How Bad Gut Bacteria Can Cause Serious Diseases

This article is a condensed version of an ABC Catalyst program dated 14 August 2014, titled Gut Reaction Pt 1. We have taken out sentences and phrases to shorten the article without detracting from its content, and added headings. You can watch the full TV program, or read the entire transcript, at

In our next blog we will cover the subsequent program, including how good bacteria can be used to treat diseases.

Could our food be making us sick – very sick?

In the first of this two-part special, Dr Graham Phillips reveals new research about the interplay between food and the bacteria deep within our guts.

I think this is one of the biggest developments in medical research. I really think we’re encountering a revolution. Maybe we can prevent diseases by simply changing our diet.

The remarkable new discoveries are telling us that our current eating habits could be making us sick. Very sick. Indeed, our food might be contributing to heart disease, cancer, asthma, allergies, arthritis, autism, depression, multiple sclerosis, diabetes – the list goes on.

We’ve been hearing for years how we should be eating healthy food. But this research is different. It’s all about the bacteria that live in our intestines. Eat good food, you end up with good bacteria. Eat badly and you get bad bacteria in your gut. Now, it turns out your gut bugs have an enormous influence on your health.

I think you can extend your life span by years, if not decades, with a healthy diet. And all the evidence is pointing to that.

How We Inherit Good Bacteria

The gut bacteria story starts at the beginning of life. During the messy process of birth, a newborn gets covered in microbes. If you were vaginally delivered, the microbes that you’re coated in initially mostly come from your mother’s vaginal community. Baby also acquires some of mum’s gut bacteria from traces of her faeces. A bit like inheriting a gene, you can also inherit the bacteria from your mother.

How we inherit good bacteria

And nature’s even provided food for those fledgling gut bugs. Mum’s milk has more than just nutrients for the baby. Breast milk contains a lot of sugars that the baby can’t metabolise, but they’re important for promoting the growth of particular kinds of bacteria in the gut that are good. Also there’s increasing evidence that the milk itself is produced with bacteria in it.

We Need Good Bacteria

Living on us and inside of us are an enormous number of bacteria. In fact, the bacterial cells outnumber ours by 10 to 1. So when you think about it, they’re not really OUR bacteria, we’re THEIR human.

Some scientists now say we’re a supraorganism, like a termite colony or a beehive, where individuals are just part of a whole. An organism that’s consisted of both human cells as well as microbial cells, all working together for perhaps the common good.

Together, the bacteria weigh about 1.5 kilograms, as much as our brains. And most live in the gut.

You eat your food, any what’s left over gets into the large intestine – the bowel. And that’s where most of the gut bacteria are. Most of us think of bacteria as generally nasty bugs rather than friendly organisms.

They Control How Our Immune System Works

We’re learning why these bacteria are critical to our health. And one of the main reasons is they help educate the body’s defences. We now know that the bacteria inside us control a lot of our immune system. They produce small molecules that regulate our immune responses.

It’s mainly in the gut that the immune system learns what to and what not to attack. And our bacteria don’t just affect physical health. They also have pathways to our brains. There are probably many different types of connections between gut bacteria and the brain. So your bacteria may influence how you think.

If our health is tied up with our bacteria, what bad effects could the modern world be having? Caesareans, for example, now account for up to 1 in 3 births. C-section babies are not readily inoculated with natural bacteria.

And in fact children born through caesarean section have got microbes that look more like the microbes that live on our skin, than children who are born in natural birth that have got microbes that look more like microbes that live in the intestine.

The literature in allergy and asthma indicates that children born to caesarean section are more likely to develop these types of disorders than children born to natural birth. Bottle feeding is also likely to result in different gut bacteria. Children that were breastfed are likely more protected against allergy and asthma than children who were fed formula. And I think these principles can extend beyond just allergies to autoimmunity, to neurological disorders.

Good Bacteria and Diet

Good bacteria and diet

While these possible health problems from entering the world unnaturally are disturbing enough, what about the unnatural diets we eat these days? Our gut bacteria change depending on what we eat. Eat bad food and you support bad communities of bacteria. And there seems to be one main bad food culprit – we’re eating too many low-fibre meals these days. Indeed, a lot of research is now pointing to low fibre being largely responsible for that long list of diseases.

It’s very exciting times now and we’re starting to understand for the first time how what we eat defines a lot of disease, and how we can actually avoid that disease by looking at diet. The people who take the highest levels of fibre are the ones that are living the longest.

Effect on Children

Effect on children

And it’s not just diet and the early years of life that are changing our gut bacteria. So are antibiotics. They’re a bit like dropping a nuclear bomb on your gut bacteria. Particularly vulnerable to antibiotics are young children.

The relationship between microbial ecology of the gut and the priming and training of the immune system is such a critical thing in the development of a child, that if you mess with that too badly, then that may be responsible for problems.

By the age of three the gut microbes look adult-like. And so I think that there is this critical window very early in life when gut microbes could affect the immune system or the metabolic and the nervous system.

OUR Diet Can Cause Chronic Inflammation

Our low-fibre diets, antibiotics and Western ways have left us with very low diversity in our gut bacteria.

The most diversity we’ve ever seen is with the Hadza (a tribe in Africa who eat a diet similar to what our distant ancestors would have). So let’s take a healthy adult in Australia. They might have 1,000 to 1,500 species of bacteria; a similar-aged Hadza might have two to three times that much.

Conditions chronic inflammation can lead to.

So all the health problems on that list may be connected to a lack of diversity and to the wrong type of bacteria disturbing the immune system, leaving our bodies in a perpetual state of inflammation. Inflammation is one of the body’s defence mechanisms and involves immune cells being released. But these defences can do harm if they’re not properly controlled.

The cells which are built to kill bacteria are actually doing damage to our own tissues. And that’s usually an inflammatory disease. That’s what happens in diabetes or in asthma or in rheumatoid arthritis. And you can add obesity to that list.

Good Bacteria and Weight

In Australia, 62% of us are overweight or obese. It’s the majority condition now.

Now, the common view is just too many calories are the cause of obesity. But could it be more complex than that? Maybe there’s more to losing weight than just exercise and eating less. Maybe you also have to change your gut bacteria.

The famous bacteria experiment.

There’s a famous experiment. They took a strain of mouse that’s genetically predisposed to obesity, rendered it free of bacteria, then they gave these mice new gut bacteria from thin mice. Incredibly, they now tended to stay thin. Gut bacteria could be helping to make the modern world fat. Back in the day obesity was a rarer thing, there could have been better gut bugs as a result of eating less processed food – in other words less sugar, fat, and more fibre. That’s a stark contrast to the modern world. But there’s good news if you’re overweight. Your gut bacteria community can be altered.

You can change it by changing your diet. And so if you manipulate the combination of protein, fat and carbohydrates in the diet, you can shift the composition – the community ecology, if you like – of the gut really quite profoundly.

In short, to do this, you have to eat a lot more fruit and vegetables. And another disease that was rarer in old times but growing at a frightening pace today is type-2 diabetes. And, again, bad bacteria from eating too much processed food could play a key role.

What About Asthma?

Dr Alison Thorburn – “It was pretty tough and annoying, because you’re always that kid in the playground with the Ventolin in your pocket. I remember my mum limiting what we could eat, which was really strange. I remember one day she said we’re not allowed to have oranges anymore ‘because you’re sister’s allergic to oranges. It makes her asthma worse.’ So I was really annoyed at my sister that I wasn’t allowed to have oranges. No orange juice. Also wheat and yeast and Vegemite at some stage. So I used to always say to my Mum, ‘Why? Why can’t I eat this?’ And she couldn’t give me an answer.”

Alison’s scientific curiosity in asthma had been sparked. Now Alison is a postdoctoral researcher at Monash University. And she’s found a new treatment for asthma – well, in mice at least – which is incredibly simple. She just puts them on a high-fibre diet.

But how does fibre fix up asthma?

“We know that when we give the mice a high-fibre diet compared to their normal diet, their gut bugs, their bacteria, change dramatically; the mice end up with more good bacteria.”

“There are really good bacteria that produce great things for our health, in particular short-chain fatty acids, which are the molecules we work on. Dietary fibre gets broken down to produce these short-chain fatty acids and then they do amazingly good things in the gut and also throughout the body.”

“One is acetate. Now, it’s important to have acetate in your body, particularly in the digestive tract, because it helps dampen the immune system. It’s a natural anti-inflammatory. Because they’re anti-inflammatory chemicals, they help prevent inflammatory diseases like asthma.”

Next time we’ll discover ways we can all have better gut bacteria and so live healthier lives.


Natural therapists have long believed that a good digestive system, including the balance of good and bad bacteria in the gut, is absolutely crucial to good health. And research such as this is helping to confirm it. In the past, doctors have generally looked at the body like a car, with parts that sometimes break down. However, it is becoming clearer to researchers that the digestive system is an ecosystem, with a huge variety of organisms (including us) interacting with each other to create a balance. Of course, some ecosystems are healthier than others, and some can even disintegrate and become toxic.

Having the right bacteria in your gut, and having the right diet to maintain your internal ecosystem, are essential to good health. Probiotics can provide the good bacteria we need, however since our ecosystems are so complex, there is no one probiotic that can sort out everyone’s system. For example, we supply ten different probiotics for different purposes.

Probex An anti-inflammatory probiotic for Irritable Bowel Syndrome
Ultra Flora Digest For healthy digestive function and improved immunity, with fibre
Ultra Flora Immune For increased immune function
Ultra Flora LGG 1. For eczema and food allergies in infants
2. Reduces the frequency of diarrhoea
Ultra Flora Plus High potency probiotic which also inhibits bad bacteria
Ultra Flora Plus Dairy Free Dairy free version
Ultra Flora Restore For restoration of healthy gut flora during and after antibiotics
Ultra Flora Restore Dairy Free Dairy free version
Ultra Flora SB Dysbiosis For the treatment of excess bad bacteria, including diarrhoea
Flora Care for Kids For a healthy digestive and immune system in children

Please note that these are Practitioner Prescribing Only products, so a trained therapist has to decide which is the correct one for you. If you are interested in looking after your digestive and immune systems, your long-term health, or if you have allergies, auto“immune problems, asthma, or other inflammation disorders, please book in for a Comprehensive Health Assessment. We can then have an in“depth look at what is happening in your body, what is causing the problem, and what can be done to sort it out. These Assessments are very thorough, and you will learn a lot about how your body is working. Our clients find them very helpful and interesting. We currently have a limited number of free Assessments available, so please contact us soon if you would like to book in for one.



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