3 Signs You Have an Unhealthy Microbiome

2 minute read

A healthy human microbiome should be resilient to outside influences. Unfortunately, that isn’t always the case. Though there isn’t one standard “healthy” microbiome, there are a few signs that you may have an unhealthy microbiome. Fortunately, there are plenty of nutritional changes you can make to your diet and lifestyle to improve the health of your microbiome!



1. You eat a lot of processed food.

Technically, “processed” food is any food that has been altered from its natural state, usually for the purpose of preservation or preparation. “Processes” include packaging, canning, freezing, and cooking. More highly processed foods — such as fast food, ready-to-eat packaged food, and pre-made meals — are more likely to contain high levels of fat, sugar, and sodium. These types of foods don’t support a healthy microbiome and, in many cases, may even support an unhealthy microbiome instead.[1],[2]

You can support a healthy microbiome with your diet, typically by eating nutrient- and phytonutrient-dense foods (fruits, vegetables, and whole grains). These types of foods — as opposed to highly processed foods — promote diversity in the microbiome and balance in the gastrointestinal (GI) tract. Put simply, minimally processed foods feed the “good” bacteria in the microbiome, and highly processed foods feed the “bad” bacteria.

Lastly, your overall eating habits, (i.e., one fast food dinner or pre-made breakfast meal) will not greatly challenge the health of your microbiome if you normally follow a minimally processed, whole food-based diet. This is great news for those of us who like to indulge in celebrations every once in a while.


antibiotic-use2. You have a history of frequent antibiotic use.

Antibiotics are prescribed to target bacteria. Antibiotic use is important to eliminate bacterial infections, but overuse or misuse of antibiotics can be detrimental to the “good” bacteria in your microbiome.[3] Antibiotics also range in specificity, so a broad-target antibiotic may kill both the intended bacteria and the unintended bacteria in your microbiome — friendly fire, if you will. If you are taking antibiotics as prescribed by your health care practitioner, you can protect your “good” bacteria by supporting your microbiome with prebiotics and probiotics.


stress3. You are super stressed.

If you feel like you’re constantly under stress, your body may also be struggling to cope. Excessive production of the stress hormone cortisol directs attention away from supporting the digestive system to instead prioritize function in vital organs like the heart and brain. This is part of our body’s natural response to stress, commonly known as the “fight or flight” response. This response is helpful in acute cases of stress, but not so helpful when you’re stressed on a regular basis.

With the digestive system and the microbiome neglected as a side effect of chronic stress, lack of natural support for “good” gut bacteria may make for an “unhealthy” microbiome.[4] “Reduce your stress” is often easier said than done, but other lifestyle changes can help mitigate the challenge of unavoidable stress. If you can’t control stress 100 percent of the time, choose instead to change the factors you can control. Build an all-around healthier life for yourself with more frequent physical activity, more fruits and vegetables in the diet and less processed food, and more time spent being mindful in whatever way works for you: meditation, yoga, or hobbies.

Fortunately, for all the lifestyle factors that may suggest you have an “unhealthy” microbiome, there are plenty of healthy changes you can make to change your microbiome health for the better! Find a supplement that supports the microbiome, adjust your diet, consider pre- and probiotics when taking antibiotics, and manage your stress with medicinal herbs and mindfulness.



[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5872783/

[2] https://nutritionj.biomedcentral.com/articles/10.1186/1475-2891-12-158

[3] https://www.nature.com/articles/d42859-019-00019-x

[4] https://www.sciencedirect.com/science/article/pii/S2352289516300509

Tags: microbiome
Meghan Hamrock, MS, MPH
About the Author

Meghan Hamrock, MS, MPH, is the Nutrition Learning Manager for Standard Process located at the Nutrition Innovation Center on the North Carolina Research Campus in Kannapolis, North Carolina. Meghan has a Master of Science in Food Policy and Applied Nutrition and a Master of Public Health in Health Communications, both from Tufts University. She is also a licensed health and wellness coach. Meghan has experience in creating personalized nutrition therapy programs through blood biomarker analysis, coordination and implementation of clinical trials, as well as classroom instruction and coaching expertise. She also has five years of experience in public health nutrition, where she designed and implemented community-based health programs. As an avid marathoner and mom of a toddler, Meghan appreciates the power of nutrition and how it plays such an important role in her daily lifestyle.

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