The Magic Microbiome What It Is And How You Can Make It Work For You

The magic microbiome: what it is and how you can make it work for you

Your microbiome impacts your heart health, your mental health, your weight, your immunity and your athletic performance. That same microbiome is also unique to you and has been dubbed the “second genome”. The big questions are, what exactly is that microbiome and how can you make it work for you?

Just a decade or two ago, although researchers were onto it, in public discussion the bacteria that live in your body were hardly spoken about in health terms, other than something that might need to be eliminated. Now, however, we know that your bacteria and other microorganisms are as vital to your health as they are unique to you. Those microorganisms have a name: they are known as your microbiota and their collective genes are known as your microbiome. These two terms are used interchangeably in the public discussion, so for the sake of simplicity, and because a biome sounds more homey than biota, we will refer to your travelling bug community as your microbiome.

The bugs of your microbiome number in the trillions and include bacteria, fungi, archaea (single-celled organisms) and viruses. Collectively they weigh between one and two kilograms in any given person, and a lot of them live in your gut, which will be the main focus of this article. Roughly, there are 40 trillion bacterial cells in your body and yes, the internet factoid is true, that means there are more bacterial cells than human cells in you because your human cells number around 30 trillion.

The bugs of your microbiome number in the trillions and include bacteria, fungi, archaea (single-celled organisms) and viruses. Collectively they weigh between one and two kilograms …

So, the question is not whether you are a “woman/man or a mouse?” but rather are you a “bacteria or a human?”. In fact, a more accurate answer is that you are a holobiont, an entity comprised of a host and many other species that live in or around it, which together form a distinct biological unit. So, fellow holobiont, why should you care about the microbiome that is part of you? The answer to that will become evident as we consider the many health implications of the composition of your own particular microbiome.

Your microbiome in action

Humans have evolved to live with microorganisms, and over the millennia during which those microbes have learned to play important roles in the human body, they’ve made themselves useful, and in turn the body has come to rely on them. We used to think that you are essentially in a sterile environment when in the womb, although we have now discovered that the placenta does in fact contain bacteria. From the moment you are born though, you are irretrievably and certainly exposed to microbes as you travel down the birth canal, and from this point your microbiome starts to form. For the rest of your life that microbiome will impact your health in a myriad of ways.

Mental health

Bacteria in the gut microbiome produce a wide range of neurotransmitters that the brain then uses to regulate memory, learning and mood. The American Psychological Association says that gut bacteria produce 95 per cent of your body’s serotonin, a calming and antidepressant neurotransmitter. On top of this, the brain is connected to the gut through literally millions of nerves, and so it likely that the gut microbiome influences brain function by affecting the messages sent through these nerves. It is no wonder then that people with psychological disorders such as anxiety and depression have been found to have different species of bacteria in the microbiome compared to healthy people. It’s possible that people with anxiety or depression might have different eating and lifestyle habits leading to that altered microbiome.

Bacteria in the gut microbiome produce a wide range of neurotransmitters that the brain then uses to regulate memory, learning and mood.

However, there are also studies that show how altering the microbiome can heal psychological imbalance, suggesting that the unbalanced microbiome is the cause rather than the effect. In one study published in the journal Psychopharmacology for instance, it was found that using prebiotics (we’ll talk about them later) to boost healthy bacteria in the gut microbiome is effective in reducing both stress and anxiety.

Heart health

The link between your microbiome and the health of your heart becomes very clear when you look at the good and the bad bacteria that can live in your gut. Good bacteria, especially lactobacilli, can help reduce overall cholesterol and triglyceride levels but, as shown in the journal Circulation Research, they can increase levels of good HDL cholesterol. By contrast, unhealthy bacterial species in the microbiome can produce a substance known as trimethylamine-N-oxide (TMAO) when they break down red meat and other animal-based foods. This TMAO contributes to blocked arteries and has been reported to increase risk of heart attack and stroke.


The basic task your body hands to the immune system is to decide what to react to and what not to react to. This task of establishing “tolerance” is fundamental to protecting you when you need to be protected and allowing things into the body when they need to be. A diverse gut microbiome established early in life, with many types of bacteria, fungi and other microorganisms, is essential to this as it teaches the cells of the immune system that not everything is bad. The balance of the bacteria in the microbiome determines the balanced response of the immune system. An unbalanced microbiome can shift the immune system to an inflamed state and has been linked to a variety of conditions such as “leaky gut”, asthma and allergy.


Increasingly, research is showing there is a link between the microbiome and weight gain. Mouse-based studies have shown that twin mice, with no differences other than their gut microbiome and eating the same diet, can yield one mouse that is obese and one that is lean. Transferring the microbiome from the obese twin to the lean twin has been shown to cause the lean twin to gain weight. In humans researchers have found that a certain strain of bacteria, Christensenellaceae minuta, is more common in the microbiome of people with a low body weight. In general, imbalance of the microbiome (also known as dysbiosis) is believed to play a role in weight gain.


Elevated blood sugar levels after a meal are a major risk factor for prediabetes and type-2 diabetes. Research has shown that in some cases this disordered blood sugar control can be due to the types of bacteria present in the microbiome.

Gastrointestinal health

Since your intestinal tract is where your microbiome lives, it makes sense that the function of your digestive tract can be impaired when your microbiome is out of balance. Gastrointestinal conditions such as irritable bowel syndrome (IBS), inflammatory bowel disease (IBD) and gastritis are suspected to be associated with microbiome imbalance.

Athletic performance

Bacteria in your microbiome produce many molecules that can affect your physiology in a variety of ways. It is not surprising that it has been found that they can also affect athletic performance. In one interesting study researchers compared the microbiome of runners in the Boston marathon to sedentary controls. The athletes were found to have significantly higher levels of one species of bacteria, Veillonella atypica, than the non-active people. Mice who were fed this bacterium were then found to be able to exercise longer. It was found that the reason the mice and humans with high levels of V. atypica were able to boost their endurance was that they were better able to convert lactate to propionate in their muscles.

Other research has suggested that people who are proficient in different sports have variances in their microbiomes, so that the microbiome of a rower is different to that of a runner. It’s not hard to see where microbiome science will soon cross over with sports science.

… imbalance of the microbiome (also known as dysbiosis) is believed to play a role in weight gain.

This is all really just the tip of the iceberg in terms of how your microbiome affects your health, but even with these few points we’ve illustrated that the influence is holistic and vital. Having established that your microbiome is critical to your wellbeing, the next challenge becomes how to maintain a healthy microbiome.

Building your microbiome

As you grow through life your gut microbiome diversifies. A high degree of diversity in your microbiome is a good thing, but harmful microorganisms can also become part of your microbiome over time. Maintaining a balance of good bugs over pathogenic organisms is the essence of a healthy microbiome and a healthy you. For better and worse, your gut microbiome is highly malleable, which means there is plenty that you can do to build a microbiome that will support you. You can sculpt your microbiome with your diet and other lifestyle choices such as exercise.


As always, a healthy diet is important in the maintenance of a healthy body, and there is no exception when considering microbiome. Excessive consumption of refined sugars, fatty foods and alcohol will promote the proliferation of bad bugs within your microbiome.

Probiotics and prebiotics

Probiotics are live beneficial bacteria that contribute to a healthy microbiome. There are many beneficial microorganisms that inhabit the human gut, including strains of lactobacilli and bifidobacteria, such as Lactobacillus acidophilus, L. casei, L. plantarum, L. rhamnosus, L. fermentum, L. bulgaricus and Bifidobacteria bifidum, B. lactis and B. infantis. Another beneficial bacterium is Streptococcus thermophilus, which has been used to enhance digestion of lactose in those who are lactose-intolerant.

It acts by producing the enzyme lactase, which breaks down the sugar lactose. The yeast Saccharomyces boulardii has also been used in both animal studies and human clinical trials to promote the growth of beneficial bacteria, without itself colonising the gastrointestinal tract.

You can sculpt your microbiome with your diet and other lifestyle choices such as exercise.

Probiotic foods, such as the fermented foods outlined below, provide good microorganisms for your microbiome, but there are also many probiotic supplements available. Supplements are generally recommended for people who have a poor diet, are taking certain medications or exhibit digestive symptoms. Probiotic supplements may also be recommended as a therapy for specific conditions. Probiotic supplements generally contain a concentrated load of viable bacteria than do probiotic foods and therefore may be more effective in producing a therapeutic effect in such conditions.

Prebiotics by contrast are the foods that feed the good bugs allowing them to thrive. With adequate prebiotics in the diet, probiotic microorganisms are better survivors. Prebiotics contain compounds such as inulin, fructooligosacharides (FOS), lactulose and derivatives of galactose and beta-glucans. Prebiotics occur in significant amounts in artichokes, onions, leeks, apples (with skin on), spinach, asparagus, chicory, bananas, seaweed, wheat and non-processed honey.

The Mediterranean diet

The “Mediterranean diet” originates from countries bordering the Mediterranean Sea and features eating primarily plant-based foods such as fruits and vegetables, whole grains, legumes and nuts; replacing butter with healthy fats such as olive oil; using herbs and spices instead of salt to flavour foods; limiting red meat to once a week; eating fish and poultry at least twice a week; and drinking red wine in moderation. There are many benefits of eating this way but the relevant one here is that it benefits your microbiome. There is plenty of research to attest to this, but to quote just one study published in the journal Gut in February 2020, eating a Mediterranean diet for just one year was found to boost bacteria in the microbiome related to healthy ageing.

Fermented foods

In many cultures around the world there is a tradition of fermented foods. Fermentation is an anaerobic process, meaning that it takes place without oxygen, that is performed by microorganisms such as bacteria and yeasts. Probiotic bacteria are naturally created by the process of fermentation in foods like kefir, yoghurt, kimchi, miso, sauerkraut, kombucha tea, natto, pickles, tempeh and vinegar. Eating lots of fermented foods will increase levels of beneficial organisms in your microbiome.


Research using rats has found that rats that exercised every day developed a more beneficial gut flora than their more sedentary counterparts. There is evidence in humans too, that exercise directly impacts the composition of your microbiome. Rugby players for instance have been found to have a much wider range of bacteria in their microbiome than non-rugby players, especially when compared to men who were overweight. Specifically, the rugby players had much higher levels of a bacteria called Akkermansiaceae which is linked to lower levels of obesity.

A microbiome on the future

The more we study the microbiome, the more we are realising that its composition goes a long way to determining your health and wellbeing. Imagine a nano-sized container with a specific bacterial mix designed to only open when it meets the appropriate “key” at the right location of your gut, for instance an enzyme or a specific pH value, so that it can deposit its payload right where you need it. Manipulating your microbiome for weight loss, illness therapy or even specific athletic performance is not too far away.

In the meantime, eat well and exercise, and you will be taking care of your microbiome so that it, in turn, will take care of you.

Terry Robson

Terry Robson

Terry Robson is the Editor-in-Chief of WellBeing and the Editor of EatWell.

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