Like many of us, Jim starts his working day with a simple breakfast of a slice of toast washed down with a cup of coffee.

By mid-morning, he’s snacked on a banana and a wholegrain muffin. For lunch, he usually heads out to a local café for a tuna salad sandwich on brown bread and apple juice ( at 56, he’s always mindful of his middle-age spread). The afternoon is taken up with preparing reports and meetings – and at least two trips to the staff kitchen for more coffee plus a few biscuits. By 5 o’clock, his thoughts are turning to dinner – takeaway or make a stir fry? he wonders. Deciding on the healthy option, he cooks up some lean chicken and a few vegetables, and finishes off with fruit and yoghurt.

By the time Jim climbs into bed and drifts off to sleep, the activity in his gut has reached fever pitch. Hundreds of trillions of microscopic bacteria are now busily breaking down the large molecules in the food he’s eaten today, converting it into fuel to power him through the next day. Most active of all is the Lactobacillus and Bifidobacterium bacteria contained in his yoghurt dessert, which have powered their way to Jim’s large intestine, and are vigorously breaking down the fibre from his dinner vegetables, fending off invasion from pathogenic species and communicating with his immune cells. The result of all this activity? Jim’s immune system receives a boost, his digestion operates like clockwork and he enjoys a restful sleep. Come morning, he wakes up happy and alert.

Your Internal War

Deep inside your belly, warring colonies of micro-organisms are bracing for battle. Every few days, entire populations rise up or perish, supported in their evolutionary struggle to survive by the food and chemicals you feed them.

When you eat, you’re not just feeding your body – you’re providing food for trillions of gut bacteria. Weighing up to two kilograms – a little more than the adult human brain – these tiny creatures breathe, feed and excrete, creating a profound effect on the food you crave, the state of your health and even how you behave.

Some species thrive on certain types of food, and others starve. This has important implications for your health. For example, having more of certain species of Prevotella bacteria in the gut – bacteria that love to eat carbohydrates, such as sugar – is linked to poor glucose tolerance and a higher

chance of developing type 2 diabetes. Other species of Prevotella prefer to eat fibre, and these help the immune system.

“We’re starting to realise that the tiny bacteria in our guts play a much more important role in our health than we ever imagined,” says Dr Amy Loughman, psychologist and microbiome researcher based at the Food and Mood Centre at Deakin University in Melbourne. “The community structure depends on the environment that’s down there. We’re only just starting to understand the relevance of these tiny cells and how they are connected to everything else. What we know now is just the tip of the iceberg.”

DNA and the Microbiome

Ancient Greek physician Hippocrates was the first to allude to the vital role the gut plays in general health when he declared, “Let food be thy medicine”. But it’s only in the last ten years or so that technology has enabled us to properly study the bacteria that live inside the human gut.

Using high-throughput sequencing technology to examine the DNA of the micro-organisms that inhabit your body, scientists have found that only 50 per cent of cells in the body are human – the rest are bacteria, fungi, viruses and even microscopic insects, living and breeding in every crevice of our skin, mouths and gut. Together, they are called the human microbiome.

As humans have evolved so, too, have these communities of tiny organisms. Different species have developed specialised roles in keeping us alive – so much so that some scientists believe human beings are more like symbiotic organisms made up of the human, the microbiome and the surrounding environment, says Loughman.

High-throughput DNA sequencing has allowed scientists to identify 3.3

ANCIENT GREEK PHYSICIAN HIPPOCRATES WAS THE FIRST TO ALLUDE TO THE VITAL ROLE THE GUT PLAYS IN GENERAL HEALTH WHEN HE DECLARED, “LET FOOD BE THY MEDICINE”

million genes in the microbes in the gut, compared to just 23,000 that make up the human genome. While there’s only ever about 0.5 per cent difference in the genes between humans, the genetic make-up of the bacteria we all carry in our belly can vary by as much as 90 per cent.

It seems the effects of the small molecules produced by bacteria in our bodies may be as important as our own DNA.

It’s All About Balance

On the weekend, when Jim’s away from his routine, he’s able to enjoy more glasses of wine, rich dinners out and sugary desserts. When he does, the colonies of good bacteria in his gut are ravaged and the colonies of harmful bacteria rise up, causing Jim to bloat and become gassy. And so, by Monday morning, more often than not, he’s feeling lethargic and depressed.

There are about 1000 different species of bacteria living in the human gut. Like the ecosystem of the Amazon rainforest, each bacteria’s survival depends on a complex pattern of interdependent relationships. Most of the time they live in harmony, but a change in their environment caused by us eating certain foods, falling ill to an infection or taking a course of medicine can kill off some species and cause others to take over.

If you eat a diet full of biscuits and soft drinks, you’ll feed the bacteria that thrive on sugar, while those that prefer protein will starve. As the bacteria help to digest food, they produce small-molecule by-products (called metabolites) that enter the bloodstream and influence your health. If you feast on protein and don’t eat enough fibre, the bacteria that thrive on this diet will produce hydrogen sulphide and ammonia, making your farts smelly.

Like the Amazon rainforest’s role in the health of the planet, cultivating a healthy gut is essential for health. Disrupt the balance, and you’re more likely to develop any number of diseases ranging from cancer to obesity, type 2 diabetes, heart disease, allergies, autism or Alzheimer’s disease.

The good news is that it’s relatively easy to change the composition of bacteria in your gut. If Jim drinks a little too much diet soft drink one week, feeding colonies of Bacteroides bugs, then replacing that artificial sugar with high-fibre fruits can help restore the balance.

“Everything you eat will in some way affect your gut,” says Loughman. “You can definitely change your gut microbiome with your diet. The tricky thing is that we still don’t fully understand in exactly which ways you would want to change it.”

The Microbiome Today

For more than 100 years, medicine has focused on killing off bacteria with antibiotics and antibacterial

cleaning products and soaps. As a result, we’re far less likely to die of the infections and diseases that once ravaged communities – but at the same time, we’re seeing a rise in antibiotic resistance and a dramatically altered gut microbiome.

Scientists think the key to good health is having many diverse species of bacteria in the gut, especially in the colon and large intestine. Some studies have looked at fossilised human remains from the Neolithic Age and from modern hunter-gatherer communities in Africa, neither of whom suffered from diseases such as diabetes or obesity that plague modern society. They have found that these peoples had a gut microbiome dramatically different and far more diverse than the microbiome most of us have today.

Our overuse of antibiotics isn’t just killing the bacteria that lead to infection – it’s killing the bacteria we need for good health, too. Even a short course of antibiotics, especially broad-spectrum antibiotics, can alter the gut microbiome for up to a year. This imbalance of the normal gut microbiome is called dysbiosis and is linked to obesity and other health conditions including cardiovascular disease and mental illness.

The impact antibiotics and hand sanitisers have on gut bacteria might also explain the ‘hygiene hypothesis’ – the theory that our modern, sterile world is giving rise to an increase in immune system problems such as allergies and asthma.

Scientists still don’t fully understand how changes to the microbiome cause disease. But studies that have analysed the gut microbiome of people with diseases such as type 2 diabetes find it’s very different to that of healthy people. “You can look at almost any disease – I haven’t found a single negative study where the microbiome is found not to be affected,” says Loughman.

It’s not just antibiotics that are altering the composition of the modern gut. The food we eat also causes dramatic changes to our gut microbiome: a diet low in fibre and high in

OUR OVERUSE OF ANTIBIOTICS ISN’T JUST KILLING THE BACTERIA THAT LEAD TO INFECTION – IT’S KILLING THE BACTERIA WE NEED FOR GOOD HEALTH, TOO

highly processed foods, preservatives and artificial sweeteners can kill off species of bacteria that are believed to be important for health, leading to inflammation and metabolic syndrome – a collection of conditions that include obesity, high blood pressure and insulin resistance.

If you eat these foods regularly, over time you’ll change the composition of bacteria in your gut for good. And worryingly, these changes caused by your diet can be intergenerational. Just as your children will inherit your genes, they will also inherit the composition of bacteria in their gut. Some mice studies have shown that pups who inherited a gut microbiome depleted from a poor diet in previous generations could not recover some of the bacterial strains they needed, even if they were fed a healthy diet.

“We’re concerned that the modern Western diet will irrevocably change the gut microbiome and health of future humans,” says Loughman.

Improving Your Gut Health

Like us all, Jim was born with a unique gut microbiome. Bacteria started to colonise his gut before birth and their make-up was influenced by his parents’ diet, where he was born, what he was fed as a baby, how many antibiotics he’s taken during his life, and the chemicals he’s been exposed to in his environment.

Much of this Jim can’t control. But there are things he can do to nurture a healthy gut microbiome and reduce his risk of diseases such as irritable bowel syndrome, obesity, type 2 diabetes and mental illness.

The best diet for gut bacteria is thought to be high in fibre, mostly plant based, and with lots of variety. That means eating more fruit and vegetables and less processed food, artificial sweeteners, sugar or saturated fat – foods that feed the ‘bad’ bacteria.

‘Good’ bacteria are especially fond of onions, garlic, artichokes, wheat, watermelon, legumes, beans, pulses and some nuts and seeds.

But other things that affect health, such as stress, exercise, sleep and environmental exposure to toxins and medications, are also important factors for gut health.

“This really is a new frontier for research,” says Dr Jane Muir, head of Translational Nutrition Science in the Department of Gastroenterology at Monash University in Melbourne. “We have the technology to identify and name all the billions of different species of bugs, and we know that by changing our diet we can change their composition. But what does it all mean? We really don’t know. It’s still early days.”

For Jim, the bloating and lethargy he feels after a few days of unhealthy eating might well be improved by a good night’s sleep, eating some yoghurt and laying off the sugar.

As the old saying goes – you really are what you eat.