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The Gut Microbiome

A graphic image of the intestines and the words My Amazing Body
How much do you know about the microbes that live in your gut?

My Amazing Body is a podcast where we explore interesting, unknown and misunderstood parts of your body with help from medical experts and stories from real Queenslanders.

This episode is all about your gut microbiome – the collection of bugs that live in your gut. With clinical dietitian Abigail Marsh, we talk everything from creating a healthy environment for your gut microbiome, to whether the microbes in your gut can control you and why some people are getting poo transplants to help gut health. Sarah, a young Queensland woman, tells us about the after-school job that wreaked havoc with her gut.

Meet our guests

Our guest expert, Abigail Marsh, is a clinical dietitian at Royal Brisbane and Women’s Hospital.

A picture of Abigail Marsh

Episode materials

Audio is great, but some things are best seen as well as heard. These materials provide more information about topics we touch on in the show.

A diagram of the digestive system

A diagram showing the digestive system

Theodor Escherich

A picture of Theordor Escherich

Episode transcript

Host: Abigail Marsh is a clinical dietitian working at Royal Brisbane and Women's Hospital. She sees patients who have serious tummy troubles, like IBS or inflammatory bowel disease. In a moment between consultations, we're sitting in an office in the basement of the hospital, and she's telling me about a new type of therapy her team are trialling in patients with recurrent C. diff infections.

Abigail: In the area I'mworking at, faecal microbial transplant is becoming a hot topic. And that's been shown to be the most effective therapy for what we call recurrent C. diff infection, which is basically when a person has really bad diarrhoea due to an infection.

Host: Faecal microbial transplant - yep, you heard that right. In lay person's terms: a poo transplant.

Abigail: A faecal microbial transplant, so that's basically a poo transplant. It's when you get a healthy poo sample from a donor with a healthy gut microbiota and this piece of poo is inserted into the person's gut. And that basically stimulates the good bacteria to grow and can help treat infections or disturbances in the gut microbiota.

It is quite gross, but it can be important, especially for those people as I mentioned who do have recurrent C.diff infection that is the go-to treatment.

Host: Hi, I'm Elise and welcome to the latest episode of the My Amazing Body podcast, where we explore interesting, unknown and misunderstood parts of your body. Today, we're learning about your gut microbiome.

Gut bacteria, or more specifically gut microbes, are tiny microorganisms that live in your gut. They're alive and, as we’ll soon find out, are usually more your friends than your foes. As a group, we call them your gut microbiome.

News readers (overlapping): Breaking news. Researchers discover almost two thousand new gut bacteria. Evidence mounts that gut bacteria can influence health. 7 things you can do now to promote healthy gut bacteria. Could gut bacteria be linked to your mental health?

Host: The gut microbiome has become a hot topic of conversation in the health science world in recent years, with research beginning to show that your gut microbiome might play a role in everything from obesity to mental wellbeing. From your stomach right through your intestines, your unseen gut bacteria are having a big impact on your life. So, what are the bugs living in your guts, why are they important, and are they secretly controlling you? Are they worth getting a poo transplant over?

Abigail: I'm currently working in surgery and doing a functional gut clinic. I'm also doing my PHD part time at the moment and I'm looking at a dietary intervention in inflammatory bowel disease and what the effects are on patient symptoms, quality of life, inflammation and their gut microbiome.

Host: That's Abi again. When it comes to your gut, Abi and the teams she works with are keen to keep your gut healthy. Because when your guts are good, you're more likely to be more healthy overall. A lot of your gut health depends on the health of your gut microbiome.

Abigail: So, there are approximately 100trillion microorganisms living in the human gut. Most of them are bacteria, but also fungi, viruses and protozoa.

Host: Since the invention of the microscope in the late 1500s and the discovery of microorganisms in the 1600s, we've known that there are tiny living creatures that exist beyond our eyesight. It wasn't until the mid-1880s, however, that an Austrian doctor called Theodor Escherich, who was studying diarrhoea in children, first discovered a living bacteria in the human gut. The bacteria he discovered was named Escherichia coli, or as you might know it, E. coli. Since then, we've learned that the microbes in our gut play a complex role in our health.

Abigail: So, we have a two-way relationship with our gut microbiome. Diseases can cause changes in microbiome. However, some changes that are initiated by say, poor diet or the environment, can cause disease. So, it's a bit cyclical.

Disturbances to our gut microbiota have been shown to contribute to many conditions so for example when looking at chronic diseases, such as obesity, inflammatory bowel disease, diabetes, metabolic syndrome, liver disease – they've all been associated with imbalances in the human microbiota. Numerous other diseases have been associated with this disbalance, so when the basically bad bacteria take over from the good bacteria, this can lead to infection, respiratory disorders, autoimmune diseases, irritable bowel syndrome and even mental or psychological disorders.

Host: Good bacteria and bad bacteria - it sounds simple, right? But is the key to our gut health as basic as a childhood story with goodies and baddies?

Abigail: Well there is good and bad bacteria so to speak. For example, the good bacteria in our body often have an anti-inflammatory effect. So, an example of one of these bacteria would be the Bifidobacterium. So, you might have heard of that because it's often heard of because it's often found in fermented foods such as yoghurt and cheese. And then other bacteria can have a more negative effect on the body and is what we refer to as pro-inflammatory for example bacteriaroids and clostridia. Some of these have been associated with intestinal infections, however, it's not that simple, nothing really about the gut microbiome is simple. When we consider a healthy gut microbiome, it's more one when there's a high alpha diversity, which is microbial richness. And there is higher ratios of the good to bad bacteria. So, disease occurs when the good bacteria is no longer able to control the bad bacteria.

So, when talking about what is a healthy gut microbiome, scientists usually look at what they call the alpha diversity. So, this is basically the number of different species living in the gut and there are trillions of these.

Host: They say that variety is the spice of life, and it turns out that's true for your gut microbiome, too. So, how do we make sure we have a diverse gut microbiome? Abi says we need to think about the big picture when it comes to making sure our gut microbiomes are healthy and diverse.

Abigail: The difference of the microbiome in adults is related to things like our diet, how old we are, where we live, any medicines we are taking and sort of things in the environment like any pesticides or pollution. So, we know that the gut microbiome is modified since birth, so whether you have a C-section or a vaginal delivery, that can influence our microbiome. And then as a baby if we're formula fed or if we're breast fed. And then as we age, our diet, antibiotics and illness can all influence the gut microbiome.

Stress, as I mentioned, can cause disturbances in the gut microbiome, so trying to think about ways to de-stress. Other things that affect gut health are smoking – that can definitely reduce the number of good bacteria and promote the growth of the bad bacteria.

Host: If you're trying to improve your gut health, looking at what you eat is a great place to start. There are lots of foods out there that are marketed to be good for our gut health, but how effective are they. We asked Abi - should we all be on a yoghurt and kombucha diet?

Abigail: Ok so basically to get a healthy gut microbiota you want to have a balanced diet, which is what we're always told. It’s especially important to ensure that we have enough fibre, especially what we call prebiotic fibre. So prebiotic fibre is the fibre that passes through the gastrointestinal tract undigested and this stimulates the growth of good bacteria in the large intestine as it is fermented. This prebiotic fibre can also help suppress the bad bacteria and that promotes an optimal environment for good digestive health.

So, where can you find this good prebiotic fibre? It’s in lots of vegetables we eat, so green beans, asparagus, beetroot, even in garlic and onion. It's found in legumes, so chickpeas lentils, kidney beans. It can be found in some fruits, so apples, nectarines, peaches; in some of our breads and cereals, so couscous, oats, barley; and in cashews and pistachio nuts. However, if you have too much of this prebiotic fibre you'll probably know because you might get a lot of gas and bloating.

Another way to promote a healthy gut is by having probiotic foods. So, probiotics are found naturally in yoghurt, cottage cheese, pickled vegetables, kombucha is a health food on the market that I'm sure you've heard of that people are drinking lots of. And probiotics are basically live microorganisms that function like the good bacteria in the gut. So, this can help repopulate the beneficial bacteria, especially when you've had say a course of antibiotics or something that has suppressed this good bacteria, probiotics foods are good as they can help repopulate the good bacteria and decrease the bad bacteria.

It's really important that we get our prebiotics and probiotics from a range of places. If you just have kombucha alone, you might get lots of the good bacteria that’s caused by kombucha but miss out on all the other good bacterium which are needed for other functions of the body. So, it is really important that we do ensure we have a balanced diet, include lots of food groups and that will contribute to optimal gut health.

Host: Is there anything we should avoid if we're trying to look after our gut microbiome? Abi says the research is still developing, but there are a few clues about the food and drink we should limit for the sake of our gut health.

Abigail: If we want to look at the foods to avoid, as they can be detrimental to the gut health, recent evidence has said foods which contain lots of artificial sweeteners can reduce the diversity of the gut microbiome. So, food additives such as emulsifiers common in many processed foods, for example ice cream, have also been shown to reduce the gut microbiome diversity. And a diet which contains lots of animal products, such and meat and dairy, can also increase the number of pro-inflammatory microbes and decrease the good ones.

And in terms of fluid, water doesn't seem to have an affect either way, it's more things like the soft drink that can have an influence on the gut microbiota, especially those sugary, sugary drinks, can cause an imbalance.

Host: When was the last time you indulged in a little bit too much 'sometimes food'? You reached for that second donut or last Tim Tam, even though you knew you didn't really need to eat it, feeling like it was somehow out of your control. Well, studies are starting to show that it's possible that your gut bacteria might be giving you a helping hand when it comes to deciding when and what to eat.

Abigail: So, can bacteria control us? That's an interesting question that’s becoming more researched in recent times. So, there is strong evidence that shows that the gut microbiota plays a role in altering appetite signalling as well as increasing the energy extraction from the food and increasing the nutrient harvesting. There has also been some research that suggests that our gut microbiota may influence our food choices. So, the kind of method behind this is that the gut microbes may manipulate the host’s eating behaviour in a way to promote their fitness at the expense of our fitness. For example, eating more sugar may increase the bacteria that feeds on the sugar inside the gut and then this bacteria grows and reproduces more quickly which in turn this over-signalling causes us to eat more sugar. So, it becomes a bit of a cycle. However, this has been mainly shown in animal models, so there is no strong evidence I guess yet that we can blame our gut for making us eat that bit of cake to say, if you know what I mean.

Host: So, we've learned that our gut health depends on a lot of factors, like our diet, sleep and environment, and our gut health can affect everything from how well we feel to what food we might crave. It's a delicate balancing act, like being on a tightrope. What happens when that balance starts to get a bit off-kilter? We spoke to one Queenslander who found out the hard way.

Sarah: I was starting to get really bad reflux every day. My stomach just wasn't feeling the best. It would always be churning and eating would be like, not painful but it was just…something wasn't right.

Host: That's Sarah. Like a lot of Queenslanders, when Sarah was a teenager, she got a casual job to earn a little extra dough. In her case, it was literal dough as well as money - Sarah worked a few days a week at her local bakery.

Sarah: So, I started working at the bakery when I was about 15 and I was there until about 18. So, it was really difficult to not eat the freshly baked bread, it was really hard working when there was fresh bread being baked, like the smell of fresh bread is really tempting.

So, the girls that I used to work with, we decided to drink sugar-free soft drink to stop us eating so much food, as it was always in front of us. So, I got to the stage where I was drinking about one of the 1.25 litres of sugar-free soft drink per shift. So, I'd normally work about five days a week…that's a lot of soft drink.

Host: Sarah and her friends thought they were making a healthy decision. They knew that eating heaps of the tempting baked treats every shift wasn't a balanced dietary choice. But, in trying to correct that behaviour, Sarah learned that too much of anything isn't good for your gut.

Sarah: So, I guess we kind of thought that if we drank soft drink it would stop us eating, so we thought we were doing the right thing in terms of not gorging on food and just drinking soft drink to kind of suppress that hunger. But it turns out it wasn't so great, at the end.

So, I went to my GP who said I'd basically messed up the acidity in my stomach by drinking so much soft drink. So, I had to go on a course of tablets to bring that acidity down.

Host: Six years on and Sarah's still feeling the effects of her soft drink overload.

Sarah: And now I've had to be really careful of drinking soft drink because the acidity in my stomach is still very volatile.

Host: Beyond a hungry tummy rumble or the times you might feel a bit bloated and gassy after a big night, you might not pay much attention to your gut health. But, as we've learned, your overall health, and the health of trillions of microbes, depend on you being mindful of what’s going on with your gut.

Thanks for joining us for another episode of My Amazing Body. My Amazing Body is bought to you by Queensland Health. With special thanks to our expert guest Abigail Marsh, patient Sarah and my podcast colleagues - Lauren our researcher, writer and producer, Carol our audio technician, Helen on sound effects, Dan our music guru and the media team at Metro North Hospital and Health Service.

Last updated: 2 July 2019