The bacteria in your intestines affects whether you’ll have allergies, your risk of depression—and even how well your medication works

Irritable bowel syndrome (IBS) is a chronic disorder that causes cramping, pain, and bloating along with constipation or diarrhoea.
While IBS can’t be cured, it can be managed through lifestyle changes. If the bacteria that live in your intestines—collectively known as the gut microbiome—are out of balance, this can contribute to this condition.
You can take probiotics—pills that contain specific strains of bacteria—to help put things in order.
After only a few days of taking the probiotics, you are likely to feel a lot better.
The state of our gut microbiome impacts many facets of our physical and mental health. But what is it, exactly? Imagine a jar of fermented food, like sauerkraut, which is full of bacteria. The bacteria that already live on the cabbage flourish when it’s covered in brine and sealed.

“The state of our gut microbiome impacts many facets of our physical and mental health”
In that oxygen-deprived space, those bacteria break down the food’s components—eg, carbohydrates—and release acid, which gives sauerkraut its tangy flavour. A similar process happens inside your intestines every time you eat: bacteria break the food down, transforming it into crucial vitamins, amino acids, chemicals, and, yes, gas.
All those bacteria start colonising you the minute you’re born. You pick up more bacterial strains from breast milk, your home, the environment outside, contact with other people, the food you eat, and even the family dog.
By the age of three, your microbiome has pretty much settled into how it will look when you’re an adult. The different types of bacteria that live in your gut can help you digest food, but they also impact other aspects of your body, including your immune system, brain, and your cardiovascular health.
Your gut is like its own ecosystem. It’s warm, humid, and wet—like a rainforest. And, like any thriving ecosystem, your gut is healthy when it’s diverse, with hundreds of types of bacteria.
Two of the most important are Firmicutes and Bacteroidetes, which feast on dietary fibre and break down complex carbohydrates. Both also churn out short-chain fatty acids, microscopic compounds that help maintain the integrity of the gut wall (that barrier is supposed to be porous in order to let nutrients through, but if it’s too porous, that can lead to inflammation). They also have anti-inflammatory properties and can promote brain health.
You should feed those two types well, because if there’s not enough food in your system, they’ll turn to a secondary source of nutrients. They will actually start to eat your gut mucus. If that happens, many bacteria in your gut will suddenly be seen by your immune system as outside agents, setting off a response that can lead to inflammatory bowel disease and other gut problems.

Signs your gut is out of balance

You have a stubborn bowel condition
Crohn’s disease and ulcerative colitis—known together as inflammatory bowel disease (IBD)—cause inflammation and breaks in the lining of the intestines, leading to pain, diarrhoea, and weight loss.
It affects less than one per cent of Europeans and its exact cause is unknown. But researchers believe affected people are genetically predisposed to an overactive immune system, and that their microbiome changes in subtle ways to prefer bacteria that thrive in that inflammatory environment. Those bacteria further activate the immune system. It’s a vicious cycle that eventually triggers IBD.
IBS, which is much more common and affects up to 11 per cent of people worldwide, shares many symptoms with IBD but without the inflammation and ulcerations. Like IBD, the exact cause of IBS isn’t yet clear, but studies have shown differences in the microbiome of IBS patients—and probiotics can help some of them feel better.

Your medications aren’t working 
The medicines doctors prescribe for various conditions don’t always work, and in some cases, the gut microbiome may be to blame. Just as microbes break down the fibre and starches in our food, they can also break down pharmaceuticals, making them act unpredictably.
In fact, a 2019 study from researchers at the Yale University School of Medicine looked at 271 drugs taken orally and found that the gut microbiome affected two thirds of them, with the bacteria consuming about 20 per cent of their active ingredients. That means, for example, that if you have too much Eggerthella lenta—a bacterium found in about one third of us—the commonly prescribed digoxin might not help your heart disease symptoms.

“The medicines doctors prescribe for various conditions don’t always work, and in some cases, the gut microbiome may be to blame”
This effect on medicine has even larger implications for cancer treatment. Recently, researchers found that the gut microbiome can affect the progression of some types of cancer, and that it also affects who responds to immunotherapy and bone marrow transplants.
All of the above has given birth to a new field: pharmacomicrobiomics, the study of how your gut microbiome affects a drug’s actions. In ten to 15 years, your doctor may be able to test your microbiome through a stool sample and then modulate the dose—or possibly prescribe a probiotic—to make your pills work better.
And clinical trials are currently investigating whether cancer patients are more likely to survive if they’re given tailored probiotics, a special diet, or a fecal transplant—a small bit of poop from someone else that could reset your gut microbiome.

You struggle with your weight
“Two decades ago, we thought that obesity and metabolic disorders were all about how much you ate,” says Chang. “But it turns out that the gut microbiome seems to play an important role.”
The connection is clearest in mice: when researchers from the Washington University School of Medicine transplanted stool samples from obese and thin people into the rodents, the animals who received fecal transplants from the obese participants gained more weight and put on more fat than the ones who received them from the healthier participants, even when the mice all ate the same low-fat diet.
There’s some evidence from humans, too: for a study two years ago, Belgian researchers gave people who had insulin resistance and were overweight or obese a bacterium that’s more common in the guts of lean men. Similar to the mice, the new bacteria lowered participants’ insulin resistance, and they lost more weight and fat than a placebo group.

You’re depressed
We think of mood disorders as originating in the brain, but your gut may also be a source of them. A 2019 study found that people with depression had fewer Coprococcus and Dialister than most people. Other research has found that mice that receive stool transplants from depressed humans get depressed, too.
Could changing someone’s gut microbiome improve their mental health? The research is still emerging, but a 2017 Australian study found promising results. It looked at people with major depression who were on medication or in therapy.
Half remained on these treatments and also tried a Mediterranean diet, which is rich in whole grains, lean protein, vegetables, and fruits. That group had a much greater reduction in their depression than the others.

You have allergies 
A diverse microbiome can help regulate your immune system, especially early in life. So if your immune system is hypersensitive because of your particular microbiome, it increases your chances of having allergies, asthma, and eczema.
That’s why exposure to a variety of bacteria from a young age is so important. Kids who are born vaginally are less likely to have allergies than those born by C-section, as are people who are raised on farms, have pets, or grow up with older siblings in the house.
According to B Brett Finlay, a microbiology professor at the University of British Columbia (UBC) and author of Let Them Eat Dirt, antibiotic use can also have a big impact: as it wipes out the bacteria making you sick, it will also indiscriminately wipe out bacteria that keep your gut diverse and healthy. That raises the risk your gut microbiome will be inadequate for preventing the conditions that cause allergies, asthma, and eczema.
In fact, Finlay and other UBC researchers found that people who had been prescribed antibiotics before age one were twice as likely to develop asthma by age five—and the risk increased with every course of the medication.
The impact of a less diverse gut persists into adulthood. When researchers with the American Gut Project analysed the microbiomes of more than 1,800 people with allergies, they found that those with seasonal and nut allergies had less diversity in their gut.