The microbiome is the name given to all the trillions of bacteria, fungi and viruses that live inside our guts. Having a healthy gut microbiome is essential for our health.

It used to be thought that the number of bacteria living in the human body (the majority of which are in the gut) outnumbered human cells by around 10:1. But it’s now known that for every human cell, there’s roughly 1.3 bacterial cells. However, the number of gut bacteria varies from person to person as it depends on our environment, lifestyle, health and diet.

The number of bacteria in our gut fluctuates all the time. What we eat, where we live, who we mix with and the medicinal drugs we take all influence how many bacteria are living inside the gut. Passing a stool can reduce their number by a few billion alone! (They’re very good at quickly replenishing themselves though, if we look after our gut.)

Although we have trillions of microorganisms living inside us, they’re so tiny that collectively they only weigh around 0.2kg. However, they play a crucial role in our health, so it’s important to keep our gut bacteria happy.

What are gut bacteria?

The trillions of bacteria and other microorganisms that live in our gut are very diverse and diversity is a very good thing! Each one of us has around 1,000 different species of bacteria, viruses and fungi living comfortably along the length of our digestive system.

The more beneficial, or good, bacteria we have, the less chance that disease-causing pathogenic bacteria can take hold and cause us to become ill.

The bacteria in our gut influence how well we digest our food, what we weigh, and some research suggests that it can also influence our mood and behaviour patterns. They also contribute to our immune system and can be associated with some health conditions.

So, it’s important that we do all we can to look after the health of our microbiome.

How does the microbiome affect the body?

Our microbiome has a huge effect on our health right from the moment we’re born. It can have both positive and negative effects.

Whilst we’re in the womb, we don’t have any bacteria in our gut. Then, as we pass through our mother’s birth canal during birth, we begin picking up bacteria. This begins our process of building up our microbiome.

Some scientists liken this to taking our first gulp of air - we ingest our first batch of bacteria, viruses and fungi from our mother as we’re born. During our mother’s pregnancy, her microbiome changes to create optimal conditions for this to happen.

If we’re born by caesarean section, we don’t get this initial surge of microbes from the birth canal. However, if we are breast-fed, then gradually we begin to grow bacteria similar to those in babies after natural birth.

Our microbiome as a baby

Once we’re born, we start picking up microorganisms from our environment, pets, parents, siblings and other family members and visitors.

If we’re fed our mother’s breast milk, our microbiome helps us to break down the sugars that are naturally present in this milk. We cannot break these sugars down ourselves and we rely on gut bacteria called bifidobacteria to do it for us.

Then during our first 2 years, our microbiome changes rapidly and becomes much more diverse. This is down to factors such as the bacteria naturally present in our mother’s breast milk, any childhood diseases we develop and the environment we live in. It will then continue to change throughout our entire life.

Our microbiome, fibre and health

Including fibre in our diet is important for our gut health. Fibre helps to keep the bowels moving and prevent constipation. There are two types of dietary fibre, soluble and insoluble – so eating fibre doesn’t have to mean forcing ourselves to eat bran flakes! We can eat fruits, vegetables and whole grains instead.

Soluble fibre helps the large intestine absorb water, making stools softer, less dry and easier to pass. Insoluble fibre bulks up the stools, allowing them to move through the gut quicker. Many foods have both soluble and insoluble fibre, but soluble fibre can be found in oats, barley, psyllium, oranges, dried beans and lentils. Insoluble fibre can be found in beans, nuts, cauliflower, green beans, potatoes and wholegrains.

A high intake of fibre can be associated with many other health benefits, too. It also keeps us fuller for longer and helps control our weight.

Our gut microbiome helps us to digest fibre, without it we wouldn’t be able to get the health benefits of eating fibre.

Our microbiome and immunity

The bacteria in our gut are responsible for the health of our immune system too. They communicate with the cells of the immune system allowing it to recognise the difference between the cells of the body and invading pathogenic microbes. It will then attack invading microbes and leave the cells of the body alone.

If the microbiome isn’t healthy, and the beneficial bacteria aren’t thriving, this line of communication can break down. This process is known as ‘dysbiosis’.

Our microbiome and brain health

This dysbiosis can be associated with changes in your mood and disorders of the brain, including conditions such as depression, Alzheimer’s and Parkinson’s disease. However, more research is needed to find a direct link between dysbiosis and disease.

It’s thought that the microbiome can communicate with the brain and impact brain function, which has led to the gut being called the ‘second brain’.

How to maintain healthy gut bacteria

Given the links between the health of the microbiome and our health, it’s crucial that we look after our gut bacteria and keep it as thriving and as diverse as possible. The more different species of good bacteria we have in our gut, and the more they flourish, the better for our health.

There are diet and lifestyle choices we can make to help maintain healthy gut bacteria.


We can eat a diet rich in ‘prebiotic’ fibre, which encourages good bacteria in the gut to grow, leaving less space for bad bacteria to thrive. Prebiotics are foods that feed the beneficial bacteria in our gut. These foods include onions, garlic, artichokes, asparagus, apples, bananas and oats.

There are also prebiotic supplements available. These supplements can contain an ingredient called galactooligosaccharides (GOS) that helps to feed the good bacteria in your gut. Taking them for as little as 7 days can help increase the number and diversity of beneficial gut bacteria.

Staying well hydrated by drinking plenty of fluids will also help keep the gut healthy.


Exercising regularly helps us to stay fit and maintain our weight, but it also helps to stimulate the muscles of the intestines. This means that food moves along the digestive tract at a healthier rate.

Aim for the NHS guidelines of 150 minutes of moderate intensity aerobic activity and 2 sessions of strength exercises such as weight lifting or body weight exercises (e.g. squats and lunges) per week.


It’s also recommended that we don’t take antibiotics unless absolutely necessary. Antibiotics are often prescribed for bacterial infections. Whilst they generally do a good job of killing the invading bacteria causing the infection, they also kill the good bacteria that make up the gut microbiome.

If you do have to take antibiotics, ensure you pay extra attention to these healthy gut tips afterwards to help build your microbiome back up again.

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