What is ‘gut health’?

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


Housed within the gut are the microbiota: a ‘community’ or ecosystem of microbes (microscopic organisms). These microbes, of which there are about 500 known species, are largely made up of bacteria, yeast, fungi and viruses. Each of us houses around 100 trillion microbes within our body, mostly within the digestive tract, although communities can be found in different parts of the body including the nose, skin and mouth.

Emerging research suggests the microbiota, along-with its collection of genomes, together referred to as the microbiome, may well influence our health as much as our inherited genes do.

Discover more digestive health recipes and tips on everything from probiotics and health benefits of fermenting to how a low-FODMAP diet can help ease IBS symptoms. Also check out our health and nutrition page for more recipe inspiration, health benefits guides and advice on special diets.

Woman eating healthy food at home

How does the gut microbiome affect my health?

One of the major roles of our gut microbes, besides that of breaking down our food, is the regulation of our immune system. Recent research has linked the health of our gut to conditions as diverse as acne, allergies and even depression.

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There is still lot for us to learn, but already scientists have found links between our gut bacteria and neurodegenerative diseases like Parkinson’s, as well as the long-term condition chronic fatigue syndrome. There is also growing evidence around the role our microbiota plays in obesity and weight management, as well as autoimmune conditions including type 1 diabetes and rheumatoid arthritis.

Why is the gut called the ‘second brain’?

Your digestive system is also known as the ‘second brain’ thanks to the millions of nerve cells or neurons that line the gut and release important messengers known as neurotransmitters. These allow the gut to keep in close contact with the brain and central nervous system, in this way it may influence our moods and emotions.

Our gut bacteria play a key role in the production of some of these neurotransmitters, including serotonin, 90% of which is manufactured in the gut. Although often referred to as our ‘happy hormone,’ the serotonin made in the gut can’t cross the blood brain barrier so is not likely to influence mood but it is involved in regulating our digestion and modulating immune function.

What can affect my beneficial gut bacteria?

Just like fingerprints, every one of us has a different mix of microbiota, and this can be influenced by a wide variety of factors, including the mode of delivery at birth, the method of infant feeding, the use of medications (especially antibiotics) and our diet. The most common culprits to affect gut bacteria include antibiotics as well as a diet low in fibre, fruit and vegetables.

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

Stress may also change the number and diversity of our gut bacteria, which in turn may dysregulate the immune system, and might explain why certain conditions, such as eczema or acne, typically flare up when we are under more increased pressure.

Raspberry kefir overnight oats

What can I do to improve the diversity of my gut microbiota?

The good news is, there are plenty of things you can do to look after your digestive system and support a healthy, diverse microbiota. Start by looking at your diet and increase the amount and variety of fibre, fruit and vegetables that you eat, as these are really good sources of prebiotics, compounds that are important for ‘feeding’ our beneficial gut bacteria. Recent research suggests that eating 30 or more different types of plant foods each week increases bacterial diversity in the gut – this isn’t as challenging as it might sound, because as well as fruit and vegetables, herbs, spices, wholegrains, nuts and seeds also count.

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 sauerkraut, kimchi and kefir, are increasing in popularity thanks to their gut-friendly benefits.

What if I am prescribed antibiotics?

If your GP has prescribed a course of antibiotics, it’s 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.

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Microbes & me – our series, in collaboration with BBC Future, looks at all the factors that affect our unique microbiomes – from dietary choices to lifestyle factors.
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Visit our Microbes & Me series hub page

Do you eat a gut-friendly diet? What are your favourite foods to support gut health? Share in the comments below…

Emer Delaney BSc (Hons), RD has an honours degree in Human Nutrition and Dietetics from the University of Ulster. She has worked as a dietitian in some of London's top teaching hospitals and is currently based in Chelsea.

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 urbanwellness.co.uk.


All health content on bbcgoodfood.com 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. If you have any concerns about your general health, you should contact your local healthcare provider. See our website terms and conditions for more information.

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