How does diet affect gut health?


Learn how healthy gut bacteria affect overall wellbeing, the best foods for digestive health and how antibiotics, sugar and stress can affect the microbiome.

Open glass jar of sauerkraut with a spoon resting on top

Our digestive system, or ‘gut’ as it is more commonly known, is a complex system comprising of tissues and organs all with a unique role to play in the digestion and absorption of our food. These include the stomach, pancreas, gall bladder, liver, and the small and large intestines.

Housed within the gut is also something known as the microbiome: a ‘community’ or ecosystem of microbes (microscopic organisms). These microbes, of which there are about 500 known species, are largely made up of bacteria. Each person carries around 10-100 trillion microbes within their body, mostly within the digestive tract, although the microbiome can be found in different parts of the body including the nose and mouth. There is emerging research to suggest that it may well influence your health as much as your inherited genes do.

How does the microbiome affect health?

One of the major roles of our gut bacteria, besides digesting our food, is the regulation of our immune system. Recent research has linked the health of our gut to conditions such as acneallergies and even depression.

There is still lots of research to be done but already scientists have found links between our microbiome (gut bacteria) and neurodegenerative diseases such as Parkinson’s, as well as the long-term condition chronic fatigue syndrome. There is also growing evidence around the role of our microbiome in obesity and weight management, as well as autoimmune conditions such as Type 1 diabetes and rheumatoid arthritis.

Woman standing on weighing scales in bathroom

Why is the gut considered to be the ‘second brain’?

Your digestive system is also known as the ‘second brain’ thanks to the millions of neurons that line the gut and release important chemical messengers known as neurochemicals or neurotransmitters. These allow the gut to keep in close contact with the brain and influence our moods and emotions.

Our gut bacteria play a key role in the production of certain neurotransmitters, such as serotonin, which is manufactured in the gut and known as our ‘happy hormone’.

What can affect gut bacteria?

Just like fingerprints, every one of us has a different microbiome and this can be influenced by a wide variety of foods, toxins and substances. The most common culprits that can affect gut bacteria include antibiotics, a poor diet (especially one high in sugar), stress, toxins and chemical exposure.

Antibiotics are used to treat or prevent some types of bacterial infection by killing bacteria in the body. While they are an important medicine, they cannot distinguish between good and bad bacteria so they wipe out both.

Sugar is inflammatory and may affect the lining of our digestive system where a lot of our microbiome live, reducing them in numbers and therefore affecting their performance.

Stress can change the number and diversity of our gut bacteria, which in turn dysregulates the immune system and may explain why certain conditions, such as eczema or acne, flare up when we are more stressed.

In our modern society, we are exposed to various toxins and chemicals through the foods we eat (from pesticides used in farming through to artificial sweeteners), cosmetics and even from pollution in the air. We cannot completely limit our exposure to all of these, but we can support good gut health through everyday diet and lifestyle.

Pot of berry bircher with probiotic ingredients such as oats and yogurt

How can I improve my gut microbiome?

The good news is that there are plenty of things you can do to look after your digestive system and support a healthy microbiome. Start by looking at your diet and reducing or cutting out refined sugars, artificial sweeteners and processed foods as this will reduce inflammation and therefore reduce damage to your gut bacteria.

Then, start to add more fruit and vegetables as these are really good sources of soluble fibre which are very important for ‘feeding’ the good bacteria. Other high fibre foods include beans and pulses such as chickpeas and lentils, wholegrain breads, brown or wholegrain rice, nuts and seeds, oats and jacket potatoes. Fermented foods, such as sauerkrautkimchi and kefir, are increasing in popularity too thanks to their gut-friendly benefits.

If your GP has prescribed a course of antibiotics it is important to follow them as directed, however, as per NHS advice, you should only take antibiotics when necessary. If you are concerned that antibiotics may have a negative effect on your gut bacteria, ask your GP about following them with a course of probiotics, which may help to reset the balance of bacteria.

Activities such as mindfulness or meditation can help you to relax and reduce your stress levels so that they don’t have such an impact on your digestive system.

More information on gut health…

What are probiotics and what do they do?
What to eat for better digestion
Digestive health recipes and tips

This article was reviewed on 11th December 2017 by registered nutritionist Kerry Torrens.

Nicola Shubrook is a nutritional therapist and works with both private clients and the corporate sector. She is an accredited member of the British Association for Applied Nutrition and Nutritional Therapy(BANT) and the Complementary & Natural Healthcare Council (CNHC). Find out more at

A registered nutritionist, Kerry Torrens is a contributing author to a number of nutritional and cookery publications including BBC Good Food magazine. Kerry is a member of the The Royal Society of Medicine, Complementary and Natural Healthcare Council (CNHC), British Association for Applied Nutrition and Nutritional Therapy (BANT).

All health content on is provided for general information only, and should not be treated as a substitute for the medical advice of your own doctor or any other healthcare professional.


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