top of page
  • Dr. Sarah Bray & Amy Loughman

Gut Microbes & Your Health 101

Updated: Jan 9, 2020

So…what is the gut microbiome anyway?

The gut microbiome is the combined genetic material of a community of microorganisms that live in various parts of the digestive tract - mainly in the large intestine. It is made up of mostly of bacteria, and also archaea, viruses and fungi. If we’re getting technical, the microbiota are the little creatures themselves, and the microbiome is their genetic material.

It turns out that almost every crevice and surface of the human body has its own microbiome, including the skin, lungs, mouth and even belly button. Each of these communities of bacteria and other microorganisms are considered important for health and disease. The gut microbiome is particularly interesting because it has been linked to diseases that occur all around the body, not just in the gut. Although we don’t normally think of ourselves as being made up of bacteria, our microbiome is definitely a part of us, and is often termed ‘the forgotten organ’. In fact the human body is approximately 50% bacterial cells! (Some earlier estimates were as high as 90%).

Salad. Photo credit: mindbodymicrobiome

How does our gut microbiome affect us?

In so many ways! The gut microbiome has been found to affect a huge number of physiological processes around the body.

Some of the key areas that the gut microbiome is known to interact with are digestion and metabolism, the immune system, and brain function. How does this all happen from the gut? Microbiota produce small molecules called metabolites that travel around the body and ‘speak the language’ of the various systems in the body.

A specific group of metabolites - neuroactive metabolites- can be produced by gut microbiota to influence brain function and our behaviour. These include serotonin and dopamine, two mood-regulating neurotransmitters. Other brain chemicals involved in social behaviour and learning are also being investigated for their relationship to gut bacteria.

Gut bacteria impact immune function in a number of ways. The first is just by making sure that pathogens we are exposed to (such as by eating something contaminated) don’t have anywhere to thrive. If a defensive army of good bacteria are already living throughout the digestive tract, then there won’t be space for pathogens to take hold and make us unwell. The richer the microbial community is, the better able it is to perform all the defensive immune functions to keep you well. Also, some cells in the lining of the gut regulate the development of the immune system, training it to recognise which foreign matter is safe and which needs to be dealt with. Early exposure to safe bacteria in the gut microbiome helps to teach the immune system how to tell the difference. By the way, a major reason for the rise in autoimmune conditions such as asthma and type 1 diabetes (where the immune system mistakes a part of the body for an invader and attacks itself), is thought to be the radical increase in hygiene and therefore decrease in exposure to harmless bacteria.

What is the link between your gut microbiome and obesity?

There are a few different ways that the gut microbiome is implicated in obesity. One way is about how much energy we extract from the food we eat. Becoming overweight or obese is more than just a simple case of calories in, calories out. Mice bred to have a genetic predisposition to obesity have a gut microbiome that have increased metabolism of carbohydrate (and probably other types of) nutrition. Basically, these mice extract more nutrients from the chow they consume than normal weight mice, thanks to their microbiota.

This microbiome-related difference in metabolism has also been shown in human studies. There is at least one documented case study where a faecal microbiota transplant administered for a nasty gut infection* has inadvertently resulted in obesity in a previously healthy-weight person. Also in Kwashiorkor, which is a particularly severe type of malnutrition, the microbiome is considered a main culprit for the loss of body mass that occurs. Mice given microbiota from children with this condition lose body mass on a standard diet, whereas mice with microbiota from healthy children maintained normal weight. (Science, always so fascinating hey!)

Kimchi. Photo credit: mindbodymicrobiome

Another way that the gut microbiome is linked to obesity is about the foods we choose to consume. Different bacteria thrive on different types of foods. So if we regularly feed our gut bugs pizza and chips (for example), the bacteria that do well on this diet will thrive, and those that prefer green vegetables will not. And because of the evolutionary drive to survive, those pizza bacteria are going to do what they can to be fed next time. How? By sending reward signals up to your brain when you eat their tucker. Pizza - bing! Chips - bing! Salad - boo (or just less bing)! This in turn helps those pizza cravings. Yes, your gut talks to your brain. Next time you feel like a Hawaiian with extra cheese, you can wonder if it is really you that feels like it, or those microbial critters inside...

* Faecal (poo) microbiota transplant is mostly used for severe, antibiotic-resistant bowel infections such as Clostridium difficile and occasionally for inflammatory bowel diseases. Because of how much is still unknown about the impact of the microbiome on human health, it’s not a treatment that is done without a pretty good reason. There is talk of transplants for all kinds of other diseases, even those unrelated to the gut, but so far there isn’t good clinical evidence for the safety or efficacy of this.

What does a healthy microbiome look like? And how do you know if you have one?

So far, the science indicates that a more diverse microbiome (a wider range of different types of bacteria cohabiting together) is better for health.

The gut microbiome of people with serious illness (e.g. colon cancer) are less diverse than those people without such illness. Also, hunter-gatherer societies who aren’t plagued by modern diseases such as diabetes and obesity seem to have a much more diverse gut microbiome. This is thought to be due to lifestyle factors such as their high fibre diet with no processed foods. However there are many versions of ‘healthy’ and individuals differ a lot, and our microbiome is equally unique. Your microbiome is affected by how you were born (vaginally vs C-section), what your mother ate during pregnancy, how you were fed as an infant, what you ate and whether you had pets in childhood, the antibiotics you have taken and many many other factors! One possible reason that a more diverse microbiome might be better for health is that the microbiome is able to perform more functions effectively. For example, as mentioned above, the gut is the host of a lot of immune system activity, and the microbiota play an active role in this.

What you can do to improve the health of your microbiome?

The great news is, your gut microbiome is kept healthy by many of the same things that nourish your body more generally! A balanced diet, regular activity, adequate sleep and not too much stress.

Pollan quote. Photo credit: mindbodymicrobiome

There are a couple of types of foods that you can eat to significantly improve the health of your gut microbiome, which are also beneficial to your overall health at the same time. These types of foods can be classified into two groups: PRObiotics & PREbiotics.

You may be familiar with the concept of consuming probiotics to help promote gut health. Consuming probiotics is a way to try to introduce new healthy bacteria to your gut to increase the diversity of the microbiota and to create an environment that is more difficult for harmful bacteria to colonise. There are many sources of probiotics, from fermented foods such as yoghurts, kimchi, sauerkraut and kefir to probiotic supplements available at the Pharmacy. Many probiotic bacteria only survive transiently in your gut, but can be particularly beneficial to consume after taking a course of antibiotics for example, which while obviously important for treating the infection it was prescribed for, often has a side effect of killing many of the beneficial gut microbes. Probiotics can help with re-colonising the gut with some healthy bacteria, however it is important to make sure you are also regularly consuming the other type of food - which can be referred to as prebiotics - in order to maintain the healthy bacteria once they are in your gut.

Arguably prebiotics are the most important type of food to be eating to promote a healthy microbiota and overall good health. Many of the ‘good’ bacteria in our gut thrive on components of dietary fibre that we (the ‘host’) can not metabolise/absorb. Western diets are typically full of processed foods, high in sugars and fats and very low in dietary fibre. If we don’t provide the bacteria with enough fibre it can lead to them trying to obtain their nutrients by eating the protective mucous layer that lines our gut instead, which can have many undesirable downstream effects. By eating a diet that contains a lot of fresh vegetables, fruits, legumes and whole grains we are providing our ‘good’ bacteria with all the dietary fibre and nutrients they need to function well - these foods can be considered prebiotic foods.

Further reading

If you would like to find out more about the gut microbiome, we would both recommend an interesting and easy-to-read book on the topic - “The Good Gut”, which is written by well-respected gut microbiome researchers Justin & Erica Sonnenburg.

If you would like to find out more about fermented foods, check out 10 Reasons Fermented Foods are Not Just Hype.

For more general information, recipes and inspiration about fermented foods, you might like to check out these websites:

For readers in Australia, there are lots of local producers of quality ferments, usually found in your local health food store or farmers’ market. Here are a few to get you started.

This blog story is a collaboration between Amy Loughman (MindBodyMicrobiome) and Dr. Sarah Bray (JetSetGo Fitness). We initially connected via Instagram, but more recently met up in person when Amy was in Adelaide for the Frontiers of Science Microbiome conference (#AusFos16). Sarah Bray is a molecular biologist, and also JetSetGo Fitness owner and personal trainer.

This article has been co-posted with permission at Sarah's blog,

717 views0 comments

Recent Posts

See All
bottom of page