Top 8 Foods That Harm the Microbiome

These foods are bad for your gut health

Credits: ​Tomasz Rynkiewicz at

Emerging research continues to demonstrate the importance of the gut microbiome in overall health, and most recently, skin health.[1] This is an area of research in need of immense exploration, for we have not defined what is considered the “perfect” set of microbial species and strains to make up the ideal gut microbiome. However, we know that communities of organisms vary greatly amongst healthy individuals, and that dietary patterns play a significant influence on the makeup of our microbiome. Changes in dietary patterns (such as animal-based versus plant-based diets) result in rapid changes in the gut microbiome.[2] In order to achieve optimal gut health, and potentially prevent or improve skin conditions or blemishes, it is important to understand what foods could be hurting our microbiome.  


1. Alcohol

Aside from increasing the risk of various diseases and cancers in almost every organ system of the body, excessive alcohol also wreaks havoc on the gut microbiome. Not only does alcohol cause intestinal inflammation and microbiome disruption, but it also causes systemic inflammation and tissue damage.[3] However, red wine in moderation may be beneficial to the microbiome.[4]


2. Artificial Sweeteners

Artificial sweeteners such as Splenda® (sucralose) and Equal® (aspartame) may be calorie-free, but they are associated with health risks. Splenda can elevate insulin and increase the risk for weight gain.[5] Aspartame, which breaks down into formaldehyde, is associated with cancer risk.[6] Additionally, non-caloric artificial sweeteners have been reported to have a negative impact on the gut microbiome, causing dysbioses and even glucose intolerance.[7]


3. Dairy

Cow’s milk and milk products (ice cream, yogurt, cheese, butter, sour cream, cottage cheese, etc.) can cause abdominal discomfort and immune reactions in people who are allergic or intolerant to lactose. Dairy is associated with diarrhea and bloating in lactose intolerant individuals, and it can also worsen acne in some people.[8] Dairy can lead to imbalances in the gut microbiome in people with lactose intolerance, which can promote gas-producing bacteria to grow.[9,10] In a study at Harvard University, subjects who consumed a cheese and meat-based diet had significantly different gut microbiota after only 2 days compared to subjects who ate a plant-based diet. In fact, cheese fungus was significantly elevated in the feces of subjects in the animal-based diet group.[2] Fortunately, if you feel you might be sensitive to cow’s milk, there are many non-dairy alternatives such as almond milk, flax milk, hemp milk, and even coconut milk and coconut ice cream.


4. High Fructose Corn Syrup

High fructose corn syrup has similar effects on the body as sugar. It spikes insulin levels and is linked with obesity, diabetes, fatty liver disease, and overall inflammation. High fructose corn syrup is a cheaper alternative to sugar and is therefore added into most junk food, sports drinks, jellies, and breakfast cereals. Eating high fructose corn syrup primes the gut to have an increase in bacteria that can metabolize it, which disrupts the balance of bacteria that are better at metabolizing healthier foods. Additionally, a Western diet including high fructose corn syrup may condition the gut microbiome to have higher amount of Firmicutes compared to Bacterioidetes species, which has been associated with obesity.[11]


5. Meat

The association between meat and heart disease may not only be due to saturated fats and cholesterol in meat, but other factors involving the gut microbiome may also be to blame. A study reported that microbial by-products from gut bacteria metabolism of meat could increase the risk for heart disease.[12] Researchers at the Cleveland Clinic believe that a compound in meat called L-carnitine can be broken down by gut microbiota to produce trimethylamine-N-oxide (TMAO), a chemical associated with plaque buildup (atherosclerosis) in arteries throughout the body. According to Dr. Stanley L. Hazen who led the study, a diet “high in carnitine actually shifts our gut microbiome composition to those that like carnitine, making meat eaters even more susceptible to forming TMAO, which helps promote atherosclerosis.”[12]


6. Processed and Refined Foods

If you are trying to improve gut health, you should say “no” to cookies, chips, crackers, packaged deli meats, microwaveable snacks, and other highly processed and chemical-loaded snacks. These foods are packed with sugar, sodium, refined carbohydrates, saturated fats, artificial sweeteners, preservatives, color additives, and calories while being devoid of almost any nutritional sustenance. This is a recipe for an altered gut microbiome and a cascade of other detrimental health effects, including insulin resistance, obesity, and diabetes.[13]


7. Sugar

Refined sugar is a prominent ingredient in the Western diet, found in cookies, cakes, candy, and snuck into sauces, marinades, and sports drinks. In addition to fueling the obesity epidemic, sugar also feeds some of the more harmful bacteria living in our guts, causing them to overgrow and disrupt the homeostasis of our gut microbiome.[14] There are other options for sweetening your food, including agave syrup, which has less of an impact on spiking insulin levels, coconut sugar, and stevia leaf.


8. Trans Fats and Hydrogenated Fats

Diets high in fats, especially trans and hydrogenated fats, are associated with unhealthy alterations in the gut microbiome. A study in the Philippines compared children who consumed a Westernized diet (>27% calories from fat) with children who consumed a lower fat diet (18% fat). The children who consumed higher amounts of fat from fast food consumption were significantly more overweight and obese than the children who did not. Additionally, the overweight group’s microbiome harbored a higher Firmicutes-to-Bacterioides species ratio and had a lower abundance of Prevotella compared to the lower fat group. Firmicutes have been highly associated with the Western Diet and obesity. This study demonstrates the significant impact that diet plays on the species of microbes living in our guts and their association with detrimental health effects, such as obesity.[15]


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