Bloating & Digestion

These Are the 10 Absolute Worst Foods for Your Gut

These Are the 10 Absolute Worst Foods for Your Gut

We like to keep things positive here at Hyperbiotics. After all, our bodies are incredibly powerful, and given the right kind of help and support, they can come back from a lot of health conditions and really thrive.

But we also know that it can be hard to make good choices that support your health if you're not aware of the effects that certain foods can have on your body, especially your gut microbiome. If you’re well-versed on the importance of gut health, you’ll know that having a good balance in this ecosystem of bacteria that lives in your gastrointestinal tract is absolutely key to supporting your physical and emotional health and well-being.

So in the interests of giving you all the information you need to make the best possible decisions for your health, we’re naming and shaming some of the worst foods for your gut...some of which may surprise you.

Here Are 10 Common Foods to Pass On––and 10 Alternatives to Try Instead

1. Gluten

Chances are you’ve heard at least one person talk about how gluten isn’t great for you. (Reminder: gluten is a type of protein that’s found in many grains, including wheat, rye, and barley). It gives foods a good texture, but can do a number on your gut. And while it’s true that some people are more sensitive to gluten than others, research has shown that even if you’re not gluten-sensitive, eating gluten can have significant, long-term effects on your gut bacteria, which in turn can affect pretty much any other part of your body.1

Try this instead: There are lots of grain-free alternatives to pretty much anything you can think of, from chips and spaghetti to rice and beyond. Experiment, and you might be surprised at what you can find! Here’s a good place to start.

2. Sugar

No surprises here––we’re all pretty on board with the idea that sugar isn’t the best for your body. (And just to be clear, this includes sugar and sweeteners in all of forms: white sugar, brown sugar, high fructose corn syrup, artificial sweeteners, etc.) But why is it so bad for your gut bacteria? It’s all about balance.

Most of the bacteria in your gut help support your body, but about 15% of the bacteria in there can have some negative impacts on your overall health. Most of the time this isn’t a problem, because as long as the good bacteria outweigh the bad by about six times, things tend to work pretty well. But if the balance of bacteria shifts, then that undesirable bacteria can start to have more of an effect, leaving you feeling less than your best.

What does this have to do with sugar? Well, just like you, your bacteria have to eat. And they get their food from the food that you consume. While some foods are prebiotic, meaning that they break down into substances that feed the good bacteria in your body, others, including sugar, feed the bad guys. The more sugar or sweeteners you eat, the more they can grow, and eventually start crowding out the good bacteria, which has all kinds of effects on your body.2,3

Try this instead: There are lots of natural sweeteners that you can use to replace sugar; honey is one of the easiest to find and use and is a potent prebiotic to boot. And remember, dark chocolate is still in: it contains fibers and flavanols that the gut can use to support your health.

3. Fried and Processed Foods

OK, you probably already know that fried and processed foods aren’t the greatest for you. But did you know why? They’re out for the same reason as sugar: they break down into components that feed the less hospitable bacteria in your gut (not to mention that they have a host of other unsavory health effects). In one memorable experiment, professor of genetic epidemiology Tim Spector found that when his adult son ate strictly fried foods and junk foods for a week, he lost about a third of the species of bacteria in his microbiome, including many beneficial ones. And among the species that stuck around, one linked to problems with weight really flourished. Similar results have been found in other studies.4

Besides the obvious issue with the inhospitable bacteria, the reduction in species of bacteria in the gut––aka gut diversity––is a really big deal. You see, the more diverse your gut microbiome is, the better your health is likely to be. While part of this comes down to easing up on our modern overzealous notions of cleanliness, another part is making sure that the foods you’re eating aren’t devastating your bacterial populations.

Try this instead: If you’re really craving junk food, try opting for healthier versions. For instance, if you’re just dying for some french fries, try having some oven-roasted potatoes or even prebiotic-rich jicama fries instead. Alternatively, you can also make fried foods somewhat healthier by changing the oil that you cook them in, so try using coconut oil or avocado oil instead of canola or vegetable oil. Unlike many other oils, they don’t break down into harmful components when heated, and so are a better choice for anything you’re frying at home.

4. Dairy

Some people are going to be more sensitive to dairy products than others. But research has shown that a diet rich in dairy products has significant effects on your gut microbiome, and it only takes a few days of increased dairy for those changes to take place.4

Another issue with dairy? The possibility of consuming antibiotics in it. While antibiotics are literally lifesavers, overusing them is a recipe for disaster. These substances have a “scorched earth” effect on the gut, getting rid of beneficial and non-beneficial bacteria alike, which really throws your microbiome out of whack.

The issue is, many of us are exposed to more antibiotics than we realize, since they sometimes show up in our food. While FDA regulations in the U.S. state that lactating cows can’t be given antibiotics, since they leach into the milk, a small percentage of farmers have been found to violate those regulations, meaning that your dairy products might not be as antibiotic-free as you’d like.5

Try this instead: Make sure you get the highest quality, organic, grass fed, rBGH free, and preferably raw dairy you can. Some people take an “organic and raw or not at all” approach and although it’s hard, it’s kind of worth it.

5. Soy

You would think that soy would be one of the healthier foods. After all, so many of the foods we consider to be healthy are made with it, and it’s an incredibly common substitute for meat. But here’s the thing—while soy that’s made in very traditional ways can be healthy, most of the soy we consume today is genetically modified and processed in ways that makes it less-than-ideal for our bodies. Studies have shown that a diet high in soy products can have rapid, large-scale negative effects on gut bacteria, particularly Lactobacillus and Bifidobacteria, two strains of bacteria that are incredibly important for microbial health.6

Try this instead: Organic soy can be healthy, especially when it’s fermented (as in the case of natto, tempeh, or miso). Just be sure to read the label carefully, and avoid GMO soy.

6. Red Meat

While having the occasional organic, grass-fed, responsibly farmed steak isn’t likely to throw your whole system off, eating a diet that’s overly meat-heavy can be tough on your body, especially if it includes a lot of red meat.7 While research is ongoing, it’s been shown that eating a lot of red meat affects your gut bacteria fast, increasing undesirable bacteria and decreasing the good guys. Another problem is that unless you’re getting really high quality, responsibly produced meat, chances are that it’s got some antibiotics in it. Crazy fact: 80% of antibiotics used in the U.S. are given to livestock!

Try this instead: Look for organic, grass-fed meat wherever you can. It’s not only much tastier, it’s much better for your health.

7. Tap Water

Staying hydrated is absolutely fundamental to good health. (No surprise, given that our bodies are 55-60% water). So while we would never recommend you putting down your water glass, it might be better to make the switch over to filtered water. While your water is absolutely drinkable when it comes out of the tap, it’s also treated with a number of chemicals, including chlorine, which can have significant negative effects on your gut bacteria.8

And don’t forget about the presence of antibiotics and other chemicals. When we consume antibiotics either as medicine or through our food supply, they get processed by our body and released into our wastewater, which is then sometimes recycled for drinking water. While it is of course processed before it makes its way back to your tap, the water can still have the residue of antibiotics in it, which in turn affects your gut microbiome.

Try this instead: This one’s an easy fix: you can easily get a filter pitcher or go for spring water instead of tap.

8. Eggs

Eggs aren’t bad in and of themselves, but how they’re produced really matters. While eggs that come from chickens who are fed a healthy diet, allowed to roam, and not dosed up with antibiotics are generally fine for your health, your standard farm raised eggs are not so great. Again, it comes down to the possibility of getting those residual antibiotics through your food.

Try this instead: Eggs are one of the easiest foods to find healthy alternatives for, so by all means, keep up the omelets––just make sure your eggs are coming from happy, drug-free, free-range chickens.

9. Farmed Fish

Conventionally farmed fish are, you guessed it, often kept in conditions and fed a diet that’s not ideal for their health. To compensate, the people raising the fish often give them antibiotics directly or in their food, which can then be passed on to you. Also, farmed fish are often fed growth hormones and genetically modified corn that can deplete your beneficial bacteria.

Another potential issue? Some types of fish have high levels of mercury in their flesh, which isn’t good for your health overall, and is also associated with lowered levels of good gut bacteria. Like so many of the other things on this list, fish are fine as long as you consume them in moderation and get them from a reputable source...otherwise, better give them a miss.9,10

Try this instead: Do your best to consume only wild-caught fish, and check out this list of species that are less likely to be contaminated.

10. GMO Foods

GMO foods are relatively new in the market, so research is still ongoing, but there are a number of potential issues with these types of foods. One of the main areas of focus is the negative effects that glyphosate (an herbicide used in growing some GMO foods) has on the gut microbiome. Other research points to changes in the genes of the microbiome: one study has shown that when humans digest genetically-modified foods, the artificially-created genes transfer into the bacteria of the gut and alter their function.11 Ultimately, the potential negative effects on your gut and overall health are reason enough for to avoid GMOs whenever possible.

Try this instead: Look for foods that are grown using traditional methods with non-GMO ingredients. Depending on where you live, the government might require companies to label GMO foods; otherwise, you may have to do a little bit of Internet searching.

In our modern Western culture, chances are you’re going to eat some ice cream or have a glass of tap water every now and then, so don’t worry that if you can’t avoid all of these things all the time that you’re doomed to poor gut health. Instead, do what you can to live a gut-healthy life by taking the best possible care of your body, and giving your microbiome the support it needs to thrive—like making healthy changes to your diet and taking a premium probiotic like PRO-15 to replenish your beneficial gut bacteria.

We know you can do it––and believe us when we say that your gut will thank you for it!

A healthy microbiome is so fundamental to your well-being, and it’s so easy to get started on your journey to optimal gut health. A switched out ingredient here, a water filter there, and you’ll have already made some great strides in supporting your gut.


1. Bonder, M. J., Tigchelaar, E. F., Cai, X., Trynka, G., Cenit, M. C., Hrdlickova, B., . . . Zhernakova, A. (2016). The influence of a short-term gluten-free diet on the human gut microbiome. Genome Medicine,8(1). doi:10.1186/s13073-016-0295-y
2. Turnbaugh P.J., Ridaura, V.K., Faith, J.J., Rey, F.E. . . . Gordon, J.I. (2009) The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice. Science Translational Medicine 1(6). doi: 10.1126/scitranslmed.3000322
3. Suez, J., Korem, T., Zeevi, D., Zilberman-Schapira, G., Thaiss, C. A., Maza, O., . . . Elinav, E. (2014). Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature, 514(7521), 181-186.
4. David, L.A., Maurice, C.F., Carmody, R.N., Gootenberg, D.B. . . . Turnbaugh, P.J. (2014). Diet Rapidly and Reproducibly Alters the Human Gut Microbiome. Nature 505(7484). doi: 10.1038/nature12820
5. Zhu, Y. Lin, X., Zhao, F., Shi, X., Li, H., Li, Y., Zhu, W., Xu, X., Li, C., Zhou, G. (2015). Meat, Dairy and Plant Proteins Alter Bacterial Composition of Rat Gut Bacteria. Scientific Reports 5(15220). doi: 10.1038/srep15220
6. Gill, I.R., Uno, J.K. (2016). The Impact of Dietary Soy on Gut Microbiome. The FASEB Journal 30(1).
7. Paul, B., Barnes, S., Demark-Wahnefried, W., Morrow, C. . . . Tollefsbol, T.O. (2015). Influences of Diet and the Gut Microbiome on Epigenetic Modulation in Cancer and Other Diseases. Clinical Epigenetics 7(112). doi: 10.1186/s13148-015-0144-7
8. Exon, J.H., Koller, L.D., O'Reilly, C.A., Bercz, J.P. (1987). Immunotoxicologic Evaluation of Chlorine-based Drinking Water Disinfectants, Sodium Hypochlorite and Monochloramine. Toxicology 44(3). doi: 10.1016/0300-483X(87)90028-X
9. Cabello F.C. (2006). Heavy Use of Prophylactic Antibiotics in Aquaculture: a Growing Problem for Human and Animal Health and for the Environment. Environmental Microbiology 8(7). doi: 10.1111/j.1462-2920.2006.01054.x
10. Claus, S.P., Guillou, H., Ellero-Simatos, S. (2016). The Gut Microbiota: a Major Player in the Toxicity of Environmental Pollutants? npj Biofilms and Microbiomes 2(16003) doi: 10.1038/npjbiofilms.2016.3
11. Heritage, J. (2004). The Fate of Transgenes in the Human Gut. Nature Biotechnology 22(2).

Rachel Allen is a writer at Hyperbiotics who's absolutely obsessed with learning about how our bodies work. She's fascinated by the latest research on bacteria and the role they play in health, and loves to help others learn about how probiotics can help the body get back in balance. For more ideas on how you can benefit from the power of probiotics and live healthier days, be sure to subscribe to our newsletter. To learn more about how a healthy microbiome can enrich your life, subscribe to our newsletter.