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What is the microbiome?

Older male in yellow jumper on a fairground swing Happy expression.
Have you heard of the gut microbiome but are unsure what it is? Learn about the bacteria in your microbiome, what it does and how you can support it, here.
Interest in the gut microbiome has increased recently, with more people understanding how good gut health can affect the body. But what is the gut microbiome?

Around 70-80% of our immune system can be found in our gut, where our gastrointestinal tract plays host to more than 10,000 species of bacteria which can be the key to a person’s immunity and health status. But how do these good bacteria help improve our gut health? And what can we do to improve it?

In this article, we’ll talk about what the gut microbiome is, how it works, and how the good bacteria affect the body. We’ll also touch on what you can do to positively affect your gut microbiome, as well as positive foods to eat to keep your gut healthy and happy.

What is the gut microbiome?

The microbiome is essentially the name for the collection of bacteria and microorganisms that live inside our bodies, their genes, and the environment they live in. There are many types of microbiomes, for example, gut microbiome, skin microbiome, and vaginal microbiome.

Our gut microbiome is originally determined by DNA and is then influenced by how we are born.2  For example, a baby who is delivered vaginally will have a microbiota that resembles the microbiota in their mother’s vagina, whereas an infant delivered by Caesarean section will have a microbiome similar to that of their mother’s skin.2

As time goes on, our gut microbiomes continue to grow and change, influenced largely by our diet and our environment.3 For example, when infants transition from breast milk to solid foods, each small change affects the gut microbiota.3

Why is the gut microbiome important?

The gut microbiome plays crucial roles in our essential day-to-day bodily operations but also has the potential to cause harm. It’s all about balance, and these ‘bugs’ tend to coexist harmoniously in healthy people.

Problems tend to start when this balance starts to tip in the favour of the harmful bacteria and our ‘good’ bacteria declines.2 But there are ways to re-strengthen these populations, which we will get onto later.

Why bacteria are so important for our health

In the fight against illness, bacteria might seem like a dirty word. However, the presence of trillions of microbes and bacteria in our bodies along with their genes and environment - known as our microbiome - is not only completely normal but also very important to our health.

This population of friendly microbes live mainly in the gut and plays a major role in the functioning of our immune system, which helps keep the whole body well.3

An imbalance in our gut microbiome leads to digestive issues such as bloating, diarrhoea, and indigestion and can exacerbate conditions such as irritable bowel syndrome (IBS).4

Where is the microbiome?

The bacteria, fungi, parasites, and viruses that make up our microbiome tend to congregate in the large and small intestine, but they can be found all throughout our bodies.

From the populous gut microbiome that helps keep our bodies functioning normally from the inside out to exterior skin microbiome ‘communities’ that can help strengthen our skin barrier and keep pathogenic or harmful organisms out, all microbiomes are important for our health.

Good and bad bacteria

Out of the trillions of bacteria that live in our bodies, so-called ‘friendly’ or ‘good’ bacteria are beneficial microbes that help the body perform vital functions.3 The ‘bad’ bacteria are the rarer type which can cause infections if the body is not able to fight them off.3

The levels of friendly bacteria in the body must be abundant for the immune and digestive systems to work effectively, so it is important that we make lifestyle choices which support our microbiome.

The latest research indicates that keeping this balance of ‘good’ and ‘bad’ bacteria is a vital part of overall health, and a healthy microbiome has been linked in emerging studies to better digestive health and fewer food allergies.5

Our gut microbiome changes with factors such as pregnancy, age, environment, stress, diet, and medications, each making an impact.3

There has been a lot of early stage research into the gut microbiome’s role in metabolism, immune defence, mood, and behaviour, and the huge role your gut plays in overall health is only just beginning to be fully understood.4

Too much of a good thing?

Many of us use products such as hand sanitisers in an effort to stay healthy and germ-free. However, these products do not discriminate and destroy our ‘good’ bacteria along with the ‘bad’, which can end up compromising our immunity defences.6

Being deprived of exposure to common bugs leads to a weakened immune system, which can then go into ‘defence mode’, triggering an inflammatory response when faced with even the most harmless of microbes.7

Excessively disinfected environments caused by hand sanitisers and the overuse of antibacterial household sprays have been linked to the increase of conditions such as asthma and inflammatory bowel disease over recent years.6

Of course, it is sensible to practise good hygiene, such as washing your hands before meals and after a visit to the bathroom to protect ourselves from potentially dangerous germs. However, excessive use of antibacterial products can be detrimental to your body’s immune response.6

7 benefits of a healthy microbiome

Here are some of the most important benefits that a healthy microbiome can help provide:

1. Immune system support

A healthy microbiome can help to stimulate the immune system and keep us defended against harmful pathogens and other harmful organisms. For example, a healthy balance of gut bacteria can help protect us from pathogenic organisms in contaminated food and water.

Certain microbes like Peptostreptococcus, Lactobacillus, Bifidobacterium and Clostridium can be found in the colon and are believed to help prevent the overgrowth of harmful bacteria. They do this by competing for nutrients and attachment sites in the gut, which is highly influential to our immunity.9

There is also growing evidence that gut health may help with the inflammatory response, which is triggered when you are unwell.10  We’ve got a full article on the link between inflammation and gut health here.

2. Can support with vitamin and amino acid synthesis

Some vitamins and amino acids can only be synthesised with enzymes found in microorganisms, like B vitamins and vitamin K.11

3. Can help with digestion

Simple sugars like the sugar in milk (lactose) and cane sugar are absorbed by the upper part of the small intestine quickly and easily.

On the other hand, complex carbohydrates like wholemeal products and starchy vegetables are harder to digest (in a good way!) and may travel to the large intestine before they are absorbed. When they get there, your gut bacteria will help to break down these complex carbohydrates with digestive enzymes.

The gut microbiota can also help ferment indigestible fibre to help the body produce short-chain fatty acids, which get used as a nutrient source by the body and play an important role in muscle function, amongst other benefits.4

Need a bit more information on how digestion works? We’ve got a full guide to digestion here.

4. May help control blood sugar

Research has shown that there is a link between the gut microbiome and diabetes, although the exact mechanics of how this works are still largely not understood.12  One 2015 study on 33 infants genetically predisposed to Type 1 diabetes found that the onset of Type 1 diabetes correlated with a drop in microbiome diversity.10 

Some unhealthy bacterial species also increased before the infants developed this condition.

5. May support brain function

Our gut is physically connected to the brain via nerves and also helps to make brain chemicals called neurotransmitters, like serotonin, that can help to regulate sleep and mood.14,15

Ever-accumulating data and research has revealed the connection between gut microbiota and the central nervous system, but exactly how this works and to what scale requires further clinical research.16

Want to know more about how this works? We’ve got a full guide on how gut health affects your mood here.

6. May support heart health

Some gut bacteria have been found to help manage cholesterol levels, which is essential for heart health.17

One study conducted in 2015 found that the gut microbiome may play an important role in maintaining healthy blood cholesterol levels by promoting ‘good’ HDL cholesterol and triglycerides independent of age, sex, and genetics.18

7. May influence gut health

There is research to suggest that a variety of diseases related to the gut, like inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) may be affected positively by a healthily balanced gut microbiome.19,20

7 ways to support a healthy gut microbiome

There are many ways to improve your gut health and one of the best ways is through the foods you eat. Here are our top seven tips for supporting and improving the good bacteria in your gut.
  1. Eat a varied diet – There is no one magic food that will cure all your ailments. The same is true of your gut. One 2016 study found that the best thing for a healthy gut was a varied and diverse diet.21
  2. Introduce fermented foods to your diet – Fermented foods have been proven to be very important for good gut health, often introducing copious amounts of good bacteria into your gut. Read more about the best fermented foods here. They might not be for everyone though, so start off with a little bit and see how your body reacts to it. 
  3. Eat more whole grains – There are plenty of good reasons to eat whole grains. For example, they are high in dietary fibre which greatly benefits gut microbiota, improving the gut microbiome.23
  4. Try gut-healthy supplements – Overhauling your diet can be overwhelming. Instead, try smaller steps – such as introducing gut health supplements into your diet. 
  5. Have more probiotic foods – Probiotic foods, such as yoghurts and cheeses, are great ways to introduce good bacteria into your gut microbiome.24  There are loads of other health benefits of probiotic foods too. 
  6. Go prebiotic, too – Prebiotic foods are sources of dietary fibre that the bacteria and other microbes in our gut like to feed on. Studies show that prebiotics support antioxidant and anti-inflammatory bacteria in the gut.
  7. Consider a plant-based diet – If you’re looking to affect your gut microbiome, there have been studies that have shown that plant-based meals are more effective than meat-based diets.26  If you’re considering switching, we’ve got a full guide to plant-based proteins here that might help.

The final say

Your microbiome plays a very important role in your overall health, from promoting healthy gut activity to supporting your immune system and helping you to get the most from your food.

If you want to support your gut microbiome and keep it happy and healthy, try to eat a varied diet, including lots of fibre-rich wholegrain foods, fermented foods, and plenty of fresh fruit and vegetables. There are plenty of great foods for gut health, so why not integrate them into your diet? Interested in finding out more about improving your gut health? Check out our ultimate guide for a happy and healthy gut.


The advice in this article is for information only and should not replace medical care. Please check with your GP or healthcare professional before trying any supplements, treatments or remedies. Food supplements must not be used as a substitute for a varied and balanced diet and a healthy lifestyle. 


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2. Stewart CJ, Embleton ND, Clements E, Luna PN, Smith DP, Fofanova TY, Nelson A, Taylor G, Orr CH, Petrosino JF, Berrington JE. Cesarean or vaginal birth does not impact the longitudinal development of the gut microbiome in a cohort of exclusively preterm infants. Frontiers in microbiology. 2017. Available at:
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12. Barlow GM, Yu A, Mathur R. Role of the gut microbiome in obesity and diabetes mellitus. Nutrition in clinical practice. 2015. Available at:
13. Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešič M, Huttenhower C, Knip M; DIABIMMUNE Study Group; Xavier RJ. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015. Available at:
14. O'Mahony SM, Clarke G, Borre YE, Dinan TG, Cryan JF. Serotonin, tryptophan metabolism and the brain-gut-microbiome axis. Behav Brain Res. 2015. Available at:
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19. Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D'Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol. 2017. Available at:
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