What is the Microbiome?

If you’ve done your research on probiotics, you will have, undoubtedly, come across the word “microbiome”. But what is the microbiome and why is it important to your gut health?

What is a microbiome?

You may not know it, but our bodies play host to a huge number of microorganisms. Ranging from fungi and bacteria to microbes and viruses, collectively they are known as the human microbiota, and the microbiome is all the genes your microbiota contains. In this definition, the microbiota is the community of microorganisms that live in and on a host, while the microbiome is the collection of their genomes (and the genes they carry) plus their functional activity in a specific environment. Scientists often debate how it should be defined, but a practical definition is useful in microbiome research. Still with us?! Don’t worry, colloquially, the microbiota and microbiome are often used like the same thing. So, all you need to really understand is that the microbiome is a collective term for all the microorganisms in your body.

What you do need to know is that 95% of them live in our gastrointestinal tract, i.e. our gut.

Now, you may think that microbes are dangerous and, in some senses, you’d be right - some microorganisms are harmful. Some microbes, called pathogenic microorganisms, definitely are and can make you sick, but others are very useful indeed and should be cultivated for good gut health. For example, some microbes are responsible for programming the immune system, providing nutrients for our cells and even preventing harmful bacteria and viruses from spreading. These microbial interactions support digestive processes, shape metabolic activity, and help the host maintain gut health and broader human health. They also provide signals that help the host’s immune system respond appropriately.

So, where do these microorganisms come from?

Research suggests that when babies are born, the actual process of birth has a huge role to play in kick-starting microbiota development in the human microbiome. However, over the years, our microbiomes change a lot due to several factors such as our environment, long-term diet, stress and the drugs we take, such as antibiotics. Environmental factors across the wider environment such as food choices, hygiene, infections, and medicines can affect microbiota composition, microbial diversity, and the risk of dysbiosis linked to disease. Other factors, such as contact with other people, animals, and environmental microbes, can also affect which organisms take hold. So the microbiome we’re born with is not the one we end up with in later life - microbiota composition and diversity shift over time.

In recent years, the specific microbiome in the gut has received a lot of attention, but did you know that you also have microbiomes in different parts of your body? The gut, skin and even vagina all have their own microbiome made of distinct microbial communities of microorganisms that do very different things. These microbial communities vary between individuals, and their composition and diversity are associated with local conditions in the environment and the host. Different species of bacteria, fungi, and other organisms can dominate in different body sites, and those species can change over time. For example, recent studies suggest that bacteria commonly found on the skin can protect against certain skin cancers, showing how microbial interactions can affect disease risk. Fascinating.

Now, for the most important bit, what can you do to support the good microorganisms in your microbiome? This is where prebiotics and probiotics come in - both are used to support microbiota composition and microbial diversity. PREbiotics are the foods microbes need in order to thrive and are found in things such as fibre and fermented food. PRObiotics are the microorganisms themselves which you can add to your gut to boost the number of good bacteria present. Used consistently, the right prebiotic food and probiotic strains can help support microbiota development, improve microbial diversity, and reduce dysbiosis that is associated with digestive disease in some individuals.

The Gut Microbiome

Most of the microbes in your gut are found in a specific part of the large intestine called the cecum, where bacterial microorganisms are especially dense. There are up to 1,000 species of bacteria in the gut microbiome, with each of them playing a different role in your body and contributing to microbial diversity. Alongside bacteria, the gut microbiome includes other organisms such as fungi and viruses, and their combined genomes contribute to key functions. For the most part, these bacterial microorganisms are extremely positive for your overall health, but some (pathogens) can cause disease if they start to outnumber the good bacteria. When the microbial community shifts, often described as dysbiosis, pathogenic microorganisms can gain a foothold, and that change is associated with inflammatory disease and poorer gut health.

Why is gut microbiome important?

Research has shown that the gut microbiome is responsible for controlling the immune system and the nervous system, which controls brain function, through microbial interactions with the host. So, it’s incredibly important to look after your gut microbiome as it affects key bodily functions and influences your overall health. Microbiome research is helping improve our understanding of how gut microbiota interactions with the host immune system and nervous system can affect human health and disease.

So, how is the gut microbiome formed?

Research suggests that when babies are born, the actual process of birth has a huge role to play in kick-starting gut microbiota development and early microbial colonisation. However, as we age, it will change and diversify, meaning it starts to contain lots of different types of microorganisms. This development involves complex microbial interactions as new microorganisms arrive, and the community’s functional and metabolic activity changes with age. Naturally, lots of the foods and drugs we consume will have an impact on your gut microbiota, affecting microbial composition and metabolic activity. These influences can alter which species thrive in the intestinal environment and how microbial communities use available food. Environmental exposures in early life and beyond can affect gut microbiota development, with changes in composition and diversity that are associated with later health outcomes. For example, when babies drink breast milk, good bacteria found in the milk begins to grow inside the intestines called Bifidobacterium. They then go onto digest the healthy sugars in breast milk that are important for growth, supporting gut development.

So, what can you do to ensure your gut microbiome stays healthy?

Unsurprisingly, what you consume plays a big role in maintaining a balance of good bacteria in the gut and supporting microbiota health. For some people, when that balance is upset, they may start experience stomach cramps, bloating, constipation, and diarrhoea. Symptoms can reflect changes in microbial composition and activity, and in some people may be associated with digestive disease. In some cases, adjusting your diet to include more foods that contain lots of gut-friendly bacteria such as fibre and fermented food can help, but for most people, taking a probiotic is a good idea to support microbiota composition.

If you’d like to find out more about how to boost your gut’s microbiome, check out our blog for more expert advice and microbiome research. Microbiome research also looks beyond the human microbiome: plant and animal microbiota respond to environmental conditions, and these host–microorganisms interactions can influence health and disease across whole systems.