Have you ever heard the phrase “be nice to your microbiome”?

(I tend to say that a lot ;) )

If so, have you then thought “what does this mean?”.

Well, this article will give you the answer to this question.

This article is the first part of my human microbiome series. Here, you will learn what the gut microbiome is and why it is crucial for our health.

Parts 2 and 3 will then discuss the function of the gut microbiome and how we can make sure the bacteria in our gut are well fed.

Before diving into this little adventure, I have to admit that research about the human 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. As you can understand there are so many and some become only clear later. This sometimes makes it really 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 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, 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. This is just because we don’t know what they need to actually grow outside of the gut. But we know one thing for sure: researchers found their bacterial DNA in human guts. So the chances are high that they actually live there.

Why do we know so much about this particular 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 intestines.

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 microbiome within the gut has been mostly studied, is 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. This is why most research focuses on understanding the interplay between diseases and gut microbiomes. All this is done to hopefully find cures or intervention therapies.

What does the gut microbiome do?

Almost every week a study on the human microbiome is currently published. This suggests that our microbiome could be involved in so many other functions within 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.

Anyway, by now we know that there are a few important players in our microbiome that seem to be highly abundant in most people’s gut. These are Faecalibacterium, Roseburia, Lachnospiraceae, Eubacterium and Akkermansia muciniphila. All of these seem 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

Part 1 here defined the basics of the gut microbiome. In the next article, we will discuss how the microbes in our gut protect us from colonisation by pathogens and how it helps us digest foods. After that, we will explore how and why we should protect our gut microbiome.