What is the gut microbiome and why should I care?

You probably have been following me on my blog or on social media for a while now. And maybe you remember reading my words “be nice to your bacteria” somewhere. And you probably also thought “what does she mean by that?”.

Well, so many things.

Today, I would like to start a blog series in which I will explain what it means to be nice to our bacteria and why we should be nice to our bacteria. In this and the following two articles I will discuss the gut microbiome, its function and how we can make sure the bacteria in our gut are well fed. 

So, stay tuned for the coming weeks by following my blog or social media!


Before diving into this little adventure, I have to admit that research about the gut microbiome is still in its infancy and some studies show controversial results. As always in research, we don’t know what we don’t know yet.

This means that some studies did not take into account all of the variables, just because there are so many and some become only clear later, which sometimes makes it difficult to come to one simple conclusion. 

However, here I will start with some simple facts and discuss what is certain amongst researchers.

What is the gut microbiome?

The gut microbiome is the microbial community that inhabits the gastrointestinal tract and comprises a diverse ecosystem of bacteria, viruses, fungi and archaebacteria. Since most studies try to understand the bacterial side of the gut microbiome and this is a blog about the bacterial world, I will solely focus on these little bugs. But please don’t forget, that there are many more players involved in all of the here mentioned processes.

The gut microbiome varies within each individual and depends on the socio-economic state, diet, age, geography, drugs, sleep and other environmental substances. Nevertheless, studies showed that each person’s gut microbiome is stable over time, even after antibiotic treatments, acute intestinal infections and modified diets. 

Generally, it is thought that the gut is a welcoming habitat for bacteria because of its temperature of 37C and a nutritious environment of partly digested food.

Surprisingly, there are still many bacteria that we are unable to research in the lab environment just because we don’t know what they need to actually grow outside of the gut. All we know about these bacteria is that their DNA can be found within the gut microbiome, so the chances are high that they actually live there.

Why do we know so much about the gut microbiome?

True, in comparison to other microbial niches within our body, the gut microbiome is probably the best characterised. But don’t forget, that this is relative; there are still so many unknowns about what is going on in our guts.

However, many studies now also try to characterise the microbiomes of other parts of our body, like different skin areas – imagine different organisms live on your feet than on your hand or under your arm pits, the ears or even eyes.

The fact that the gut microbiome has been mostly studied, if probably due to the accessibility of samples. The sample comes out of our body, so you can directly use it without swapping anyone. 

Second, the gut microbiome plays important roles in so many diseases that most research focuses on understanding the interplay between diseases and the gut microbiomes. All this is done to hopefully find cures or intervention therapies.

What does the gut microbiome do?

Almost every week a study is currently published that suggests that the gut microbiome could be involved in another function of our body. As I said, most of these correlations are not well explained yet, and a lot of research needs to be done to understand these correlations better. 

The gut microbiome plays an important role for our overall wellbeing. It protects us from pathogens, support our immune system and helps us digesting food,

Anyway, by now we know that there are a few important players of our gut microbiome that seem to be highly abundant in most people’s gut. These are Faecalibacterium, Roseburia, Lachnospiraceae, Eubacterium and Akkermansia muciniphila. All of these were so far shown to have beneficial functions in our gut and they help us to

  • protect the gut from colonisation by pathogens
  • digest complex sugars to so called short-chained fatty acids (SCFAs) 
  • support our immune system

Having defined the basics of the gut microbiome, in the next article I will explain in more depth how our gut microbiome protects us from colonisation by pathogens and how it helps us digesting foods. After that, we will explore how and why we should protect our gut microbiome.

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