The Ultimate Guide to Your Gut

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

Vanessa Milne Published Feb 24, 2022 18:48:45 IST
The Ultimate Guide to Your Gut Illustrations by Kevin Moran

A decade ago, Kaitlyn, a 28-year-old support worker living in Ontario, Canada, became very ill. She had painful constipation and was contracting fevers and losing weight. “If I ate too much, I would vomit,” she says.

After tests ruled out Crohn’s disease and colitis, Kaitlyn’s family doctor diagnosed her with irritable bowel syndrome (IBS), 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. A dietitian suggested to Kaitlyn that the bacteria that lived in her intestines—collectively known as the gut micro-biome—might be out of balance, contributing to her condition. She recommended Kaitlyn take probiotics—pills that contain specific strains of bacteria—to help put things in order. 

After only a few days of taking the probiotics, Kaitlyn felt a lot better. “The pain and fevers went away, and I was able to eat without getting sick,” she says. She still needed to avoid specific foods that trigger her condition, but gained back some of the weight she had lost.

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. In that oxygen-deprived space, those bacteria break down the food’s components—e.g., 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 colonizing 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, 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 help you digest food, but they also impact other aspects of your body, including your immune system, brain and cardiovascular health.

“Your gut is like its own ecosystem,” says Sean Gibbons, a microbiome researcher and assistant professor at the Institute for Systems Biology in Seattle, Washington. “It’s warm, humid, and wet—like a rainforest.” And, he explains, 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 mucous,” explains Gibbons. 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.


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 affect an estimated 1.5 million people in India. Dr Eugene Chang, director of the Microbiome Medicine Program at the University of Chicago, says its exact cause is unknown. But, he adds, 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 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. 

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 10 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 foecal 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 foecal 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 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 analyzed 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.


There isn’t one magic prescription for everyone, though researchers are hopeful that within five years, microbiome tests will be detailed enough to prescribe personalized probiotics or make other patient-specific recommendations. But there are some changes that can help right now. 

1. Eat More Fibre

One of the most well-proven connections between lifestyle and gut health is that eating more fibre creates a better microbiome. Fibre is the main food source for the most important gut bacteria, so not getting enough starves them, and many of them die. That means they may produce fewer short-chain fatty acids and other important components of your diet, and begin consuming your gut’s mucous lining. 

To get your daily requirements, focus on eating five servings of fruits and vegetables each day, as well as a whole-grain carbohydrate at every meal.

2. Diversify your Diet 

Your overall goal should be to create a diverse gut microbiome. And it’s not just fibre that provides sustenance for good bacteria—other things in our meals do, too. If you eat a large variety of foods, including many different types and colours of fruits and vegetables, that variety will promote a healthy gut. 

On the other hand, high-fat processed foods deplete healthy bacterial strains and make your gut less diverse in general, says Chang. If you were to suddenly stop having salads and instead eat fries, he adds, “Your microbiome would change within 24 hours, with a decrease in the healthy microbes that plant fibre promotes.” 

3. Go Easy on Antibiotics

Antibiotics are a lifesaver when needed, but they tend to throw our gut microbiome off balance by killing even the healthy bacteria that help maintain the gut wall. Usually, they are able to crowd out bacteria that can make you sick, just as it’s harder for weeds to establish themselves in a lush lawn than in unplanted soil. But when antibiotics do their job of destruction, bad bacteria can take over before the good have a chance to reestablish themselves. Then, the clue that something is wrong is often diarrhoea. While most healthy gut microbiomes can bounce back from that, if yours is already unbalanced, Gibbons says antibiotics could lead to issues like IBS. 

To help prevent antibiotic-caused diarrhoea, talk to your doctor about taking a probiotic the same day you start your antibiotics. A 2017 University of Copenhagen review found that only eight per cent of people who took probiotics developed diarrhoea when they took antibiotics, compared with 18 per cent of those who took placebos. 

Most importantly, make sure you really need an antibiotic before you take it. According to the US-based Centers for Disease Control and Prevention, at least 30 per cent of antibiotic prescriptions are unnecessary. 

4. Consider Probiotics 

Probiotics may also protect against diarrhoea when we travel to countries where the bacteria in the food and water are different from those at home. And, as mentioned, probiotics could help people with IBS. It’s best to try them at the direction of a health-care provider, who can suggest specific types. 

In the meantime, scientists are working to better understand probiotics. “Within the next five to 10 years, I believe we’ll start to see medical grade probiotics on the market,” says Gibbons. 

5. Stay Active 

Regular exercise improves your gut microbiome. A 2016 UBC study found that athletes with the best cardio-respiratory fitness levels—a marker that measures how well your body can move oxygen to where it’s needed—also had more diversity in their gut. Another study, from Spain, found that women who did three hours of exercise a week—even just brisk walking—improved the composition of their gut microbiome. 

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