What is the composition of our Gut Microbiome and what is the role of the major species?

Gut health has become an increasingly popular topic in recent years, driven by the rise of the wellness industry and a growing body of research exploring the role of our gut in overall health. When we talk about ‘gut health’, many people may assume that we are only focusing on our stomach – however what most people do not realise is that our ‘gut’ refers to the entire system and pathway that food travels down, starting at the mouth and ending at the anus. We also sometimes refer to this as our ‘digestive tract’. 

The gut microbiome

Within our gut lives over 100 trillion different ‘microorganisms’, which include things like bacteria, fungi, viruses and archaea. These microorganisms play an important role in our health, helping with things like our digestion, supporting our immune system and contributing to metabolic functions. Gut microbiota composition varies along the digestive tract – for example, the small intestine may contain less microbes compared to regions like the large intestine, due to factors like pH levels, transit time and bile concentrations. 

Let’s take a closer look at some of these microorganisms and their specific roles.

Important note: Our gut microbiome can vary hugely from person to person, depending on factors like diet quality, genetics, lifestyle and things like stress. 

Bacteria

Bacteria make up the majority of the microorganisms in our gut microbiome, and for this reason, they are the most well studied of all the microbes too. When it comes to groups or different classifications of bacteria in our gut, we often see that the two main “phyla” present there are Firmicutes and Bacteroidetes. 

Firmicutes

There can be hundreds of different types or ‘genera’ of Firmicutes found within our gut such as Clostridium, Lactobacillus or Enterococcus. Each one of these can be broken down again into various different ‘species’ with different roles helping to boost (or even harm) our health. For example, some healthy people may find higher amounts of Clostridium butyricum in their gut which acts as a probiotic, helping to also break down and ferment fibre we eat to then produce a health boosting molecule called butyrate.

Butyrate is a short chain fatty acid that can help to support the gut barrier and help to reduce inflammation. Other species of Firmicutes like Lactobacillus acidophilus may lower pH in parts of the gut, reducing the ability for other harmful bacteria to grow, and may even help to lower cholesterol in the body. We may also see various strains of Enterococcus faecalis (which makes up around 1% of an adult’s gut) helping to support our immune system and acting as a probiotic. 

Bacteroidetes

There are many different types or ‘genera’ of Bacteroidetes found in our gut, but the most common ones we see in healthy people are Bacteroides and Prevotella. Some of the main species include Bacteroides vulgatus, Bacteroides uniformis and Bacteroides fragilis, which can provide protection from some harmful bacteria, help to supply some nutrients for the gut and also may have some anti-inflammatory effects.

Prevotella copri is the most common type of Prevotella found in the gut and may improve insulin sensitivity, help to break down fibre in our diet, and there is some evidence that specific strains present in mothers during pregnancy may potentially play a role in protecting against allergies in their offspring. 

Archaea 

Included as part of our gut microbiome are also archaea, which share some similarities with bacteria. Archaea and bacteria have a bit of a co-dependant relationship; bacteria produce compounds that help archaea survive, and archaea help to create the right environment for bacteria to thrive in. Archaea typically make up around 1.2% of our gut microbiome (but this can vary from person to person), and research is slowly discovering that archaea may support our health by:

1. Helping with digestion. Species like Candidatus M. intestini and Methanobrevibacter smithii, (which is estimated to make up as much as 10% of the gut microbiome in healthy adults), can absorb some of the hydrogen produced by gut bacteria which may help to aid digestion. 

2. May play a role in reducing cardiovascular disease risk. In some studies, there have been links showing that some species of archaea may play a role in preventing something called ‘trimethylamine oxide’ from forming in the body – which is a compound linked to increased cardiovascular disease risk. 

It’s also important to note that not all archaea are good, and many have also been linked to harmful conditions and diseases. In order to boost the good type in the gut, it’s best to eat a balanced diet with plenty of dietary fibre and plant variety. 

Fungi

Although we may associate the word fungi with things like mushrooms found outside in nature, did you know that fungi can also be found hiding in our gut too? Candida albicans is the most prevalent fungal species within the gut microbiome, and it can both boost our health (for example helping to educate our immune system) and also cause harm (particularly when we see an overgrowth of it in parts of the gut). 

Viruses

We refer to the community of viruses living in our gut as the “gut virome”, and this is an important regulator of our immune system. Although many of the viruses in the gut can cause harm, there are a few which may benefit our health too.

For example, it has been found that some viruses may play a role in helping to control inflammation, and others play an important role in shaping the composition and evolution of our gut bacteria. The adult gut virome is generally stable in healthy people, although it can be altered through things like a poor diet, unhealthy habits like lack of movement or access to nature, or even disease. 

How to boost the gut microbiome

If you are someone looking to boost the health of your gut microbiome, then I recommend eating more plant foods, getting in 30g of fibre (or more) each day, getting outside into nature, eating more fermented foods like kimchi, miso, Biotiful Kefir and sauerkraut, as well as reducing stress levels.