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5 Common Gut Microbiome Saboteurs + Ways To Counteract Them

Stephanie Eckelkamp
Author: Expert reviewer:
Updated on November 29, 2020
Stephanie Eckelkamp
Contributing Health & Nutrition Editor
By Stephanie Eckelkamp
Contributing Health & Nutrition Editor
Stephanie Eckelkamp is a writer and editor who has been working for leading health publications for the past 10 years. She received her B.S. in journalism from Syracuse University with a minor in nutrition.
Ashley Jordan Ferira, Ph.D., RDN
Expert review by
Ashley Jordan Ferira, Ph.D., RDN
mbg Vice President of Scientific Affairs
Ashley Jordan Ferira, Ph.D., RDN is Vice President of Scientific Affairs at mindbodygreen. She received her bachelor's degree in Biological Basis of Behavior from the University of Pennsylvania and Ph.D. in Foods and Nutrition from the University of Georgia.
November 29, 2020
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Ten years ago, the word "gut" was hardly trendy, and no one was talking about probiotics—except for maybe that guy at the health food store who was fermenting his own sauerkraut in a Mason jar. But now, you can't go more than a day without hearing about a gut-centric protocol, fancy new probiotic drink, or a study on how the gut microbiome seems to influence everything from digestion to mental health to immunity.

The uptick in microbiome research and awareness we're seeing is crucial—but an important question we also need to be asking is, why does gut health seem to be under attack now more than ever? With the help of some prominent gut experts, mbg explored an array of modern-day gut saboteurs—and what you can do to counter them:



There's no question that modern, processed diets are bad for the gut. Due to the vast majority of farming subsidies going to producers of corn, wheat, and soy, prices for the foods containing these crops (many of which are high in sugar and refined carbohydrates and low in meaningful vitamins, minerals, micronutrients, and fiber) have dropped—making them cheap and readily accessible for consumers. 

Fiber—found in vegetables, fruits, and a variety of whole grains—promotes gut microbial biodiversity and feeds beneficial bacteria in the GI tract. In fact, these "good" bugs use fiber food to produce gut-healthy, anti-inflammatory compounds called short-chain fatty acids (SCFAs). But the average American gets just 15 grams of fiber per day, when we should be getting at least 25 to 30 grams. "Part of the problem we're seeing today could be due to three to four generations of progressively diminished fiber consumption," says gastroenterologist Will Bulsiewicz, M.D., author of Fiber Fueled, referencing a groundbreaking 2016 study1 in Nature by Stanford University microbiome researcher Justin Sonnenburg, Ph.D. 

For the study, researchers fed mice a low-fiber diet over multiple generations. After one generation, there was a decline in microbial biodiversity in the gut, which was reversible when fiber-rich foods were returned to the diet. But with each subsequent generation, there was a progressive loss of biodiversity that was harder to reverse (and impossible to completely reverse). 

"Compared to the Hadza of Tanzania2, some of the last remaining communities of hunter-gatherers, people in the U.S. have about 40% less microbial diversity in the gut," says Bulsiewicz. "This leads us to believe that we've essentially lost 40% of what we're supposed to have as humans. To an extent it's reversible, but this study shows that we might be in a place where we're impaired from the get-go."

Excessive consumption of animal products (particularly in the absence of fiber-rich foods) may also have a negative impact on the gut microbiome. This was illustrated in a 2014 study by Harvard researchers in which they put the same group of people on two drastically different diets—an animal-based diet3 of foods like bacon, eggs, salami, and pork rinds; and a vegan diet of foods like rice, tomatoes, lentils, squash, and fruit—and measured the effects of each. What they found: On the animal-based diet, there were significant increases in the bile-tolerant gut microbes, which are necessary for breaking down fat but also associated with inflammatory processes.

Additionally, excessive refined carbohydrate and sugar intake has been shown to reduce the microbial biodiversity and feed bad microbes. "Someone who's eating way too much sugar is going to become a fertile ground for yeast to grow in their gut," a form of gut imbalance, says Vincent Pedre, M.D., integrative physician and author of Happy Gut.


Antibiotics (in medicine and the food supply)

Although antibiotics are necessary and even lifesaving, the Centers for Disease Control and Prevention (CDC) estimates that 30%4 of antibiotics prescribed in the outpatient setting are completely unnecessary. And this is extremely dangerous, as inappropriate antibiotic use can not only mess with the gut but contribute to the rise of antibiotic-resistant superbugs. "Overprescribed antibiotics are the No. 1 reason for gut imbalance," says Pedre. "They're why so many patients come to see me."

That's because antibiotics don't just act on the bad bacteria that cause us issues; they also affect your resident, good microbes. For example, a 2008 study found that treatment with the antibiotic ciprofloxacin5 "influenced the abundance of about a third of the bacterial taxa in the gut, decreasing the taxonomic richness, diversity, and evenness of the community." And while many of these bacterial groups recovered by four weeks post-treatment, some didn't—even after six months.

But even if you've managed to avoid an antibiotic prescription recently—there's still a possibility that you're being exposed. A 2018 paper featuring findings from the American Gut Project—an ongoing project in which researchers at U.C.–San Diego analyze fecal samples from individuals around the country to gain insight into the gut microbiome—revealed how scientists detected agricultural antibiotics in samples from people who hadn't taken any antibiotics the year prior. Not-so-fun fact: "Around 80% of the antibiotics in our country are actually being administered to livestock as a part of animal agriculture," says Bulsiewicz.

Much more research is needed to determine the implications of this discovery, but it could mean the antibiotics given to animals could end up in human bodies and affect the gut. That said, at this point, there's no study defining the likelihood of being exposed to antibiotics via food.


Being out of touch with nature

As the world has industrialized, people have become increasingly nature-deficient—which, according to Bush, is one of the biggest culprits in overall declining gut health. Let's consider the Hadza again—remember how they have 40% more gut biodiversity? Well, that's not just due to the variety of fiber-rich plant foods they're gathering; it's also because they're in constant contact with the natural world around them, and with each other.  

"What we've come to learn about [the Hadza] through the American Gut Project is that their gut is really an extension of their greater environment," says Bush. "They actually have bacteria in the gut that are specific to zebra skin—they're really touching nature all the time and therefore reinforcing this extremely diverse microbiome. There's also an enormous amount of skin-to-skin contact—they're wearing no clothes much of the time, children are always on the backs, bellies, or shoulders and passed around from person to person."

All of this, of course, is in stark contrast to how many of us in the U.S. live our lives today (personally, I'm lucky if I get out for a hike once a week), and "as we narrow our contact with nature, animals, and other humans, we get a more narrow microbiome," says Bush. 

For a crazy example of just how protective contact with the natural world can be for the gut, consider this: When the Hadza were being studied by the American Gut Project, a missionary group came and gave them boxes of antibiotics in case they got sick. Not really being familiar with the concept of infection, they sat around that night and ate all the antibiotics, thinking it was candy from the West. The crazy part? In the genomic studies of their gut, scientists found that the very next morning—and in the months following—there was no change in their microbiome. 

"So what that shows you is that if you're in touch with your environment adequately, you're pretty impervious to damage because the ecosystem is constantly reinforcing your recovery," says Bush. "If we stop touching nature, then something like an antibiotic becomes really damaging because we can't recover."


Herbicides and pesticides (like glyphosate)

Increasingly, glyphosate (the active ingredient in the weedkiller Roundup) is showing up in food and in people's bodies: A 2017 study, which obtained urine samples from a group of California residents between 1993 to 1996 and then again from 2014 to 2016, found that the number of individuals who tested positive for glyphosate6 increased by 500% in that time period, and the levels of glyphosate detected went up by 1,208%. And in recent tests by the Environmental Working Group (EWG), glyphosate was found in 21 popular oat-based cereal and snack products. 

Of course, many experts debate what all this means for gut health and the extent to which glyphosate (and other herbicides and pesticides) affect the gut microbiome, but according to Bush and Pedre, there is some cause for concern. "Glyphosate acts by chelating minerals—it starves crops of nutrients by chelating minerals in the soil, and it does the same thing if it gets into the gut," says Pedre. "It can kill bacteria by chelating essential nutrients that they need to replicate and consequently cause dysbiosis."

Research by Stephanie Seneff of MIT supports this idea and proposes that glyphosate is a major driver of the gut-related autoimmune condition celiac disease. A 2013 study authored by Seneff states that "Deficiencies in iron, cobalt, molybdenum, copper, and other rare metals associated with celiac disease can be attributed to glyphosate's strong ability to chelate these elements7," and that "Fish exposed to glyphosate develop digestive problems that are reminiscent of celiac disease." 

Even more experts are concerned about glyphosate's effect on soil quality—which can indirectly affect the gut and overall health by stripping our crops of nutrients. "Human health is proportional to soil health," says Bulsiewicz. "There are interesting studies comparing foods of today to the same foods 70 years ago, and they were more nutrient-dense 70 years ago."

Keep in mind, though, food may not be the most direct way you're exposed to glyphosate and other pesticides. "The third-largest 'crop' grown in the U.S., behind corn and soybeans, is lawn," says Bush. "So backyards, schoolyards, and other green spaces cover 40 million acres, and many are heavily sprayed with Roundup. That can be public enemy No. 1 within an urban community." (Bush recommends talking to your town and school district about their Roundup spraying practices, and, if you're up for some advocacy, asking them to stop.)


Excessive stress and poor sleep

Chronic stress and inadequate sleep—which often go hand in hand—can both interfere with the gut in different ways. Your gut and brain talk via the gut-brain axis. Not only does that mean poor gut health can negatively influence your mental health, but lots of stress or emotional turmoil can also mess with your gut.

Bulsiewicz believes the effects of stress can be huge. "As a gastroenterologist, the most challenging patients that I take care of are the patients who have been victims of trauma or have dealt with an eating disorder," he says. "You can sleep, you can exercise, but if you're not properly managing your stress or something traumatic that happened to you, you're not going to have a healthy gut."

As for how sleep affects gut health, it has to do with circadian rhythms. "Circadian rhythm disturbances cause alterations in the gut microbiome," says Pedre. "I see a lot of people who fly long distances, and they can't lose weight; it really does a number on the gut." In fact, in a 2014 study8, researchers induced artificial jet lag in mice (simulating the changes in sunlight that would occur on a flight from Tel Aviv to San Francisco) and found that the gut very quickly transitioned to a type of microbiome that promotes insulin resistance and weight gain. And while staying up until midnight scrolling Instagram probably won't affect your gut to the same extent as a trans-oceanic flight, it's still disrupting your body's ideal circadian rhythm.

What can you do to support your gut?

As you can see, you're not quite as in control of gut health as you'd like to think. That said, "we know more about how the body functions today than we've ever known in human history," says Bulsiewicz. "So when we talk about these things, what we're doing is identifying where the problems exist, then phase two is to create solutions to those problems."

One solution you've probably heard the most about is probiotics, the bacteria that help support good health, especially in the gut.* So when you take a probiotic supplement, you add more of these good bacteria to your gut.* "Think of probiotics as your little helpers that restore order and help maintain harmony in your gut ecosystem," Pedre previously told mbg. There's a lot of evidence that probiotics are beneficial for managing gut issues like regularity, bloating, and gas, among other benefits.* (You can check out Pedre's guide for choosing the right probiotic.)

There are also other lifestyle practices to help support your gut microbiome, like eating more plants, opting for organic produce, exercising regularly, spending time with animals, meditating to ease stress, getting plenty of sleep, and supporting sustainable agricultural initiatives.

You won't be able to change your gut overnight, but taking these small steps may help reinforce a healthier, better microbiome in time.

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Stephanie Eckelkamp author page.
Stephanie Eckelkamp
Contributing Health & Nutrition Editor

Stephanie Eckelkamp is a writer and editor who has been working for leading health publications for the past 10 years. She received her B.S. in journalism from Syracuse University with a minor in nutrition. In addition to contributing to mindbodygreen, she has written for Women's Health, Prevention, and Health. She is also a certified holistic health coach through the Institute for Integrative Nutrition. She has a passion for natural, toxin-free living, particularly when it comes to managing issues like anxiety and chronic Lyme disease (read about how she personally overcame Lyme disease here).