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A Bite-Sized Journey Into The Gut Microbiome: How We Shape It, And How It Shapes Us

Trillions of bacteria live in our gut, and they make vital contributions to our health. From digesting our food, to supporting our immune system and mental health, we wouldn't be much without them. The food we eat can influence the bacteria and the role they play in our health, either for bad or for good.
Isabelle Sadler
August 31, 2022

The human body is covered in microorganisms. From the top of our heads to the tips of our toes you’ll find them everywhere, on your eyes, inside the nose, even in the bladder. 

Microorganisms (microbes) are tiny single-celled organisms impossible to see with the naked eye. They include bacteria, archaea, viruses, and fungi and whilst some can be bad for us, most do a lot of good. 

Each of us provides a home for trillions upon trillions of them, right now you have more microbial cells than human cells in your body 1

These microbes form a community called the human microbiota and the human microbiome, which is all the genes that your microbiota contain.  

These microbes make us who we are. They affect almost all of our physiological functions to the point where we don’t know who or what we’d be without them. 

We can control the levels of good and bad bacteria that live within us, and diet is the key.  

The gut microbiome 

Your gastrointestinal tract (better known as the gut) houses the busiest and most important ecosystem of microbes in the body, home to 100 trillion of them 2

It predominantly contains bacteria that are split into several main groups, most of which fall into the Firmicutes and Bacteroidetes. These groups contain hundreds of different types of bacteria, a mix of good guys and bad guys. 

From the moment we’re born we start to shape and develop our microbiome. We first journey through the birth canal, where upon our exit we’re bathed in vaginal microbes. This continues into breastfeeding, where over 200 chains of sugars called human milk oligosaccharides have evolved as prebiotics in the mothers breast milk. These have no nutritional value to the baby, instead they feed the growing gut microbiome that protects us for the rest of our lives 3 4

The microbiome develops a lot in the first 2-3 years of life, based on diet, environment and upbringing 3 5. Even exposure to household pets can increase the abundance of certain bacteria (Ruminococcus and Oscillospira) that are associated with a lower risk of obesity and allergic disease 6. Now there’s an argument I wish my younger-self knew when begging for a family puppy!

Different bacteria thrive under different conditions, so as we continue to grow, live in new places, eat different foods and interact with different people your microbiome can continue to change and adapt 7

Microbiomes are incredibly unique. Even though you share 99.9% of your genome with all other humans, your microbiome can be 80-90% different to other people 8.

Why is the gut microbiome so important? 

Only now are we beginning to fully understand the power of the gut microbiome over our health and wellbeing. Experts call it the virtual organ because of its endless functions and importance in our survival 9 10

Firstly it helps to digest your food and extract important nutrients 11. This is vital for our digestion and metabolism whilst also giving the microbes something to eat, so everyone’s a winner. 

They also maintain the health of our immune system, fight off disease and protect us against pathogens. The gut microbiome makes essential bioactive compounds like vitamins and messenger molecules that communicate with distant organs including the brain, lungs, skin and joints 12 13

It’s crucial for maintaining the structural integrity of the gut barrier, which separates your insides from the external world and prevents unwanted substances getting in 2.

For all this to run smoothly, you need to have the right balance of numbers and types of bacteria in the gut (that favors the good guys). 

If there is an imbalance, known as gut dysbiosis, it puts you at a higher risk of most chronic conditions, are you ready for the lengthy list? 

Dysbiosis can contribute to 14

  • Rheumatoid arthritis 
  • Type 1 diabetes
  • Eczema
  • Asthma
  • Inflammatory bowel disease
  • Irritable bowel syndrome
  • Cardiovascular disease
  • Type 2 diabetes
  • Non-alcoholic fatty liver disease
  • Chronic kidney disease
  • Mental health disorders 

Whew! Now take a breath. 

It’s not as doom and gloom as the list may seem, because if your gut microbiome is healthy, it can actually protect you against these diseases. 

What does a healthy gut microbiome look like? 

We know it’s important to have a healthy gut microbiome, and you may be wondering, what does that actually look like? 

Because of the uniqueness of the gut microbiome, there isn't one optimal composition of bacteria 2. What researchers agree on is the importance of richness and diversity. 

The richer and more diverse the gut microbiome, the better it is at dealing with external threats and maintaining our health 2. A healthy gut that’s full with good bacteria doesn’t leave much space or resources for pathogens to enter and cause havoc. 

More beneficial types such as Lactobacillus, Bifidobacterium, and butyrate-producing bacteria are reduced in patients living with illness such as type 2 diabetes and colorectal cancer 2.

In the state of gut dysbiosis, potentially pathogenic types such as E. coli, Streptococcus, Escherichia and Shigella are more prominent. These are related to inflammation, and diseases such as Allzheimers, colorectal cancer, and inflammatory bowel disease 15

There are symptoms of dysbiosis including diarrhea, constipation, gas bloating, belching, and abdominal pain. Other cases of dysbiosis may have less obvious symptoms and may contribute to rashes, fatigue and illnesses without accompanying digestive issues. 

How can you improve the health of your gut microbiome?

Research shows us that genetics have very little influence on the gut microbiome, and that diet is the most important factor influencing the bacteria living in our gut. 16

Some types of bacteria prefer certain foods to others, so we can influence the bacteria that live in our gut with the food we eat.   

Dietary fiber is fuel for the gut microbiome and has a huge impact on the diversity and richness of the residing bacteria 17. Only certain gut bacteria breakdown fiber and use it to build short chain fatty acids (SCFAs) that are crucial for the health of us and our gut. They support the immune system and cancer responses of the gut, as well as blood sugar and lipid control, reducing the risk of obesity and type 2 diabetes 18

Fiber is found exclusively in plant foods and is abundant in a plant-based diet. It’s completely absent from all animal foods and low in a western-style diet, most Americans don’t eat nearly enough of it. 

Increasing the number and diversity of plant-foods in the diet, along with eating more fermented foods are also key to increasing good gut bacteria diversity. The wider the variety of food you eat, the wider the variety of gut bacteria you’re feeding 19 17

Sleep, stress, exercise, time outdoors, and your home environment also matter and represent other ways we can control our gut microbiome.

Too much stress can change the composition of bacteria in the gut and may contribute to gut dysbiosis 20

It’s never too late to nurture your gut microbiome

What if you’ve spent most of your life stressed, not exercising, and following an unhealthy Western style diet? Has the damage to your gut been done for good? 

Not at all. Thankfully, your gut microbiome responds incredibly quickly to dietary changes 21

Dr. Will Bulsiewicz, a board-certified Gastroenterologist says “no matter what you’ve done and what you've been through, your gut microbiome forgives you. And wants to have a good, healthy relationship with you”. 

Dr. Bulsiewicz is the New York Times best selling author of the microbiome book Fiber Fuelled. He goes on to explain that “when you change what you eat, in less than 24 hours you will see changes in your gut microbiome. That's how malleable it is”. 

Brilliant news for us, we have the control here, not the microbes. So it’s never too late to swap what you eat and start feeding the good bacteria. 

The Bottom Line 

The next time someone says 'we're only human' you can tell them that's far from the truth. The trillions of microbes living in our gut make us who we are, and affect every part of our health.

We have control over how negatively or positively the gut microbiome controls our health. Being able to control our gut microbiome gives us greater control over our health, or at least more confidence in understanding the control we had all along. 

By eating more fiber, and a wide variety of plant foods, the good guys can thrive and keep the bad bacteria at bay. 


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2. Rinninella, E. et al. What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms 7, E14 (2019).

3. Derrien, M., Alvarez, A.-S. & de Vos, W. M. The Gut Microbiota in the First Decade of Life. Trends Microbiol. 27, 997–1010 (2019).

4. Masi, A. C. & Stewart, C. J. Untangling human milk oligosaccharides and infant gut microbiome. iScience 25, 103542 (2022).

5. Rampelli, S. et al. Pre-obese children’s dysbiotic gut microbiome and unhealthy diets may predict the development of obesity. Commun. Biol. 1, 222 (2018).

6. the CHILD Study Investigators et al. Exposure to household furry pets influences the gut microbiota of infants at 3–4 months following various birth scenarios. Microbiome 5, 40 (2017).

7. Dill-McFarland, K. A. et al. Close social relationships correlate with human gut microbiota composition. Sci. Rep. 9, 703 (2019).

8. Tomova, A. et al. The Effects of Vegetarian and Vegan Diets on Gut Microbiota. Front. Nutr. 6, 47 (2019).

9. Losno, E. A., Sieferle, K., Perez-Cueto, F. J. A. & Ritz, C. Vegan Diet and the Gut Microbiota Composition in Healthy Adults. Nutrients 13, 2402 (2021).

10. Mills, S., Stanton, C., Lane, J., Smith, G. & Ross, R. Precision Nutrition and the Microbiome, Part I: Current State of the Science. Nutrients 11, 923 (2019).

11. Shreiner, A. B., Kao, J. Y. & Young, V. B. The gut microbiome in health and in disease: Curr. Opin. Gastroenterol. 31, 69–75 (2015).

12. Belkaid, Y. & Hand, T. W. Role of the Microbiota in Immunity and Inflammation. Cell 157, 121–141 (2014).

13. Zheng, D., Liwinski, T. & Elinav, E. Interaction between microbiota and immunity in health and disease. Cell Res. 30, 492–506 (2020).

14. Vijay, A. & Valdes, A. M. Role of the gut microbiome in chronic diseases: a narrative review. Eur. J. Clin. Nutr. 76, 489–501 (2022).

15. Cattaneo, A. et al. Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly. Neurobiol. Aging 49, 60–68 (2017).

16. Rothschild, D. et al. Environment dominates over host genetics in shaping human gut microbiota. Nature 555, 210–215 (2018).

17. Sonnenburg, E. D. et al. Diet-induced extinctions in the gut microbiota compound over generations. Nature 529, 212–215 (2016).

18. Cronin, P., Joyce, S. A., O’Toole, P. W. & O’Connor, E. M. Dietary Fibre Modulates the Gut Microbiota. Nutrients 13, 1655 (2021).

19. Heiman, M. L. & Greenway, F. L. A healthy gastrointestinal microbiome is dependent on dietary diversity. Mol. Metab. 5, 317–320 (2016).

20. Madison, A. & Kiecolt-Glaser, J. K. Stress, depression, diet, and the gut microbiota: human–bacteria interactions at the core of psychoneuroimmunology and nutrition. Curr. Opin. Behav. Sci. 28, 105–110 (2019).

21. David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559–563 (2014).

About the author
Isabelle Sadler
Isabelle majored in Human Biology at the University of Birmingham in England, and she leads scientific copywriting for the Mora team.

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