For those who follow health news, you might be familiar with words like ‘probiotic’, ‘kombucha’ or even hard-to-pronounce bacterial names like bifidobacteria or lactobacillus. Gut-related messages are everywhere, both in popular media and in science too. With the arrival of so many new supplements, health drinks and advertisements promising to heal all of our health woes (by correcting problems we didn’t realise we had), it can be difficult to understand the real function and importance of the bacteria that populate our guts. Here we provide a back-to-basics introduction on the gut microbiome, and why it is important to your health.

What is the Gut Microbiome?

Your ‘gut microbiome’ is made up of the trillions of microorganisms and their genetic material that live in your intestinal tract. These microorganisms, mainly comprising bacteria, are involved in functions critical to your health and wellbeing. These bacteria live in your digestive system and they play a key role in digesting food you eat, and they help with absorbing and synthesising nutrients too. Gut bugs are involved in many other important processes that extend beyond your gut, including your metabolism, body weight, and immune regulation, as well as your brain functions and mood. There are many factors that influence the type and amount of bacteria we host and although most of us belong to a certain ‘enterotype’ – similar to having a certain blood type – each person has a unique bacterial footprint.

How does the Gut Microbiome Develop?

Your gut began to populate with bacteria very early in life. Indeed, some research suggests that this begins while we are still in the womb. When you’re born, there are many factors that influence the types of bacteria that will live and flourish in your gut – the genetics and health of your parents, whether you are delivered vaginally or by caesarean, and if you’re breast or bottle-fed. As you grow, there continues to be many things that can shape the bacteria that live in your gut. Some of these things are difficult to change, like genetics, stressful events or illness, but some are factors we can modify or control, such as our lifestyle behaviours – particularly what we eat.

What is a ‘Healthy Gut’?

We all live our day-to-day lives in different environments with different combinations of habits and surroundings. Because of this, each of us has a gut microbiome that looks at least slightly different to that of our parents, siblings or overseas friends – your microbiome is like a bacterial fingerprint, specific to you. For this reason, and also because there is so much about our microbiome that we have yet to fully understand, it’s difficult to say exactly what makes up a healthy gut microbiome. Generally speaking, a healthy gut itself has a barrier that is effective at keeping the contents of the gut, such as its microbiome, undigested food particles and toxins, from escaping into the bloodstream. A healthy gut has several other important jobs, including helping to fight off infection, as well as performing all of its usual digestive and regulatory functions, like absorbing and synthesising nutrients that are essential to keeping your body running at its best.

At the Food & Mood Centre, we tend to think, based on the existing evidence, that having lots of different, diverse types of bacteria living in our gut is a good thing. Such diversity may mean that your gut is in a better position to fight off and resist pathogens. Plus, if one strain of bacteria is for some reason unable to do its job, then another similar type can step in and keep things running smoothly. We do not yet know how, exactly, to ensure or even to measure a healthy gut microbiome and for now the health of the gut is best measured by how well it is performing its important jobs, rather than a specific prescription of types and amounts of bacteria. This means that instead of focusing on a specific type or amount of ‘good bacteria’, you might like to focus on broader behaviours that promote a well-functioning gut microbiome, like eating a healthy diet, having adequate exercise and sleep, and reducing your exposure to stress.

What is ‘Dysbiosis’?

In some instances, the gut microbiome becomes imbalanced or disrupted – this is called dysbiosis. This can be caused by lots of things, including stress, illness, overuse of antibiotics, or unhealthy eating. In fact, diet is the most important modifiable factor affecting the composition of bacteria living in our gut. Eating a diet composed many ultra-processed foods, and not having enough healthy whole-foods, appear to compromise the barrier lining our gut. If your gut barrier is weakened, then small particles like bacteria or small bits of food, are able to escape into your bloodstream, where they are marked as intruders and trigger your immune system into action. This is known as ‘Leaky Gut’ and there is rapidly expanding evidence for this as a factor in disease. Continuous immune activation and the inflammation that goes with it puts us at risk for a range of diseases and can compromise both our physical and mental health.

What can I do?

Happily, there is good evidence showing that there are several things you can do to keep your gut microbiome healthy, balanced and functioning optimally. How you eat, your exercise habits, and how frequently you take antibiotics are examples of happy-gut factors within our control (here’s more about the influence of a diverse diet, exercise, and antibiotic use on the microbiome). Research happening now at the Food & Mood Centre will help us all to understand how to prevent or treat disorders that are related to gut health.


  • The gut microbiome is made up of billions of bacteria and other microorganisms that co-exist with other human cells in the large intestine
  • The gut microbiome helps with digestion, metabolism, immune function and brain health
  • Our gut microbiome begins to develop in very early life, and is influenced by genetics, delivery method, age, stress, illness, environment, medication use, and diet
  • There is no one ideal ‘Healthy Gut’. Everyone’s gut is different, and it’s important that bacteria are able to function at their best, rather than having specific types and numbers of bacteria
  • The ‘balance’ of our gut can be disrupted by several factors, and this can promote inflammation – a risk factor for physical and mental disorders
  • There are several things that we can do to help our gut microbiome become or remain healthy and balanced; many of these are discussed in our other articles!