Dr Alena Pribyl: What Is A Healthy Gut Microbiome?

By Women Love Tech
on 27 November 2018

When it comes to health, one of the emerging trends is to investigate the community of microorganisms that live in our gut, collectively called the gut microbiome. Over the last decade, thousands of studies have demonstrated there is a strong link between these microbes (or microorganisms) and our health. For example, the gut microbiome has been correlated to numerous physical and mental disorders including inflammatory bowel diseases, colon cancer, heart disease, arthritis, diabetes, Parkinson’s disease and even depression1. Studies are also showing the gut microbiome plays an important role in the development of the immune system during the first three years of life2. As a result, having a healthy gut microbiome is increasingly being identified as an important factor for maintaining overall health.

So, what does a healthy gut microbiome look like and how do we know if we have one? Unfortunately, there is no clear answer yet. Most of the bacterial species that live in our gut have yet to be identified and studied, meaning scientists do not yet know what role they may play in our gut. Research is progressing at a fast pace though and we are learning more about this important part of our body every day. Below are a few of the findings so far about what we do know about a healthy gut microbiome:

One size does not fit all

It is estimated that somewhere between 1,2003 to 40,0004 different bacterial species could inhabit the gut of people, globally. However, any one person will typically only have up to a couple hundred of these species. This means there is a large range of what a healthy gut microbiome can look like, and the microbial community that is healthy in one person can look very different from what is healthy in another person. This is in part due to the large variety of factors that can influence bacterial species in the gut such as diet, ethnicity, geography, medication use, and personal genetics among many others5–7, making everyone’s microbiome unique.

Function over form

Studies that use metagenomic sequencing, an advanced type of DNA sequencing, can look at all the genes within a bacterial species. These genes act as a blueprint for what a bacterial species can do, such as producing compounds linked to health and disease. By sequencing these genes, you can see what unidentified species are capable of, even if the species has not been grown in the lab to be studied. This research has found that the function of gut bacteria tends to be more similar across individuals compared to the species present,8 suggesting that understanding what your gut bacteria can do as opposed to who they are might be more important in deciphering what is a healthy gut microbiome. If your gut microbiome lacks some of the well-known species associated with health, it could very well be you have other species performing the same function that are not as well studied.


As scientists learn more about the different functions of gut bacteria, important functions associated with health have surfaced. One well-studied function is the ability to produce a short chain fatty acid called butyrate, the main energy source for the cells lining our intestine. Butyrate plays an important role in maintaining the intestinal cell barrier9 and has anti-inflammatory effects in the gut10.  Studies have shown that increasing your intake of prebiotic fibres, especially resistant starch11, can increase butyrate production by the gut microbiome.


Another important function in a healthy gut microbiome is the ability to break down fibre. Fibre is the main energy source of gut bacteria, who break it down into beneficial metabolites such as short chain fatty acids and B vitamins12. An insufficient amount of fibre in the diet can result in a reduction of beneficial bacteria that break down fibre and an increase in gut bacteria that can use alternate sources of energy, such as the mucus lining the gut13.

Microbial diversity

Although the identity of a bacterial species may not be as important as their function, it does appear that how many different bacterial species you have and how evenly distributed they are is important. This is called diversity and numerous studies have indicated that healthy individuals have a more diverse gut microbiome than unhealthy individuals14.

Pathogenic or pro-inflammatory species

A high number of pathogenic or pro-inflammatory species is often associated with an unhealthy gut microbiome. Many of these species can produce toxins or other compounds that can trigger an inflammatory immune response, such as the Shiga toxin in some strains of Escherichia coli or specific types of lipopolysaccharides found in species from the bacterial group Gammaproteobacteria15.

If you are interested in learning who is in your own gut and what they might be doing, it is possible to have your gut microbiome sequenced by a commercial company. Most companies can tell you who is in your gut, but only a few can also tell you what the bacteria might be doing (e.g. the presence of genes involved in butyrate or fibre degradation). For this, a test that uses metagenomic sequencing methods is necessary. Because there is still so much to learn about what makes up a healthy gut, these tests are not diagnostic and for informational use only.

Eating a wide variety of foods high in fibre is important for a healthy gut

There is still much to learn about what makes a healthy gut microbiome, but what is clear is that diet is a very important factor. In particular, consuming a wide variety of foods high in fibre is necessary to promote microbial diversity and the growth of gut bacteria that produce compounds associated with health. 


  1. https://doi.org/10.1016/J.ENG.2017.01.008
  2. https://doi.org/10.1038/nm.4142
  3. https://doi.org/10.1038/nature08821
  4. https://doi.org/10.1097/MOG.0b013e3282f2b0e8
  5. https://doi.org/10.3402/mehd.v26.26164
  6. https://doi.org/10.1038/s41591-018-0210-8
  7. https://doi.org/10.1016/j.cell.2014.09.053
  8. https://doi.org/10.1038/nature11550
  9. https://doi.org/10.1194/jlr.R036012
  10. https://doi.org/10.1038/ctg.2015.34
  11. https://doi.org/10.3945/jn.110.128504
  12. https://doi.org/10.1007/s00394-017-1445-8
  13. https://doi.org/10.1016/j.cell.2016.10.043
  14. https://doi.org/10.1186/s13073-016-0307-y
  15. https://doi.org/10.1016/j.jaci.2014.09.036

Women Love Tech would like to thank Dr Alena Pribyl, Senior Scientist at Microba, for this article



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