How the microbiology in your gut can affect your brain and mood

How the microbiology in your gut can affect your brain and mood

When we think about microbiology, we may assume this refers to just your gut. Yes, our gut is a part of our microbiomes, but this also includes the mouth and other areas that house different forms of bacteria. It can be surprising just how interconnected the mind and body are- the vagus nerve serves as a highway to the brain from the gut, reporting back to maintain internal equilibrium. The bacterium in your gut also breaks down the fibres in our diets and affects our immune system. Our microbiomes play a pretty big role in how we think and feel, so why not cultivate a beautiful little ecosystem all for ourselves?

Why is it important? 

A rapidly growing pool of research seems to show a significant connection between our microbiomes and mental makeup. Our guts contain a whole myriad of bacteria and fungi and are always changing- it’s a whole new world! Research suggests that this system is in a fragile state of balance and that any sway in conditions can have an adverse effect on our physical and mental health. There is evidence that microbiomes seem to have some influence over factors like the likelihood of developing depression or anxiety, as well as how we deal with social situations. 

Microbiomes begin to take shape in early life and grow with us. Approximately two thirds of our internal flora is completely unique to us. The microbiomes continue to change over the course of our lives, shaped by our diet and environment. These tiny internal systems create very specific internal reactions. 

Ways we can have a say in our microbiomes

There are innumerable factors that can influence our internal flora, so it’s certainly useful to be aware to help keep ourselves steady and healthy. This guide demonstrates some of the ways we can shift our daily lives to make things that little bit easier for our insides. 


Stress has been linked to weight gain in the past, with an emerging theory now suggesting that it causes a significant decrease in the variety of microbes that help us to excrete fat. Stress can cause an inflammation of the gut when the balance is shifted, yet an imbalance in the gut can also (ironically) cause inflammation. This two-way street can be hard to tackle because both causes essentially play off one another. The best way to avoid this is to encourage a consistent and diverse array of gut flora, and to try and keep tabs on our stress levels where possible.

Some studies have found that those with weaker biomes who haven’t been exposed to a wide variety of bacteria tend to be more vulnerable to outside influence. Because they haven’t adapted as well, they are more likely to fall ill or experience bigger internal changes. Depression is another pretty big factor in our internal balance. Approximately 90% of serotonin (the happy hormone) is manufactured in the digestive tract. When we are depressed it affects our gut health, which in turn can make us feel worse. 

There has been some success in moving specific bacteria from one organism to another- and moving specific emotional states over as a result. The aim here is to be able to transplant certain types of bacteria to help cultivate the ideal internal system in the future. We aren’t there just yet, but it’s a fascinating prospect in medicine and demonstrates just how important our gut health really is. 

Sleep patterns

If you have trouble sleeping it can cause fundamental changes to your gut flora. This can have unfortunate side effects as it’s been linked to weight gain. Gut flora is also capable of affecting your sleep patterns, so improving the health and variety of your gut flora can solve two problems at once. Studies have found that poor sleep can have an adverse effect on cognition as lower levels of the microbes that help with cognitive function seemed to decline. The connection between sleep and our microbiomes is an area of new interest and increasing research, but the suggestion seems to be that our guts function the same way the rest of us does- on a circadian rhythm that can be swayed to perform for better or worse.


Within two days of changing your diet, your gut species will have changed. Different bacteria will thrive in different environments, while others will starve and die out. One of the main ways that we can change our microbiome is through our diet. Certain foods, particularly those which are fermented or high in fiber help to maintain a healthy system. Fermented foods are sometimes able to colonise your gut and help shift the internal balance in the right direction. 

Some examples of good gut foods:

  • Garlic
  • Onions
  • Leeks
  • Fruit
  • Nuts
  • Kimchi 
  • Kombucha

Different areas in the world have developed vastly different microflora because of environment and dietary variations- where you live and what foods you have access to can change your microbiomes considerably. There is a large contrast between the guts of urban and indigenous populations due to distinctions in their diet and lifestyle. It’s good to remember that things have changed for all of us- the types of food we eat have a considerably different makeup to what they once did  because of processing  and changes in environment, and so do we. Our fiber intake is far lower than it would have been back in the hunter-gatherer days, so it’s always good to try and boost this however we can.

Be consistent

Making big changes to your diet can wreak havoc on your sensitive internal systems. Rather than changing it up every day, try to gradually change your diet so your gut has time to adapt to these changes. 2A varied diet is good make no mistake, your body will change it up to match your variety, but try and increase the selection steadily as to not give it a fright. 

Avoid high saturation foods

Sugar feeds the microbes that attack your stomach lining, as well as speeding straight through your gut without feeding any of the good microbes. If these microbes starve it can lead to a whole host of problems, particularly complications with your immune system. Try reducing your intake of processed foods and sugars where possible to make sure your gut can get what it needs.

Choose food and drink with high levels of polyphenols 

Evidence has shown that polyphenols can cause an increase in healthy and diverse microbes and reduce harmful pathogens in your gut. Examples of foods that contain polyphenols are nuts and berries, but one of the best sources of polyphenols is tea. Black tea reduces the body’s ability to absorb fat and sugars, whereas green tea increases your body’s ability to excrete fat. 


Probiotics are a natural phenomenon in our guts and are an essential part of the process of keeping us balanced and healthy. There are ways to increase the number of probiotics in our system, including the yogurts we often see advertised. There are lots of suggestions that these yogurts can potentially help keep our gut healthy, but the actual link that this evidence provides is a little on the vague side. It’s more likely that they don’t cause any harm, or even do promote gut health somewhat, but the actual extent that these products benefit us is still up for debate. If these supplements are coupled with the natural probiotics found in the foods listed then there isn’t a downside, but it's worth seeing all sides of the research before making decisions about your health and diet.

A healthy balance of many different bacteria stops one from ruling over the others. The balance is what seems to keep things running smoothly. Many scientists consider us to be symbiotic creatures- co-existing with intricate systems that are believed to be critical to our continued existence. It’s true that some gut flora can do more harm than good, but to do battle with them is to fight with ourselves. The best way to maintain healthy and diverse microbiomes is to work with what we know. Encourage growth of the areas you want to improve and cultivate a stable and diverse system that supports you beautifully.

Additional Reading

Genevieve Wanucha (2018) The Gut Microbiome and Brain Health, MBWC, online, available:

Kristen Sanchez (2020) The Harmful Effects Of Stress On The Gut Microbiome, honeycolony, online, available:

Leigh Stewart (2021) Stress, Anxiety, Depression and Mood: The Gut Microbiome Is Involved, AtlasBiomed, online, available:

Michael Einstein (2020) The hunt for a health microbiome, Nature, online, available:

University of Oxford (2018) How microbes living in the gut affect the brain and behaviour, Phyorg, online, available: