Guide to microbiome

It is a bit mind-blowing to think about, but we all have trillions of microorganisms from thousands of different species living inside our bodies and their collective term is microbiome.1

Each person has a totally unique microbiome (aka, microbiota) consisting of not only bacteria, but parasites, viruses and fungi, too.

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

As time goes on, our microbiomes continue to grow and change, influenced largely by our diet and our environment. For example, when infants transition from breast milk to solid foods, each small change affects the gut microbiota.2

The microbiome both plays crucial roles in our essential day-to-day bodily operations but also has the potential to cause harm. It’s all about balance, you see, 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. But there are ways to re-strengthen these populations, which we will get onto later.

Where is the microbiome?

It’s here, there, and everywhere!

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.

What is a healthy microbiome?

A healthy microbiome is one that benefits the body and helps it function as normal.

What are the benefits of a healthy microbiome? 7 of the best

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 microorganisms in the gut 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 help prevent the overgrowth of harmful bacteria.3 They do this by competing for nutrients and attachment sites in the gut, which is highly influential to our immunity.4

2. 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.5

3. 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 lower to the large intestine before they are absorbed.

When they get there, a healthy microbiome will help to break down these complex carbohydrates with digestive enzymes.

The gut microbiota can also help ferment indigestible fibres 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.6

4. May help control blood sugar

Gut microbiome could help our bodies control blood sugar, which could reduce the risk of diabetes.

One 2015 study on 33 infants genetically predisposed to type one diabetes found that the onset of type one diabetes correlated with a drop in microbiome diversity. Some unhealthy bacterial species also increased before the infants developed this condition.7

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 serotonin8, that can help to regulate sleep and mood.9 Ever-accumulating data and research has revealed the connection between gut microbiota and the central nervous system, which is already known to influence brain behaviour and function.10

6. May support heart health

Some microorganisms in the microbiome have been found to help manage cholesterol levels, which is essential for heart health.

One study conducted in 2015 found that 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.11

7. May influence gut health

There is research to suggest that a variety of diseases related to the gut, like inflammatory bowel disease (IBD)12 and irritable bowel syndrome (IBS) 13 may be affected possitively by a healthily balanced microbiome.

What is microbiome testing?

A microbiome test is sometimes recommended to find out just what is going on with all those microorganisms inside your gut.

These tests almost always require a poo sample, which is usually collected in a container and sent to a lab to be analysed.

Sometimes people get them to specifically look for infectious bacteria, much like you would if you had a urine infection. Whereas other tests aim to analyse the composition of gut microbiome, and then offer you a ‘solution’ (usually probiotic or prebiotic products) to help improve it.14

How do I improve my microbiome?

There are many ways you can support your body’s microbiome, here are 5 of the best ways we have found.

How to support a healthy microbiome: 5 ways

There are many ways to support your gut microbiome, here are 5 of the best.

1. Your diet

As a lot of your microbiota live in your gut, it makes sense that everything that we eat and drink has a significant effect on our microbiome.

What foods are good for the microbiome?

A bit of everything

Variety is the spice of life; If the food we eat is diverse, it can also help our microbiome become diverse. Researchers believe that a varied microbiome-friendly diet can help to create an gut environment that’s better equipped to deal with harmful bacteria.15

Try and pack in as many different healthy foods as possible into your daily diet to not only support your microbiome, but to also support your overall health.

Prebiotic foods

Prebiotic foods are sources of dietary fibre that the bacteria and other microbes in our gut like to feed on. Think of them as the compost and fertilisers you would add to your garden to help your plants grow strong and healthy – except we’re talking friendly bacteria here, not roses!

Not all fibre-rich foods can be classes as prebiotics, but most prebiotics can be classified as dietary fibres.16 Here are some examples:
  • Garlic
  • Artichokes
  • Legumes, e.g. beans, lentils, chickpeas
  • Leeks
  • Onions
  • Asparagus
  • Wholegrain products
  • Oats
  • Barley
  • Bananas
  • Apples
  • Cocoa
  • Flaxseeds
  • Wheat bran
  • Seaweed


Ah, wholegrains – all the fun and taste of refined carbs but with tons of extra benefits, especially when it comes to our microbiome.

Wholegrains fall into the prebiotic category. They are full of heart- and gut-healthy fibre that supports digestion, as well as essential vitamins and minerals like B vitamins and zinc.

Research also suggests that wholegrains can have positive effects of our microbiome. A systematic review of 40 studies on the effects of wholegrains on the gut microbiome suggests that eating them can increase both microbiota diversity and abundance – 2 key indicators of a healthy and balanced microbiome.17

Popular wholegrain foods include:

It’s quite easy to swap refined carbs like white bread, pasta and rice for some of the grains above, and your gut will be sure to thank you later!

Go plant-based

Vegan and vegetarian diets are full of fibre (which our microbiota love) and also appear to promote more stable and diverse microbiomes when compared to a typical omnivorous diet.18 First of all, fibres only come from plant-based food and most consistently increase lactic acid bacteria in whoever eats them.19 Multiple studies have found that microbial diversity correlates positively with protein consumption20. However, a diet high in animal protein, has been seen to have lower bacteria abundance21 than a diet high in plant-derived proteins like pea protein.22 This may have something to do with the fact that high-protein diets based around animal-derived protein e.g. beef, will have significantly less carbohydrates and fibre compared to a high-protein plant-based diet which tends to be more carbohydrate- and fibre-rich.23

Fermented foods

Yoghurt, kimchi, kefir, kombucha and sauerkraut are some of the most popular fermented foods and drinks that could help support your microbiome. They all contain healthy bacteria, which is made during the fermentation process, that can help introduce and strengthen different bacteria in the gut, as well as help reduce more harmful species.24 Just make sure to choose unpasteurised versions as pasteurisation kills the natural bacteria.

Foods containing polyphenols

Polyphenols are micronutrients in some plant-based foods and drinks. They are packed full of antioxidants and can help to increase the abundance of friendly bacteria like Lactobacillus and Bifidobacterium. These bacteria have been seen to have anti-inflammatory effects (like antioxidants) and support heart health.25

You can find polyphenols in some plant-based foods like:

  • Vegetables
  • Fruits
  • Seeds
  • Tea
  • Cocoa products
  • Wine
One found that even drinking cocoa-based drinks could positively affect the growth of some bacteria in humans. The results revealed that the group drinking a high-cocoa flavanol drink for 4 weeks has a significantly higher abundance of Bifidobacterium and Lactobacillus in their faeces, compared to the group drinking a low-cocoa flavanol drink.26

2. Breast feeding

If you have a baby, one of the best things you can do for their developing microbiome is breastfeeding them for at least 6 months. This will be one of the first and most important substances they digest and will help set up their microbiome for the rest of their lives.

One study found that children who has been breastfed for a minimum of 6 months had higher levels of the beneficial bacteria Bifidobacteria than infants who were bottle-fed a milk formula.27

3. Probiotic supplements

Probiotic supplements contain cultures of live bacteria intended to replenish levels in the gut that may have dwindled due to illnesses or treatments like antibiotics.

The NHS advises that there is some evidence that probiotics could help to help ease the symptoms of irritable bowel syndrome (IBS) and prevent diarrhoea when taking antibiotics.28 They can be an easy way to ‘top up’ on friendly bacteria like strains of Lactobacillus and Bifidobacterium.

4. Only taking antibiotics when medically necessary

There has been a shift away from the routine use of antibiotics to treat infections for a number of reasons, including antibiotic resistance.

This is when strains of bacteria develop resistance to many different types of antibiotics and gain ‘superbug’ status, which make them increasingly hard to treat and ultimately dangerous.29

Your microbiome may also be affected by overuse of antibiotics when they are not needed, as they do not differentiate between ‘friendly’ and ‘unfriendly’ bacteria in the gut and kill everything.

Always follow the advice of your GP when receiving treatment for illnesses and infections.

5. Keep your vitamins topped up

Vitamins and other macronutrients are essential for the healthy function of our bodies, including our gut – and they could influence our microbiome, too.

When we eat vitamin-rich food, bacteria in the gut synthesise those vitamins to feed themselves and any they don’t use, they excrete and return to us. In fact, some gut bacteria secrete vitamin B12 and vitamin K to help us reach our daily goals.30

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.

Your diet is one of the most integral aspects to get right if you want to keep all of those bacteria, fungi and other microorganisms healthy and flourishing.

Try to eat a varied diet of food, including lots of fibre-rich wholegrain foods, fermented foods, and plenty of fresh fruit and vegetables.

Consider taking a probiotic supplement to help replenish your microbiome if you have been taking courses of antibiotics recently.

Shop Acidophilus & Friendly Bacteria

Last updated: 18th January 2021

Related Topics

Digestive Health
Donia Hilal

Donia Hilal,

Joined Holland & Barrett: Jan 2018

Bsc in Nutrition, Registered Associate Nutritionist and Certification in Pre and Post Natal Nutrition

Donia started her career as a freelance nutritionist, later she joined Nestle as their Market Nutritionist to help support their healthier product range, before joining the team at Holland & Barrett in January 2018.

Donia has over 6 years experience as a Nutritionist and also works with clients on a one to one basis to support their goals which include weight loss, prenatal and postnatal nutrition and children’s health.