Gut Health Part 1: How our microbes impact our physical and mental health

“You are what they eat”  – Alanna Collen, PhD – biologist

Germs are bad…right?

David Vetter was 12 years old when he died from a common herpes virus. This virus doesn’t even cause symptoms in most people but David suffered from a rare disease that caused his immune system to be pretty much non-existent. Therefore he spent his entire life living in a sterilised environment in a plastic dome. It gained him the nickname “Bubble boy”. He was considered the ultimate germ-free human (1) but, on the contrary, he was in no way healthier. Quite the opposite.

Traditionally bacteria have had a bad name and for good reason: many infectious diseases caused by microbes have been a major problem for most of human history. With the invention of antibiotics we got a bit carried away trying to kill all of them because all germs are bad right? Only recently have we started to understand that we need the millions of microbes that inhabit our guts to stay healthy just as much as they need us. When our microbiome is in a state of dysbiosis, disease can be the result. Hippocrates understood this long before microbes were discovered when he said:

So what is our microbiome, how can it affect our health and what can we do to keep our friendly bacteria happy?

“All disease begins in the gut”  – Hippocrates 460 – 375 BCE

Why every microbiome is special

For every cell in your body there are 9 bacteria in your gut (3). This community of bacteria is what we call our gut microbiome. It plays a very important role in our health and in our response to certain foods. Research is difficult because no 2 gut microbiomes are the same: every human has a microbiome that is as different as their DNA. This is because we all have a unique exposure to different bacteria depending on the microbes we inherit from our mother during birth (yes this really does occur in the way you are thinking – babies are born with a sterile gut and the first colonisers are bacteria from the mother’s birth canal and faeces) as well as through breastmilk. Further colonisation occurs by exposure to the environment, and the foods we eat.

Your genes also play a role, certain genetics make our gut a better place for some strains than others. Our microbiome also changes over time, as we age but also after each meal (5).

Not all bacteria are equally desirable to us, some are very useful, others just take up space, and some can make us ill. In a healthy person pathogens are kept in check by other microbes. A healthy gut microbiome has a lot of different species that are constantly competing with each other for a place to live in the gut. In a state of dysbiosis one pathogen can overcrowd others and cause problems. Dysbiosis can be a consequence of use of medications such as antibiotics, poor diet, disease and obesity (6).

Gut flora friends and the impact on physical health

The human body has approximately 23,000 genes of which some provide information to create enzymes to break down food. Our gut microbiome has over 3 million genes that can produce thousands of enzymes. These can help us with digestion and absorbing more nutrients from our food that our body could not otherwise. Germ free mice (mice without microbiome) for example, gain less weight on the same amount of calories than normal mice. Their guts are simply not as efficient in breaking down food and absorbing the nutrients (1).

Furthermore, some bacteria produce useful compounds for us such as vitamin K, B12, biotin, folic acid and short chain fatty acids (SCFA’s). The main SCFA’s are acetate, propionate, and butyrate. Propionate reduces food intake in mice and butyrate can mute your immune response. This is great news if you have Crohn’s disease as this is in part an overreaction of the immune system. Butyrate is the main food of the cells that line your colon and protects against colon cancer (4).

SCFA’s also play a role in satiety signalling, insulin sensitivity and appetite regulation. High levels of SCFA’s correlate with lower diet induced obesity. However, causality is a problem here: are people obese because of their microbes or are the microbes a result of obesity and poor diet? Research implies the latter (3). Obese people have a less diverse microbiome than their healthy counterparts. Germ free mice that receive microbes from obese people gain more weight from the same diet than germ-free mice that receive microbes from healthy humans (1).

It is important to realise that this does not mean that your microbes are all determining whether you will become obese or not. You still need to be in an energy surplus consistently to gain weight. Obesity appears to alter your microbes and make it more difficult to lose weight once you are already obese. However, it is not impossible and the microbiome can change again depending on what you feed it (2). Health, or the absence of it, is rarely a matter of one single factor.

Mental health and the Gut-Brain Axis

Apart from your physical health, our microbes also impact our mental health. Gut diseases linked to dysbiosis of our microbiome such as IBS and Crohn’s disease also increase the risk of mental illnesses such as depression and anxiety (3).  The exact mechanisms aren’t fully understood yet but the gut microbiome seems to communicate with our central nervous system through the “second brain”, or enteric nervous system that covers our GI tract.

This is called the gut-brain axis and there seems to be a two-way traffic between them. Mental stress for example alters the environment of our guts in favour of pathogenic microbes. It makes our gut lining more permeable to pathogens and reduces mucus production (2).  

Microbes also communicate with our brain by producing the same neurotransmitters that the brain uses – serotonin and dopamine: stuff that makes you feel happy. This is how your microbes can impact our mood (1) and partially explains why food makes us feel good.

There is also evidence that cravings aren’t actually yours, but that these are your microbes telling you what they want. Germ free mice like sugar more than regular mice. Sugar is a high energy food, the favourite fuel of all our cells. Without a balanced microbiome also demanding other useful compounds such as protein and fats, this craving takes over. This could be an indication that sugar cravings are a symptom of poor gut health. People exposed to a lot of stress crave sugar more than others, this can be seen as an attempt of the body to load up on energy to prepare for the fight or flight response (1).  

Check out part 2 which includes our top tips on how to improve your gut health!


  1. Anderson, S.C., Cryan, J.F. and Dinan, T. (2017). The Psychobiotic Revolution: mood, food and the new science of the gut-brain connection. Washington: National Geographic Society.
  2. Carabotti, M., Scirocco, A., Maselli, M. A., & Severi, C. (2015). The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems. Annals of gastroenterology, 28(2), 203-209.
  3. Collen, A. (2015). 10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness. UK: William Collins Publishers.
  4. Lin, H.V., Frassetto, A., Kowalik, Jr. E.J., Nawrocki, A.R., Lu, M.M., Kosinski J.R., et al. (2012). Butyrate and Propionate Protect against Diet-Induced Obesity and Regulate Gut Hormones via Free Fatty Acid Receptor 3-Independent Mechanisms. PLoS ONE. 7(4): e35240.
  5. Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G.A.D., Gasbarrini A., and Mele, M.C. (2019). What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms, 7(1).
  6. Valdes, A.M., Walter, J., Segal, E. and Spector, T.D. (2018). Role of gut microbiota in nutrition and health. The British Medical Journal, 361: Supplement 1.
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Published by Georgia Chilton

In her teenage years, a love of food and rowing led Georgia into this field as she wanted to know how to optimise performance through nutrition. With a BSc in Nutrition and an MSc in Sports and Exercise Nutrition, she has the skill set to help you track towards your goals and maximise your potential.