How the Bacteria in Your Digestive System Is Impacting Your Health

By Zoe Buratynsky

reviewed by amadou barrow

Did you know your digestive system plays one of the most important roles in determining your overall health? While the organs within the digestive system are essential for the functioning of the human body, the invisible, microscopic organisms that line these organs play an even larger role. These helpful bacterial microbes, commonly referred to as the gut microbiome, inhabit our intestines and colon and have a significant impact on our overall health and wellbeing.


The relation between bacterias and our bodies

The human gut is populated with as many as 100 trillion microorganisms of anywhere from 500 to 1000 different species. While some microbes can cause illnesses like the stomach flu, most bacteria in the digestive system are good and improve our health. These microbes that live within us have a mutually beneficial relationship with our bodies, as we provide them with a living environment and food while they mediate and contribute to numerous functions within our bodies in return. These functions range from determining our body size and shape to the functioning of our digestion, to the state of our mental wellbeing.


Gut microbiome and digestion

Our gut microbiome aids in our digestion. These microbes survive off the food we ingest and aid in the process of breaking it down. This reduces stress on our digestive system and has been shown to increase the absorption of two vitamins:

  • Vitamin K: A vitamin present mainly in leafy vegetables that the body needs for blood clotting, helping wounds to heal, and keeping the bones healthy.
  • Different kinds of vitamin B, especially vitamin B6, which helps the body cells carrying oxygen around the body, and B12, which keeps the nervous system healthy. 


In addition to this, these microbes live off of the insoluble fiber found in certain complex carbohydrates as well as fruits and vegetables. Studies show that bread, cereals, pasta, and legumes, for example, contain oligosaccharides, and the gut microbiome helps the body digest and transform them into rapid energy for our system. The gut microbiome also helps the body with metabolization and immunization by absorbing different compounds found in plants, fruits, and plant-derived products (tea, cocoa, wine).


Microbiome and mental health

While the gut microbiome is very influential on digestion, it has also been proven to have significant effects on our mental health. Changes in the gut have been linked to changes in behavior, personality, and brain chemistry, as certain microbes are involved in producing neurotransmitters. Neurotransmitters are chemical messengers that act in the brain to regulate body processes like sleep and hunger, as well as emotions. For example, the neurotransmitter serotonin is responsible for regulating sleep, happiness, and anxiety, and studies have indicated that low levels of serotonin are related to depression and anxiety disorders. This is directly impacted by the gut microbiome, as 90% of all serotonin is created in the gut. The connection between the gut microbiome and mental functioning and health is so strong that the term “gut-brain axis” has been developed as researchers delve deeper into the relationship between the two.


What can you do to achieve optimal health?

So, in light of all of this, how can we influence our gut microbiome to achieve optimal health? 

  • Be mindful about processed fats and added sugars: Studies have shown that our diet is so influential on our gut health that all it takes is a single day of eating a diet high in processed fats and sugars to significantly alter the structure and functioning of the microbiome. To prevent these effects, it has been shown that a diverse diet rich in fresh fruits and vegetables as well as beans and legumes is very beneficial. This is because these foods contain large amounts of nutrients and fiber which help our gut bacteria thrive.


  • Increase the consumption of whole grain foods and fermented foods: Other studies have indicated that a diet high in fiber-rich complex carbohydrates, such as whole grain foods (popcorn, oat groats, brown rice, or quinoa, among others) is also very beneficial. On the contrary, low fiber intake can produce detrimental metabolites, which can develop chronic diseases. In addition to this, fermented foods (such as yogurt, kombucha, kimchi, and sauerkraut) enhance the diversity and function of the gut microbiome. Studies have shown that whole grains are not only beneficial for the gut microbiome; they are also a good source of nutrients such as proteins, lipids, vitamins, or minerals, among others. Whole grains also reduce risk of obesity, diabetes, hypertension, dyslipidemia, and various cancers.


  • Incorporating prebiotics in our diet: Another significant element is incorporating prebiotics into our diet, which can be found in foods like oatmeal and asparagus. Probiotics are live bacteria and yeasts that, when administered in a viable form and in adequate amounts, are beneficial to human health. They are usually added to yogurts or taken as food supplements. This is important as these foods provide food for the microbes and thus further promote the growth of good bacteria. Finally, a high quality probiotic supplement can also largely benefit gut health. This is because probiotics can change the composition of our gut and support metabolism. Studies have shown that these dietary changes can aid in weight loss, as well as reduce blood pressure, cholesterol, and heart rate while also decreasing the number of toxin-producing bacteria in the gut and replacing them with beneficial gut bacteria.


  • The effect of antibiotics: Besides food, antibiotics and other medication can also affect the gut microbiotics. Antibiotics are also used to increase the growth and weight of livestock and, therefore, they can be consumed indirectly with food.


From physical health, like improved digestion, to mental health, through the production of essential neurotransmitters, the bacteria in our gut are a huge determinant of our overall health and wellbeing. Through small dietary changes, like incorporating more fermented foods and lots of fresh fruits and vegetables, we can ensure that our microbiome is functioning as well as possible. As a result, we can experience significant improvements in mental and physical health that can translate into an overall improved quality of life. 

Zoe Buratynsky
I’m a Canadian writer, sailor, world traveler, and health and wellness enthusiast. When not learning about nutrition, I’m often found outside hiking, reading, and exploring.

Amadou Barrow

My areas of expertise center around climate change and global health; Reproductive, Maternal, Newborn, Child and Adolescent Health (RMNCAH); environmental and occupational health; health education and promotion; and health risk communications. I have experience as a lecturer at both university level in the area of health psychology, health education & promotion, water supply & sanitation, biostatistics, epidemiology and research methodology. I have published several scientific manuscripts in various reputable journals on maternal & child health morbidities and mortalities in LMIC settings. I am a passionate digital health enthusiast with a special focus on holistic wellbeing at all levels.

Christian Milani, Sabrina Duranti, et al. (2017). The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. Microbiology and Molecular Biology Reviews 81 (4), e00036-17; DOI: 10.1128/MMBR.00036

Bultosa (2016) Functional Foods: Dietary Fibers, Prebiotics, Probiotics, and Synbiotics. Editor(s): Colin Wrigley, Harold Corke, Koushik Seetharaman, Jon Faubion. Encyclopedia of Food Grains (Second Edition). Academic Press, Pages 11-16.

Ghaisas, S., Maher, J., & Kanthasamy, A. (2016). Gut microbiome in health and disease: Linking the microbiome–gut–brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases. Pharmacology & Therapeutics (Oxford), 158, 52–62.

Jandhyala, S. M., Talukdar, R., Subramanyam, C., Vuyyuru, H., Sasikala, M., & Nageshwar Reddy, D. (2015). Role of the normal gut microbiota. World journal of gastroenterology, 21(29), 8787–8803.

Robertson, R. (2016). 10 Ways to Improve your Gut Health, Based on Science. Healthline. Retrieved from

Valdes Ana M, Walter Jens, Segal Eran, Spector Tim D. Role of the gut microbiota in nutrition and health BMJ 2018; 361 :k2179

Vitamins and minerals – Vitamin K. (2021). Retrieved 12 February 2021, from,may%20help%20keep%20bones%20healthy.

What I’ve Learned [YouTube]. (2018). How the Gut Microbiome affects the Brain and Mind. Retrieved from

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