Log in Log inRegister

Forgotten your password?


Sorry, your email or password is incorrect.
15% OFF when you SUBSCRIBE & SAVE*
| Use code: SAVE15  

Ways to Improve Your Gut Microbiome

by Matt Durkin
MSc Nutrition Specialist

The impact that the gut microbiome has on our health is certainly a contemporary topic in the field of nutrition. The gut has been referred to as the ‘forgotten organ’, seeing there is an apparent lack of understanding on the topic, despite its importance. 

Although there are many gaps to fill in our knowledge of the subject, there have been significant advancements in the last decade that have indicated just how important our gut is to overall health. In this article, we are going to explore what the gut microbiome is, what role it plays in the body and how we can improve it to experience these benefits. 

What Is the Gut Microbiome? 

The gut microbiome, previously known as the gut flora, is the name given to the whole host of bacteria, viruses, fungi and other microorganisms that thrive in our intestines. It is thought that there are around 1000 different strands of bacterial species living in our gut, which totals up to 40 trillion individual cells. Considering that there are only 30 trillion human cells, we can be thought of as more bacteria than human!

The microbiome is however not all good news. In the gut there exist bacteria which can be harmful, so it is important to have a diverse and rich amount of ‘good’ or ‘friendly’ bacteria to ensure a balance for the betterment of our health. 

Why Is the Gut Microbiome Important to Health?

As elucidated earlier, research has only really scratched the surface in regards to our understanding of the gut microbiome. From our current knowledge, these are the ways in which the gut microbiome influences our health: 


It is common knowledge that the bacteria in our gut work to help digest the food we eat so that we receive the nutrients we need for maintaining good health and energy levels. Additionally, our gut microbes can create short-chain fatty acids such as butyrate, which is proven to calm inflammation in the gut, subsequently reducing a variety of gastrointestinal issues. It is for this reason that many people with issues such as Irritable Bowel Syndrome find benefit from taking a probiotic supplement that increases the number and diversity of gut microbes. 


Depending on the state of the bacteria in our gut, we can either be prone to suffering from illnesses and infections or somewhat protected. This is because the gut microbiome plays an integral role in the function of the immune system.
As we have already found, the bacteria in our gut can help to combat inflammation. However, it can also promote inflammation. Before you get worried, it is important to understand that acute inflammation is perfectly healthy; it is chronic inflammation that is a cause for concern.

When foreign pathogens enter the digestive tract, a healthy microbiome will stimulate an inflammatory response to help attack the potential virus or bacteria. It is useful to think of a healthy gut microbiome as a barrier to stop pathogens multiplying in the gut or entering the bloodstream. 

Due to the impact that a healthy gut microbiome has on immunity, it is an area that has been researched heavily. Numerous studies have shown that a probiotic supplement can both ward off illnesses and shorten the duration and severity of symptoms when taken at the first sign of illness.  So if you are someone with suffers from regular illnesses despite having a good intake of the classics such as vitamin C and zinc, a probiotic supplement would be an evidence-based choice. 


Scientists have uncovered the link between our gut bacteria and different types of cancer. Specifically, it has been found that certain strands of bacteria can cause lymphoma – a cancer of the white blood cells and also stomach and colorectal cancer. 

Making positive lifestyle changes can help to decrease the action of harmful bacteria, thus decreasing the risk of certain cancers. We touched on butyrate earlier, a short chain fatty acid. High amounts of this in the digestive system have been shown have a protective effect by actually decreasing the risk of colon cancer.

As in all areas of gut microbiome research, it is really in its infancy, but we expect to see much more conclusive and diverse findings in the next few years. 

Brain Function

If you told people that the bacteria in their guts could influence their brain function and mental well-being, they would probably give you a funny look, laugh at you, or a mixture of the two. As after all, there doesn’t seem to be any logic in this. However, there exists something known as the gut-brain axis – a line of communication between our brain and our gut that can have a big influence on one another.

Many of us will have heard of the neurotransmitter called serotonin, which is often referred to as the body’s ‘happy hormone’ given that it governs our mood. Although serotonin exerts its actions in our brain, 95% of it is actually produced by our gut bacteria. 

It should come as no surprise that scientists have therefore found associations between the condition of our gut bacteria and our mental health. One study of note found that in as little as 3 weeks, a group receiving a probiotic supplement had lower levels of anxiety, negative moods and stress hormones compared to the group that received a placebo. It was once thought that the gut-brain axis was one-way traffic, but now we know this is not the case. 

Body Composition & Metabolic Health

Metabolic health is the umbrella term used to describe how healthy and efficient the chemical processes in our body are. This encompasses aspects such as blood pressure, cholesterol and sugar levels. Aside from these aspects, body-fatness, especially around the waist is a key indicator of poor metabolic health, massively increasing our risk of numerous chronic illnesses. 

One of the most interesting and relevant findings in recent years is that our gut microbiome may either dispose us to metabolic illnesses and obesity or provide a protective effect. Research from 2014 found that genetics can in-fact determine our likelihood of obesity, as one strain of bacteria known as Christensenellaceae Minuta was much more common in lean people than obese people.

This link was strengthened when this gene was studied in greater depth. It was found that introducing this strand into the digestive system of mice led to substantially less weight-gain than mice without the strand, when subject to a high-calorie diet. In contrast, there are other genes that have been shown to exacerbate weight-gain. Even though these genes are for the most part shaped by genetics, it would be prudent to suggest that our lifestyle could certainly play a part. 

To complement these findings, there is also research showing how our microbiome can influence the amount of good and bad cholesterol in our blood and also how we manage our sugar levels. Scientists are also confident there is a link between our microbiome and illnesses such as type 1 diabetes, coeliac disease and Crohn’s disease. 

The above conditions are all examples of autoimmune diseases, and as we now know our gut bacteria can help to strengthen our immune system and levels of inflammation. Due to this, it wouldn’t be a surprise if concrete evidence came out soon linking these diseases to an issue with the gut microbiome. 

Production of Essential Nutrients 

Another fascinating way that our gut microbiome affects our health is through the production of certain essential nutrients. Specifically, it is known that in healthy individuals our gut bacteria have the ability to make certain amounts of thiamine (Vitamin B1), biotin (B7), folate (B9) and cobalamin (B12). The B vitamins are water-soluble nutrients which mean they cannot be stored and therefore need to be ingested on a daily basis for optimal health. 

It, therefore, seems that another benefit of a healthy gut microbiome is that it can ensure we have enough of certain B vitamins if our diet is inadequate. As a whole, the B vitamins have a central role in helping to turn the food we eat into energy, thus contributing to mental performance and the reduction of tiredness and fatigue. 

Providing an example of their individual roles, vitamin B1 is an important nutrient for the heart, B7 is influential in the condition of hair, skin and nails, B9 is key for the immune system and also in pregnancy and finally B12 is needed for red blood cell formation. 

Alongside the four B vitamins, certain strands of bacteria have the ability to synthesise vitamin K2. Unlike vitamin K1 which has a role in blood clotting, K2 is important for heart and bone health through a related mechanism. K2 is needed to activate calcium transporters, which help to shuttle calcium into our bones and muscles and away from our blood vessels where it could cause plaque build-ups and blockages. 

How to Improve the Gut Microbiome

Now that we have discovered the diverse benefits of a healthy microbiome and the potential health consequences of an unhealthy one, I am sure you are keen to understand what can be done to ensure we provide a gut environment where friendly bacteria can flourish.

Fortunately, only a third of our microbiome is genetically determined, meaning our diet, lifestyle and environment can shape the vast majority of our gut health. Here’s what we can start doing today to exert a positive impact.


Out of the lifestyle factors, that can influence our gut health, diet is certainly the key player. There is overwhelming evidence that eating a diverse range of foods is crucial to a healthy gut environment. Alongside ensuring we achieve an adequate intake of vitamins, minerals and other essential nutrients, this is why health experts always recommend ‘a varied and balanced diet’. Try to add a wide range of foods to your shopping basket each week and also experiment with new foods.

As well as consuming a wide range of foods, we should also focus on consuming a high fibre diet, as those who increase their fibre intake to a healthy level have been shown to experience an increase in colony size and the diversity of bacteria strands. Most importantly, however, certain fibres are a fuel source for friendly bacteria, helping them to become stronger and more efficient in their myriad of roles.

Now let’s get onto the topic of probiotics and the lesser known prebiotics. Probiotics are foods or supplements that contain active friendly bacteria, which when consumed help to introduce these microbes into the gut. Good examples of probiotic foods are fermented foods (sauerkraut, miso and kefir), live-culture yoghurts, pickles and certain cheeses – especially Swiss cheeses. 

To complement this activity prebiotics, which are types of fibre, work by feeding the bacteria that is already present. Inulin is the prebiotic fibre which has received the most attention, as it can not only influence our microbiome but also works to control cholesterol and sugar levels whilst suppressing appetite. Inulin can naturally be found in onion, garlic, leeks, bananas, artichokes, asparagus and chicory root – which is the best-known source. 

On a final note, it is known that children who have been breastfed have a healthier gut microbiome than children who have not. So to complement the other benefits of breastfeeding such as a decreased risk of illnesses, obesity, diabetes and heart disease, breast milk helps to promote a gut bacteria profile that sets the child up for a healthy life. 


Exercise is universally recognised for its ability to reduce the risk of a plethora of diseases. Another lesser-known benefit of exercise is how it can strengthen the immune system, at least in moderate amounts. 

Scientists have known for some time that exercise can help to increase our body’s content of white blood cells and antibodies that ward-off pathogens. However, novel research has shown how in as little as a few weeks, a structured exercise regime can stimulate marked improvements in our gut microbiome.

This suggests that exercise could partially be beneficial to our health because of how it improves our gut environment, which as we know subsequently influences our health on numerous fronts. This preliminary research showed that performing as little as 30-60 minutes of continuous exercise 3 times per week was all that was required to see a significant benefit. The participants also did not change their diet, so it would be reasonable to suggest that making positive dietary changes on top of the increased exercise would lead to even more impressive results. 


Even if we have our diet on point and an exercise program nailed down, there are some other lifestyle factors that can damage the equilibrium of our gut microbiome. 

We all know smoking is one of the worst habits we can have for our health, but many of us don’t know that it can also negatively affect the balance of bacteria in our intestines. Although there are much worse health concerns from tobacco smoke, if you are interested in improving your gut microbiome, quitting if you do smoke is one of the best things you could do.

Another massive problem in the developed world is the misuse of antibiotics. We are all to blame for this, as doctors are often too quick to prescribe them and we do not question this. There is no doubt that antibiotics have a huge role in the health of people that need them, but we all need to take responsibility to use them wisely. This is because people are now becoming resistant to their actions, meaning that when we do in fact need them, they aren’t as effective. 

Given their name, it should come as no surprise that antibiotics destroy microbes in our gut. Unfortunately, antibiotics don’t differentiate between friendly or harmful bacteria. Research has shown that it can take up to a year to redevelop a healthy microbiome, just after a single course of antibiotics. Although we don’t know the health consequences of this, it is unlike to be good. The bottom line: Only use antibiotics when you really need them.  


Hopefully, this article has outlined the importance of the gut microbiome and what we can do to improve it. By doing so, we can hopefully render it less of a ‘forgotten organ’. Although the current evidence is impressive, the dense and diverse nature of the gut microbiome means that there is so much scope for further work. We will make sure to keep you informed on future advancements on the topic, but in the meantime, here are the key points of what we know so far: 

•    Our gut is home to around 1000 different strands of bacteria, with individual microbes to the quantity of 40 trillion. Given their importance, there is a relative lack of research into the area, but the current evidence is both impressive and fascinating. 

•    With a healthy gut microbiome, we can expect to experience benefits to our digestion, immune system, metabolic health, body weight, psychological health whilst reducing the risk of certain types of cancer. On top of this, a healthy gut has the ability to create certain essential nutrients, thus making up for dietary shortcomings. 

•    Genetics only make up a third of our gut microbiome; meaning how we live has a massive bearing. By eating a prudent diet, incorporating regular exercise and having a sensible lifestyle, we will go a long way to ensuring we have a healthy and diverse gut environment.

•    Specifically, eating a high-fibre diet that incorporates a wide range of foods, especially ones with pre and probiotic properties is the best way forward with regards to nutrition. From an exercise perspective, 3 sessions of a moderate intensity every week seems the goal based on the current evidence. 

•    Finally, quitting smoking if you are a smoker and only using antibiotics when you need them are good things to aim for. This should help you to develop a gut environment where microbes can flourish, subsequently leading to a range of proven health benefits. 


view all articles