The Body's Second Brain: Understanding Microbes & Gut Health

Joseph Gregorio
Written By: Joseph Gregorio
September 18th, 2018
Updated: June 13th, 2020
Categories: Articles Nutrition
8K Reads
The Body's Second Brain: Understanding Microbes & Gut Health
Your overall gut health can affect your overall mental health. Learn why, how, and what you can do about it to help the microbes living in your gut.

Did you know: From the day you were born, microbes in your gut played a key role in helping you develop a healthy brain and nervous system?

Scientific evidence continues to suggest that microbes can affect certain areas of the brain which have an impact on your overall health and wellbeing.1

More specifically, having a gut full of friendly microorganisms has been linked to lower rates of obesity, digestion problems, increased lifespan and an improved mood.2

Your gut is the second largest collection of nerves in the body (with the brain being the first) and is often named as your ‘second’ brain.

Astonishing, right?

Your brain and gut are connected through a series of complex signals which relay back information between each other that help to control multiple functions; in particular, eating and digesting food.

The relationship between your brain and gut is so vast - it has been proven to have a net effect on your overall mood.

Doctors have long known that an upset gut can send signals back to your brain to induce feelings of nausea and prevent the need to eat which can lead to depression (albeit relatively short-term).

There are known to be around 16 chemicals which transmit messages released from the intestines into the bloodstream which sends signals to the brain to eat more or less. Your genes, and what you put in your mouth, are the two things which control this behavior.

How Stress Affects Gut Health

Is There a Connection Between Microbe Diversity and Stress?

In times of stress, the brain can alter the movements of the bowel through your emotions, which has a knock-on effect on hormonal function. This in turn creates a virtuous cycle of symptoms which can cause massive disruption of microbiomes and feelings of depression.

Through further scientific research, it has become clear that your body’s immune system also plays a key role in the connection between your gut and brain.3

Related: Gut Health - The Next Big Thing in Health & Fitness

Regulatory T Cells, which are responsible for controlling and regulating the immune system’s response to foreign cells to prevent autoimmune disease, are in continual contact with both your microbes and brain acting as a messenger between the two.3

One of the most common complaints associated with the gut is that of irritable bowel syndrome (IBS). This is usually more prevalent in woman as opposed to men and is more common for those aged between 30 - 60 years old. Whilst the cause is still unknown, stress is said to be a big factor.

In fact, 50% of IBS-related cases are merely down to psychiatric symptoms such as anxiety, stress and depression which are purely created either by the conscious or subconscious mind.4

Improve Your Health with Fermented Foods

Whilst stress management will help to offset the effects of some of the mentioned psychological effects (from compromised microbes in your gut), eating fermented (probiotic) foods will ensure you have a diverse range of healthy microbes to improve your overall health and wellbeing.

Some of these include:

  • Natural Yogurt;
  • Kimchi;
  • Tempeh;
  • Miso
  • Sauerkraut;
  • Soybean Milk.

These foods are high in live microbes such as lactobacilli, a type of ‘gut-friendly’ bacteria found in your digestive, urinary and genital systems to keep it healthy and to prevent disease.

Yogurt Can Improve Gut Health

Bottom line: Including fermented foods in your diet can enhance your body’s microbe function which in turn reduces the development of disease-causing bacteria in your gut.

Ultimately, variety is the spice of life. Eating a diverse range of food will ensure your body produces a good mix of microbiota which will contribute to your overall health (something which is far underappreciated today given a societal focus on convenience-based foods).

The western diet is high in fat and refined sugar which dampens the development of gut-friendly bacteria. As we’ve come to expect, this has led to a rise in the number of people suffering from psychological and physical ailments such as depression, overeating and various types of cancers.

Therefore, if you want to stay fit and healthy - both mentally and physically, it is important to not neglect the role fermented foods play in your diet.

Can Regular Exercise Positively Alter Your Gut Microbes?

According to a study published by ‘Medicine & Science in Sports & Exercise’,5  32 adults were selected to review how frequent exercise is associated with altered gut microbial composition.

They consisted of 18 lean female subjects and 14 obese female subjects who participated in an endurance-based training program over the course of 6 weeks for 3 days a week each consisting of 30 - 60 minutes exercise on those days.

Related: Prebiotics, Probiotics, & Poop: 3 Questions Every Person Should Ask

During the 30 - 60 minutes of exercise, this would alter between moderate intensity (60% of the subject’s heart rate reserve) and vigorous intensity (75% of the subject’s heart rate reserve).

Once the study period was finished, the subjects were asked to revert to a sedentary lifestyle for 6 weeks as a ‘washout period’.

Throughout the study period, samples of the subjects feces were collected before and after the 6 week endurance training program as well as before and after the subjects underwent a 6 week sedentary washout period.

After the researchers carried out beta diversity analysis, they found that all test subjects experienced an increase in short-chain fatty acids (SCFA). It was shown that cardiorespiratory fitness was positively linked to increased bacterial diversity and butyrate-producing bacteria.

However, the increased levels of SCFA declined when the test subjects underwent a sedentary lifestyle as all exercise-induced changes in microbes was quickly reversed.

The lean subjects saw the greatest increase in bacterial diversity from the production of SCFA, whilst the obese subjects experienced a ‘moderate’ increase in gut microbiomes that produce SCFA.

Overall, researchers from the study concluded that frequent exercise has a positive net effect in functional changes to human gut microbiota. This is especially the case the leaner you are, although everyone will experience some sort of increase independent of diet.

Exercise Improves Gut Health


Microbes play a key role in your life and are responsible for the healthy development of your brain and nervous system.

The relationship between your gut and your brain is so sophisticated, it has been proven to have a key influence on your mood which dictates how much you are likely to eat (important if you are following a strict diet).

In times of stress (either caused by lack of sleep or some other stress-based stimuli), your body negatively alters the movements of your bowels which can disrupt the natural production of healthy microbes.

It is important to manage your stress well (to suppress your body’s level of cortisol) to increase your performance mentally and physically.

Including some of the mentioned foods as part of your nutrition program such as kimchi, tempeh and natural yogurt followed by a diverse range of fruits, vegetables and whole-based foods will put you in good stead to optimize your capabilities (both inside and outside of the gym) and will go a long way in ensuring you lead an overall healthy life.

Finally, frequent exercise plays a crucial role in your gut microbial composition. Aim to get at least 30 - 60 minutes of exercise every day, or every other day, to benefit from the increased production of bacterial diversity and butyrate-producing bacteria to keep you lean, fit and healthy.

Posted on: Thu, 11/01/2018 - 20:01

Solid info! Thanks

Joseph Gregorio
Posted on: Mon, 11/12/2018 - 20:28

Thanks Palmer. Glad you found the info useful!