Eating for Gut Health: How Diet Affects Your Microbiome | Daily Dose

Eating for Gut Health: How Diet Affects Your Microbiome

March 05, 2021 6 min read

Papaya, limes, and mango for gut health

The gut is a complex system that plays a central role in the digestion and absorption of nutrients from food. Housed within the gut is an ecosystem of microbes, forming what's known as the microbiome. These microbes primarily consist of bacteria—both good and bad—and they impact virtually every aspect of health. 

In the microbiome, hundreds of microbial species coexist. Most are symbiotic, or good for the body, while a few are pathogenic or disease-causing. In a healthy body, pathogenic and symbiotic microbiota coexist without problems. However, imbalances brought on by infections, certain diets, or the prolonged use of antibiotics can provoke dysbiosis, interrupting these sound interactions. As a result, the body may become more susceptible to illness.

When your gut is healthy, the rest of your body often is too. That's because the microbiome in your gut influences everything from digestion to cognition to proper immune functioning

On the other hand, if your gut microbiome is weakened or overruled by harmful bacteria, you may encounter health issues. These issues range from bloating, constipation, diarrhea, and indigestion to poor concentration, fatigue, skin problems, and autoimmune disorders. 

Fortunately, the foods you eat can have a tangible impact on the state of your microbiome. By adopting gut-healthy eating habits, you can foster the proliferation of healthy gut bacteria while weeding out the bad. In this article, we'll talk about what those healthy eating habits look like and how you can incorporate them into your lifestyle.

Can diet affect your microbiota?

In addition to factors like medication, genes, and your environment, diet plays a significant role in determining the bacteria that reside in your gut. 

In one experiment published in Cell Host & Microbe, 34 healthy volunteers were asked to record every morsel of food they ate and every drink they consumed for 17 consecutive days. Researchers then analyzed participants' stool samples and confirmed a link between diet and gut bacteria. 

In analyzing results, the researchers could predict changes in the microbiome based on what participants had eaten in the days prior. They also noticed that participants responded to foods differently, illuminating the need for a personalized approach to studying diet-microbiome interactions.

In general, fiber-rich whole foods are particularly beneficial for the microbiome. When dietary fiber is broken down and fermented by bacteria, short-chain fatty acids (SCFAs) are formed. The presence of these SCFAs lowers the pH level of the colon and makes it acidic, thereby limiting the growth of certain harmful bacteria. 

Foods rich in prebiotics and probiotics help maintain a balanced gut microbiome. But beware of introducing too many prebiotic foods into your diet at once, as they can lead to gas and bloating. Instead, slowly ease them into your diet for a smooth transition.  

What to avoid eating for gut health

Artificial sweeteners

Popular artificial sweeteners such as aspartame, saccharin, and sucralose come in contact with the microflora in the gut and induce toxicity in the microbiome. 

Several animal studies point out that artificial sweeteners like Splendaaspartame, and saccharin cause changes in the gut ecosystem, increasing the number of harmful bacteria while reducing beneficial strains. They also caused glucose intolerance in some subjects.

In any case, keep an eye out for these artificial sweeteners on the labels of processed food, yogurts, granolas, and drinks like diet sodas and other snacks that claim to be zero-calorie. 

Processed and refined foods

Limiting highly processed foods loaded with questionable ingredients is one of the best things you can do for your microbiome. Most processed foods lack fiber and micronutrients, and they're often packed with empty calories and preservatives. 

While your taste buds may prefer processed foods, your gut bacteria thrive on diverse nutrients and polyphenols from fresh, whole foods.

Red meat

Red meat has a chemical compound called L-carnitine, which alters the gut microbiota in a way that is harmful to the heart. A study conducted at Cleveland Clinic demonstrated that red meat could increase the risk of developing arteriosclerosis (narrowing or obstruction of the arteries) by producing greater amounts of trimethylamine N-oxide (TMAO).

A diet rich in L-carnitine makes you more susceptible to forming TMAO and suffering its artery-clogging effects. Those on plant-based diets have a reduced capacity to synthesize TMAO from carnitine, making these diets preferable for heart health. 

Hamburger and fries to avoid for gut health

Foods containing antibiotics

Most animals raised for consumption, such as poultry and cattle, are treated with antibiotics to reduce the risk of infection in crowded farms. Of note, animal agriculture comprises 70% of American antibiotic use

When you consume meat from animals injected with antibiotics, you're consuming those antibiotics as well. This elevates your risk of antibiotic resistance, which occurs when your gut bacteria are repeatedly exposed to antibiotics and evolve to resist the drugs. It also puts the healthy bacteria in your gut at risk as the antibiotics work to eradicate the harmful bacteria. 

To combat these risks, try to limit your meat intake and opt for organic and sustainably raised meat whenever possible. It may be marginally more expensive, but it's a small price to pay for your health. 

Fried foods

By now, you're probably aware that frying food destroys its nutritional value and does more harm to the body than good. The frying oil multiplies your caloric intake while adding harmful trans fats to your meal. 

Frying foods at high temperatures heats oils to the point of hydrogenation, altering their chemical structure into a state your body struggles to digest. In the gut, these hydrogenated fats feed the bad bacteria in your gut and may even promote their growth. 

In one single-subject study, Tom Spector, a genetic epidemiology professor, found that when his son ate only fried junk food for a week, his microbial diversity decreased by about one-third. What's worse, the majority of bacteria lost were beneficial strains. The strains that remained were largely those promoting weight gain. 


Dairy is hard on your digestive system, even if you're not lactose intolerant. Studies have shown that dairy consumption can change your gut's bacterial makeup within days, allowing strains linked to intestinal disease and inflammation to flourish.

Genetically-Modified Organisms (GMOs)

Genetically modified crops are resistant to certain pests, diseases, and herbicides, making them a valuable tool for farmers. One of the primary concerns regarding genetically modified crops is glyphosate, a broad-spectrum herbicide commonly applied to kill weeds competing with crops for resources. 

Aside from the potential carcinogenic properties of glyphosate, studies have found that consumption of GMO foods can reduce the beneficial bacteria populations in the gut. Common GMOs include corn, soy, canola, and animal products.

Eating for gut health

Women holding green leafy vegetables in a basket

Eat your vegetables

This may seem like a no-brainer, but it's worth repeating. The reason vegetables, especially the green leafy varieties, are so good for your gut is because they're loaded with fiber and phytonutrients. This fiber feeds the healthy bacteria in your gut, encouraging them to thrive.  

Fruits also supply ample fiber and micronutrients to benefit your microbiome. The best approach is switching up the fruits and vegetables in your diet to provide a diverse supply of micronutrients and fibers to your gut bacteria.


Probiotics are microorganisms or bacteria that provide a health benefit to your body. They've been used to treat a host of gastrointestinal issues for decades and are great for people with occasional constipation, diarrhea, and other digestive troubles.

You can get your probiotics from naturally fermented food sources or in the form of high-quality probiotic supplements. If you're on antibiotics, your doctor might prescribe a probiotic supplement to repopulate the good bacteria that get wiped out from the treatment. 

Not all strains of probiotics are the same. While there are hundreds available, those stemming from the Lactobacillus or Bifidobacterium genera are the most common. Once you've identified the problem you're looking to solve, you can research from there to find the probiotic that fits your needs.

The efficacy of your probiotic may depend on the strain, dose, and pH level in your body. Since no conclusive studies prove that the bacteria you ingest via probiotics stay in your system for extended periods, it's a good idea to incorporate them into your regular routine. 

Some of the natural foods rich in probiotics include kefir, sauerkraut, kimchi, kombucha, tempeh, and yogurt. Foods contain lower doses (CFUs) than probiotic supplements, so you can include these in your diet whether you're supplementing or not.  


While prebiotics don't contain bacteria, they create an environment that fosters the growth of good bacteria in your gut. Prebiotics are fibers that cannot be digested by humans but can be digested by your gut bacteria. They help provide nutrients to the gut microbiota and support healthy digestion and immune functions. 

While there are many natural sources of prebiotics, you can also supplement with a synbiotic (probiotic + prebiotic) to make sure you get your daily dose of prebiotics. 

Some natural sources of prebiotics include onions, artichokes, garlic, legumes, oatmeal, and apples. 

In summary

Trillions of microorganisms spanning hundreds of species make up your gut microbiota. This delicate ecosystem, often referred to as the microbiome, is responsible for healthy digestion and immune functioning.

Each person has a unique microbiome influenced by their DNA, environment, and diet. Diet plays a significant role in determining the nature of the gut microbiota. Foods high in sugar, refined carbohydrates, and trans fats are harmful to the microbiome as they kill the good bacteria and create a conducive environment for the bad ones.

On the other hand, foods rich in fiber, probiotics, and prebiotics are great for the gut microbiome. You can get probiotics and prebiotics from a number of natural sources, or you can opt for a high-quality probiotic and prebiotic supplement.

It's interesting to note that just like fingerprints, no two guts are the same. So while this article provides general guidelines on the kind of food to eat and avoid, you may be the best judge of the combination of foods that work for and against you. 

Ramya Satheesh - Contributing Writer, Physician's Choice


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