5 Worst Things You're Doing to Your Gut

Keeping your gut bacteria happy may lead to better overall health.

Updated on May 2, 2022

Woman eating a cheeseburger
1 / 6

It’s estimated that about 39 trillion bacterial cells reside in the human body, the vast majority in the colon. Together with other microbes, these bacteria make up the gut microbiome.

While scientists know the microbiome aids in digestion and influences our immune and nervous systems, they’re only beginning to understand the extent to which it affects our health overall. Recent studies suggest that gut bacteria may also shape our risk of developing a range of conditions, including obesity, diabetes, and some cancers. The research, however, is largely new and limited in scope, and has been done mostly on animals.

“It’s in its relative infancy compared to other aspects of medical science,” says R. Stuart Bridge, MD, a gastroenterologist at St. Mark’s Hospital in Salt Lake City, Utah. “And clinical applications of this kind of knowledge of the microbiome are still being developed.”

In the meantime, we can help the most beneficial members of the microbiome flourish—in terms of numbers and variety—by practicing a healthy lifestyle and avoiding some potentially detrimental habits. Here are some of the worst things you can do for your gut and its community of helpful bugs.

Woman with a cold drinking hot tea and taking cold medicine
2 / 6
Taking antibiotics unnecessarily

While they’re great for treating bacterial infections, antibiotics are often prescribed unnecessarily for symptoms and illnesses for which they won’t do much good—like colds, which are caused by viruses. And since antibiotics are not finely targeted drugs, says Dr. Bridge, in the process of killing “bad” bacteria, they end up killing a lot of the normal bacteria that reside in our colon and small bowel.

Restoring the gut’s bacterial balance after periods of overusing antibiotics can take time, he says. And a lingering imbalance may result in long-term health effects, including gastrointestinal disruption “and even other forms of disease that we haven’t necessarily linked up quite yet.”

What to do: Bridge recommends carefully evaluating the need for antibiotics in certain situations, “limiting them to the bacterial infections that would benefit from them.” Additionally, it’s important to always take medications as directed by your healthcare provider (HCP) and for the full duration required. If you have any left over, safely dispose of them using Food and Drug Administration (FDA) guidelines, or hand them in at official collection sites, such as on a semiannual National Prescription Drug Take Back Day. Don’t save unused antibiotics.

Overweight man lying on couch and watching tv
3 / 6
Being a couch potato

Physical activity is likely good for your gut. One 2020 review of studies in the Journal of the International Society of Sports Nutrition linked exercise to a greater number of good gut bacteria and a more diverse microbiome, among other benefits. A 2014 study published in the journal Gut suggested as much when it compared 40 professional rugby players to similarly sized, healthy people who didn’t exercise. Though their diets were also an important factor, the athletes’ microbiomes were much more varied than those of the control group, with more plentiful good bacteria. What’s more, in multiple small studies on rodents, scientists have found that animals who engage in workout regimens are better off, bacterially speaking, than those who don’t get much physical activity.

What to do: Get moving. “Exercise in general just has so many beneficial effects across multiple organ systems,” says Bridge, that remaining sedentary doesn’t make sense. In addition to its cardiovascular and weight control perks, working out can help lessen inflammation all over the body. Regular exercise over the long term is best, but any physical activity may contribute. If you don’t have a regimen already, start out walking a few minutes every day, and work your way up from there.

Man smoking a cigarette
4 / 6

As if there weren’t enough reasons to kick the habit, studies suggest that smoking may also reduce the amount and diversity of beneficial gut flora, while increasing the number of harmful bacteria. There are several theories as to why. Smoking may:

  • Alter the pH balance in the gut, potentially making it more hospitable to bad bugs and less comfortable for the good ones
  • Introduce toxic chemicals that change the composition of the microbiome
  • Lead to excess production of harmful free radicals

Smoking is also a risk factor for Crohn’s disease, an inflammatory bowel condition that causes chronic pain, bleeding, and diarrhea. And if you already have the condition, smoking can exacerbate these symptoms.

What to do: If you don’t smoke, don’t start. And if you do, quit. Here’s a step-by-step plan to put you on the right track.

Stressed out businesswoman at work
5 / 6
Not managing stress

It’s well known that stress can affect your digestive system. When you’re anxious, for example, you may develop diarrhea or become constipated. “That people get butterflies in their stomach when they’re nervous is a real effect,” says Bridge. Some early studies indicate stress may stifle the production of good gut bacteria, as well, and make you more susceptible to infectious illnesses.

As it turns out, your gut may affect your emotions, too. That’s because it houses a division of the nervous system called the enteric nervous system, sometimes referred to as the “second brain.” Bacteria there create chemicals that send signals to the central nervous system. Scientists speculate that this influences behavior and mood, including stress-related conditions like anxiety and depression. While we’re a long way from adjusting gut flora to improve mental health, many researchers are intrigued by the possibilities.

What to do: Some experts believe stress-busting activities may boost good bacteria. “No one thing has been proven to be better than another,” says Bridge, “but things that reduce stress are certainly worthwhile.” So, find one that works for you. Exercise is a proven stress reliever, with yoga and tai chi often recommended as being particularly helpful. Many patients swear by mindfulness and meditation practices, as well. Try a meditation app to get started (such as the Sharecare Windows experience available in iOS and Android from Sharecare), or explore different methods to discover the best fit.

Pizza, fries and burger
6 / 6
Eating an unhealthy diet

Diet is intimately connected to gut health, and many experts believe eating plans that go heavy on saturated fats, added simple sugars, and processed foods—and light on natural fiber—do a number on gastrointestinal flora. For example, several studies on both humans and mice suggest that high-fat diets, particularly those high in saturated fats, may alter the microbiome to promote inflammation.

What to do: Though no single eating plan has been proven best for your gut, it’s generally agreed that a balanced, fiber-rich, plant-heavy diet benefits your whole body—including, likely, your microbiome. So, try to minimize your intake of saturated and trans-fats and added sugars. Shoot for a wide range of colorful produce, whole grains, legumes, and lean proteins. Include a moderate amount of good fats, like those found in walnuts and oily fish. Among other health benefits, it’s thought that the omega-3 fatty acids in these foods can promote the production of anti-inflammatory compounds and help maintain healthy intestines.

Remember, too, that fresh and minimally processed foods are better for you than highly processed ones and can help you maintain your weight and keep your body’s organ systems in good shape.

Slideshow sources open slideshow sources

Sender R, Fuchs S, & Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biology. August 2016. 14(8), e1002533.
Abbott A. Scientists bust myth that our bodies have more bacteria than human cells. Nature. 08 January 2016.
U.S. Department of Veterans Affairs. How a Healthy Gut Makes for a Healthier You. June 5, 2017. Accessed May 2, 2022.
Foster JA, Rinaman L, & Cryan JF. Stress & the gut-brain axis: Regulation by the microbiome. Neurobiology of Stress. December 2017, 7, 124–136.
Singh RK, Chang HW, et al. Influence of diet on the gut microbiome and implications for human health. Journal of Translational Medicine. 2017; 15: 73.
Harvard Health Publishing. Can gut bacteria improve your health? October 2016. Accessed May 2, 2022.
Langdon A, Crook N, & Dantas G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Medicine. 2016; 8(1), 39.
Mohr AE, Jäger R., et al. The athletic gut microbiota. Journal of the International Society of Sports Nutrition. 2020. 17(1), 24.
Mach N & Fuster-Botella D. Endurance exercise and gut microbiota: A review. Journal of Sport and Health Science. June 2017. Volume 6, Issue 2, Pages 179-197.
Douglas Main. Rugby Player Study Suggests Exercise Diversifies Gut Bacteria. Popular Science. June 11, 2014. 
Monda V, Villano I, et a. Exercise Modifies the Gut Microbiota with Positive Health Effects. Oxidative Medicine and Cellular Longevity. 2017, 3831972.
Savin Z, Kivity S, et al. Smoking and the intestinal microbiome. Archives of Microbiology. 2018 Jul;200(5):677-684. 
Lee SH. Intestinal permeability regulation by tight junction: implication on inflammatory bowel diseases. Intestinal Research. January 2015. 13(1), 11–18.
GI Society. The Effects of Smoking on Inflammatory Bowel Disease. 2015. Accessed May 2, 2022.
American Psychological Association. That gut feeling. September 2012. Accessed May 2, 2022.
Saulnier DM, Ringel Y, et al. The intestinal microbiome, probiotics and prebiotics in neurogastroenterology. Gut Microbes. January 2013. 4(1), 17–27.
Holscher HD. Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut Microbes. 2017; 8(2), 172–184.
Sawicki CM, Livingston KA. et al. Dietary Fiber and the Human Gut Microbiota: Application of Evidence Mapping Methodology. Nutrients. February 2017; 9(2), 125.
Costantini L, Molinari R, et al. Impact of Omega-3 Fatty Acids on the Gut Microbiota. International Journal of Molecular Sciences. December 2017; 18(12), 2645.

More On

What is irritable bowel syndrome?


What is irritable bowel syndrome?
Experts aren’t sure what exactly causes irritable bowel syndrome (IBS), they know certain triggers can exacerbate symptoms. In this video, Kevin Soden...
You've Been Pooping Wrong Your Whole Life


You've Been Pooping Wrong Your Whole Life
Turns out, there's a proper technique you should know about.
9 Ways to Help Kids With IBD


9 Ways to Help Kids With IBD
Communicating openly and planning ahead can help prevent stressful situations.
Eat right to ease IBS symptoms


Eat right to ease IBS symptoms
If you have IBS, you know how you eat is as important as what you eat. In this Health Smarts video, Kevin Soden, MD, outlines several easy-to-follow n...
People with IBD need to safeguard their heart health


People with IBD need to safeguard their heart health
If you suffer from an inflammatory bowel disease like Crohn's disease or ulcerative colitis, you may be at increased risk of having a heart attack or ...