut microbes than someone who only ate ten.

For microbiome health we are more interested in counting colours than counting calories. The following diagram shows how eating the rainbow not only supports gut bacterial diversity but also offers the body a large array of phytonutrients (‘phyto’ = ‘plants’) with a wide mix of vitamins and minerals, necessary for overall good health and mental wellbeing.

In my clinical work, it is sometimes necessary to implement a restrictive short-term therapeutic diet. Ultimately though, the aim is to make the diet as inclusive as possible, as it is the diversity of foods that is so important for a healthy gut microbiome. Nourishing the intestinal lining and supporting the gut ecosystem back into a more balanced place is necessary before the reintroduction of foods that may have once been problematic to the individual.

A rainbow of colourful plant foods

Helen Ross is a Registered Nutritionist ® specialising in gut health and IBS support.

My Simple Gut ReSet is designed to help us get to the root cause or causes of your health issues. The aim is to nourish and support the gut lining to assist it back to a healthy state. A robust intestinal lining is an essential first step for finding freedom from painful, frustrating and embarrassing symptoms of IBS and other gut-related symptoms and health problems.

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For more information see:


1. Ordovas, J. M. et al. (2018) ‘Personalised nutrition and health’, BMJ (Online). doi: 10.1136/bmj.k2173.

2. Mathers, J. C. (2019) ‘Paving the way to better population health through personalised nutrition’, EFSA Journal. doi: 10.2903/j.efsa.2019.e170713.

3. Toribio-Mateas, M. (2018) ‘Harnessing the Power of Microbiome Assessment Tools as Part of Neuroprotective Nutrition and Lifestyle Medicine Interventions’, Microorganisms. doi: 10.3390/microorganisms6020035.

4. Rinninella, E. et al. (2019) ‘Food components and dietary habits: Keys for a healthy gut microbiota composition’, Nutrients. doi: 10.3390/nu11102393.

5. Dimidi, E. et al. (2019) ‘Fermented foods: Definitions and characteristics, impact on the gut microbiota and effects on gastrointestinal health and disease’, Nutrients. doi: 10.3390/nu11081806.

6. Singh, R. K. et al. (2017) ‘Influence of diet on the gut microbiome and implications for human health’, Journal of Translational Medicine. doi: 10.1186/s12967-017-1175-y.

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