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 mouth, oesophagus, 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 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.

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.

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 acne, allergies 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 factors, including the mode of delivery at birth, the method of infant feeding, the use of medications (especially antibiotics) and the diet. The most common culprits that can affect gut bacteria include antibiotics and a diet low in fibre, fruit and vegetables. 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.

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.

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 increase the amount of fibre, fruit and vegetables that you eat, 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 sauerkraut, kimchi and kefir, are increasing in popularity too thanks to their gut-friendly benefits.

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.

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.

Microbes & me

Our new series, in collaboration with BBC Future, looks at all the factors that affect our unique microbiomes – from dietary choices to lifestyle factors.

We’ve worked with dietitian Emer Delaney to bring you expert information and specially selected recipes that will help you to understand how to eat for better digestive health.

Find out more...

BBC Future: What we do and don't know about gut health
What are probiotics and what do they do?
Gut-friendly vegan recipes
Visit our Microbes & Me series hub page

This article was reviewed on 2nd January 2019 by dietitian Emer Delaney.

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.


Do you have any questions or thoughts about how diet affects gut health? We'd love to hear from you in the comments below.

Comments, questions and tips

Choose the type of message you'd like to post

Choose the type of message you'd like to post