In the previous article, we concluded that our gut microbiome helps us with three main functions. They help us digesting food, protects the host from pathogens and enhance the immune system.

To understand how exactly the gut microbiome helps the immune system, I would advise you to read other sources, as my knowledge on that area is rather limited.

In this article, we will focus on the other two roles of the gut microbiome.

Why is it important that the gut microbiome helps us digesting food?

Gut bacteria play a very important role in food digestion. Some of the foods that we eat, we can’t fully digest ourselves, like many complex sugars. In this case, the bacteria in our gut break down these indigestible molecules and produce compounds that we otherwise would not have.

For example, they produce gasses and certain molecules called short-chained fatty acids (SCFAs). While the gasses eventually make their way our of our gut, the SCFAs play important roles for our overall well being.

These SCFAs are super important to keep the gut-lining cells healthy, so to keep our gut intact. SCFAs also decrease the pH of the gut to inhibit growth of pathogenic bacteria. The SCFAs also strengthen our immune system and promote the growth of beneficial bacteria.

Additionally, SCFAs reach different organs of our body. Some studies even suggest that SCFAs have health benefits as well, but this needs further conclusions.

How does the gut microbiome protect its host from pathogens?

Now my favourite part – bacteria interacting with other bacteria :)

Our microbiota developed many strategies to ensure that any invading pathogenic bacterium feels very unwelcome in this new environment.

Imagine one single pathogenic bacterial cell somehow made its way to our gut where it encounters billions and trillions of bacteria that already live there. Our gut microbiota is already a settled community that interacts with each other and helps each other where needed. This one pathogenic bacterium has to face a huge war for food and space in order to settle down and to try to grow on its own. This exclusive effect of our gut microbiota is the first line of defence to keep the bad guys out.

Plus, our gut microbiota has its own metabolic activity that reduces the oxygen content in the gut. Not many pathogens can actually live in environments with low oxygen concentrations and will eventually die.

Also, some bacteria in our gut produce compounds that slow down the growth of pathogenic bacteria. This again stops them from settling down and getting comfortable in our guts.

Another strategy is that our resident bacteria actively try to kill these invaders. They can do this by producing toxic compounds that are lethal to the pathogen. Or, as you might be aware of by now, bacteria in our gut also carry some highly toxic and lethal weapons. Bacteria specifically aim these weapons to kill other bacteria.

So, these are the mechanisms that our resident bacteria use to get rid of invading pathogens, but in case a pathogen was successful in colonising our gut:

What does an unhealthy gut microbiome look like?

This is actually a bit of a trick question. As I said before, every person has a unique gut microbiome and we still don’t really know what the “normal” gut microbiome actually looks like.

Or better, what are the perfect conditions for a normal and healthy gut microbiome to grow?

What we do know by now is that when it comes to the gut microbiome, diversity is key!

To study this, researchers compare strains in the gut microbiomes from people with a specific disease (for example Crohn’s disease) with gut microbiomes from people that do not have that disease.

Generally, what they find is, that the people without the disease have a broader variety of bacteria living in their guts. So, somehow all those different bacteria grow together and work as a team to keep us healthy.

This means, one or two bacterial species are usually more present in the microbiomes of people with diseases. For example, the bacterium Faecalibacterium prausnatzi likely has beneficial effects on our gut health. However, in samples from many unhealthy people, the abundance of this strain is often reduced.

In other studies of patients with Crohn´s disease, researchers found increased levels of Escherichia coli populations. Here, it is not yet clear, what this means, as this bacterium usually lives in our gut.

This shift in our microbial gut flora is what researchers call a gut dysbiosis. However, whether this shift is the cause or the result of the disease is still not clear. My guess would be that it is kind of both, but let’s see what researchers will find out.

Generally, in a gut dysbiosis, bacteria that produce SCFAs are massively reduced. Similarly, quite often bacteria that degrade the mucus layer of the gut are increased. Our gut also needs the mucus layer to be healthy and intact, so its degradation is certainly not a good thing.

Gut dysbiosis was correlated with many chronic diseases so far, like type 2 diabetes, obesity, inflammatory diseases or Crohn’s disease, and many others. But again, it is not clear, whether such disease is the cause or the result of the gut dysbiosis.

Now you know why we need our gut microbiome and how it is protecting us from pathogenic bacteria. In the following article, I will explain how you can make sure your gut microbiome stays healthy.