Diversity of our microbiome

One ecosystem
As in the natural ecosystems around us, high diversity of the microbiome means resilience and low diversity means vulnerability to perturbations. Fewer microbial species means a diminished ability to withstand perturbations such as infections (by pathogenic bacteria, viruses living in our gut), poor diet, or medications. 

Within our digestive system we have low diversity zones such as the stomach and small intestine as well as large diversity zones in the large intestine.

The large intestine has more microbes than any other location in our body and the largest diversity of microbes. 

And how to support our gut?
The ultimate goal is to create a stable healthy state of diversity which creates resilience in our small and large intestine. And just like diversity in nature, resilience in our gut microbiome means that we have to nourish ourselves diverse (meaning fibers, probiotics, pre-biotics, vitamins, minerals, and so forth.)

A number of longitudinal studies have been on the composition of the microbiota, they seem to show that dietary changes, the use of drugs (especially antibiotics), and immune function can bring shifts from a healthy state into another state in our microbiota.

  • This shift can be temporarily or persistent resulting in chronic disease. 

The most common perturbations are antibiotics, infections, inflammations, or stress.


Where does diversity begin?
It all starts already within our mother’s womb. The microbiota living in the gut of a newborn has a low microbial diversity when they´re healthy, and for good reasons. The newborns microbiome needs flexibility in order to create a pattern of communities of gut microbes during the early programming period which is unique for each individual. The vaginal microbiome needs flexibility in order to adjust its function to the unique demands of reproduction and delivery (E.Mayer, 2017).


Nature has developed clever alternative strategies to ensure the stability of these unique habitats and protect them from infections and disease. Both habitats are dominated by lactobacilli (the bacteria you find in our raw, fermented veggies) and bifidobacterial (mostly from added yoghurt cultures). These bacteria can produce many antimicrobial substances, and they have the unique ability to produce enough lactic acid to create an acidic milieu that is hostile to most other microorganisms and pathogens. 

A growing scientific literature demonstrates that disease such as obesity inflammatory bowel disease, and other autoimmune disorders are associated with reduced gut microbial diversity often as a consequence of repeated exposure to antibiotics. Other disease may join this list in the future. 

In order to increase your own microbial diversity, probiotic intervention on the health of your gut microbes may be greater during the first few years in life. Year 1-3 is the time when the microbiome is developing most. This is why it is our responsibility as parents to ensure a well-balanced diet including pro/ and prebiotic foods as well as maintaining a lower stress level in general. Raw, fermented Kraut, Kimchi, and other veggies are one way to implement more lactobacilli bacteria in any diet with regular consumption of it. 


They key is stability and resilience 
Friendly gut microbes can return quickly even after a very stressful period in life or after an antibiotic treatment when the right diet is in place. This allows them to keep up their beneficial activities over time and makes the microbiome resilient – it’s in our own hands to take care and become strong and resilient from the inside out. 

It is important to mention that we cannot expect that any simple intervention by itself, such as a particular diet, will optimize your gut microbiome, while not paying attention to all the other factors that influence gut microbial function, like the influence of unhealthy gut reactions associated with anger, anxiety, and our daily stress. 

Meaning simply eating probiotic foods such as sauerkraut, kimchi while continuing a high-animal fat, high sugar diet will not do the trick. Furthermore, drastic diet changes such as becoming gluten free, no fat, or only raw food are also not considered to be the change you may need. None of these interventions by themselves will improve the chronically disturbed connection between your gut and your brain. 

Science clearly points it out more than ever that changing your diet is not enough. We need to modify our way of living and working as well, I truly believe now is the chance to work on that more than ever before. 

Stay tuned within the gut-mind journal to learn more about this fascinating topic and how you can take your gut-immunity in your own hands. 


  • Emeran Mayer, The mind-gut connection, 2016
  • Rodney dietert (PHD), The human superorganism, 2016 
  • Hartmann, A. L., Behrendt, R. A., & Frøst, M. B. (2019). Fermentation as a driver for food innovation
  • Breidt, F., McFeeters, R., Perez-Diaz, I., Lee, C. (2013). Fermented Vegetables. Food Microbiology: Fundamentals and Frontiers 

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