12 Signs of an Unhealthy Gut Microbiome

How in tune are you with your gut? Many people these days have at least heard of the term 'gut microbiome', which refers to the ecosystem made up of trillions of microbes that live in your digestive system. As a matter of fact, our gut is home to over 100 trillion bacteria and there are up to 1,000 different species, each with a different function. 

More people are becoming aware that the balance of the types of these microbes in our gut plays a major role in our health. These bacteria help with regulating digestion and metabolism, but they also impact other facets of your health, like allergies, immunity, mental health, and more. 

When the balance of this bacteria ecosystem is jeopardized, countless chronic health issues can arise, such as skin disorders, insomnia, anxiety, brain fog, fatigue, food intolerances, and autoimmune diseases, to name a few. 

In this article we'll address which warning signals to watch out for from an unhealthy gut, the different factors that can affect digestive health, and ways in which to support your gut health and help it thrive. 

Oftentimes, it seems like modern culture has normalized digestive issues, brushing off digestive upset as an ordinary part of life. But the truth is, while some symptoms like gas and bloating are common, they shouldn’t be happening consistently or excessively. 
In reality, these symptoms – and many more – could be a sign of underlying health issues or an imbalance of your gut microbiome.

The gut microbiome is a fragile environment that is influenced by many factors, including age, diet, stress, lack of sleep, toxins, antibiotics, and other prescription medications [2]. Digestive conditions like lactose intolerance, celiac disease, acid reflux, and more, can also play a role. 

Over time, many of these elements can add up and lead to issues in the digestive system. When this happens, a condition called gut dysbiosis occurs. This is when the bacteria in the gut becomes unbalanced and there is more “bad” bacteria than “good” bacteria, which can lead to health issues. While no bacteria is inherently good or bad, the “bad” bacteria are thought to cause disease, while the “good” bacteria promote health.

1. Excessive Stomach Upset


As mentioned previously, occasional gas or bloating is common, as it is a normal part of the digestive process. However, if you experience these symptoms frequently or they make you feel uncomfortable, it could be a sign of an underlying issue, like lactose intolerance or gut dysbiosis. 

2. Unhealthy Bowel Movements


While it may not be appealing, maintaining awareness of your bowel movements can help you stay in tune with your digestive system. Every body is different, but on average, bowel movements should be occurring about 1-3 times per day. Healthy transit time is around 21-24 hours after eating. The easiest way to track this is by eating a meal rich in corn or beets – corn often shows up partially undigested and beets will result in a red coloration. 

If your transit time is way off, or you’re not having 1-3 bowel movements each day, it may be a sign of an unhealthy gut. Frequent diarrhea, constipation, or undigested food (besides corn) in your stool are also indications that something is off. 

3. Fatigue


Chronic fatigue, where you feel tired often or all the time, could be a sign of an unhealthy gut. If naps or caffeine (or both) are a necessary part of your day, you might have gut dysbiosis. 

Your digestive system uses energy to function, so if there is a gut imbalance, it will have to work overtime to digest your meals. This means you’ll have less energy for other bodily functions. Chronic fatigue is common among people who struggle with irritable bowel syndrome (IBS). 

4. Insomnia


If you have difficulty sleeping or have been diagnosed with insomnia, an unhealthy gut may be the culprit. The majority of your body’s serotonin is made in the gut – serotonin is a neurotransmitter necessary for making melatonin, the sleep hormone.

If your body has difficulty producing serotonin due to an unhealthy gut, then it will reduce the amount of melatonin your body produces, negatively impacting your ability to fall asleep and your sleep quality. 

5. Poor Immunity

Almost 70-80% of our immune system cells live in our gut. If you are the type of person that is always getting sick, it may be due to a gut imbalance. For example, the “good” bacteria Lactobacillus, commonly seen in yogurt, helps support your immune cells. Less “good” bacteria in your gut can result in a lowered immune system.

6. Unhealthy Skin 


The health of your skin is often a direct reflection of what is happening inside your body. An unhealthy gut can lead to internal inflammation, which has been linked to chronic acne and other skin conditions like eczema and psoriasis [2]. If your skin is constantly dry, irritated, acne prone, or anything else abnormal to your usual, it could be an indication of an unhealthy gut.

7. Poor Brain Function


Brain fog – difficulty with focus, memory, thinking, or concentration – is one of the main symptoms of IBS and inflammatory bowel disease (IBD). When gut dysbiosis occurs, it leads to inflammation in the body, which can disrupt the neurotransmitters that support brain and mental function. Poor gut health also means difficulty absorbing vitamins and minerals, which are important building blocks of brain health and cognition. 

8. Poor Mental Health


Not only can an unhealthy gut impact your brain function, but it can also negatively affect your emotional health and lead to mental health issues like anxiety and depression. Serotonin, which is primarily made in the gut, is also known as your body's natural “feel good” chemical because it helps regulate mood.

Have you ever gotten butterflies in your stomach from stress? Or felt angry or upset when your stomach isn’t feeling well? Our feelings and emotions are deeply intertwined with our gut health, a phenomenon known as the gut-brain connection. 

9. Unintentional Weight Changes


Unplanned significant weight gain or loss is usually a sign of an underlying health issue. When you have an unhealthy gut, your digestive system struggles to absorb nutrients and regulate blood sugar. Unexpected weight fluctuations could be due to an overgrowth of “bad” bacteria or a lack of nutrients. 

However, other health conditions (like thyroid issues or menopause) can also lead to unintentional weight changes, so it’s important to visit your doctor for further testing if this is happening to you.

10. Food Intolerances


Do you notice digestive upset or symptoms like bloating, gas, rashes, nausea, inflammation, heartburn, or pain after eating certain foods? This may be a sign that you have a food sensitivity or intolerance. A food intolerance occurs when your body has difficulty digesting certain foods. It can happen with common allergens, like gluten or dairy, or sometimes other foods that seem less obvious.

Unfortunately, some food reactions don’t happen directly after eating a meal, and can occur up to 72 hours after consuming an irritating food, which can make it difficult to figure out what is causing your symptoms. If you think you may have food sensitivities, visiting a health professional to get further testing can help.

11. Food Cravings

Do you have a sweet tooth? Extreme food cravings, especially for sugar, can be a sign of an unhealthy gut. That’s because the microbes can actually generate food cravings for the types of food that they use as fuel, even going as far as making you feel sad or upset until you satisfy the craving [3]. 

Eating excess sugar feeds the “bad” bacteria in the digestive system, causing them to flourish and out-balance the “good” bacteria. This can lead to gut dysbiosis, candida overgrowth, leaky gut syndrome, and other long-term health issues.

12. Autoimmune Problems


Too much “bad” bacteria in the gut has been linked to autoimmune conditions like thyroid disease, rheumatoid arthritis, multiple sclerosis, and type 1 diabetes [4].

Just as there are many factors that can affect gut health, there are many ways to improve it. You will likely need to incorporate a variety of different treatment protocols into your life to support digestive health. 

First of all, it is important to consult a medical professional and talk about your issues to see if you need a gastrointestinal (GI) test, food intolerance testing, or other types of exams. Testing can help you determine if you have any underlying health conditions, as well as guide you towards which steps to take for addressing your unhealthy gut. You may need to avoid certain foods or take specific supplements based on your unique individual gut health.

Diet plays a huge role in your digestive health. Focus on eating foods that feed the “good” bacteria, like probiotic rich foods such as yogurt, kefir, sauerkraut, beet kvass, kimchi, jun and kombucha. Eating a plant-based diet rich in high fiber foods is also supportive of a healthy gut. Avoid eating large amounts of foods that boost “bad” bacteria, like sugar, yeast, and alcohol.

There are also a wide variety of digestive herbs that you can incorporate into your diet or consume in the form of teas, tinctures, digestifs, and more. However, learning about healing plants is only one part of the holistic healing practice. Other lifestyle factors that can help support gut health include exercise, drinking adequate amounts of water, and participating in self-care activities that lower your stress levels. 

Our digestive system is a collection of complex organs. Every body is different and every gut is different, therefore, there is not one exact protocol to follow for good gut health. It’s best to work with a nutritionist and other health professionals to find the best healing plan for you.

Article Written By Melissa Szaro

1. Robertson, R. (2017). Why the Gut Microbiome Is Crucial for Your Health. https://www.healthline.com/nutrition/gut-microbiome-and-health

2. Mahmud, R., Akter, S., Tamanna, S.K., Mazumder, L., Esti, I.Z., Banerjee, S., Akter, S.,  Hasan, R., Acharjee, M., Hossain, S., & Pirttilä, A.M. (2022). Impact of gut microbiome on skin health: gut-skin axis observed through the lenses of therapeutics and skin diseases. Gut Microbes. 14(1): 2096995. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9311318/

3. Alcock, J., Maley, C.C., & Aktipis, C.A. (2014). Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms. Bioessays. 36(10): 940–949. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270213/

4. Frederick Health. (2021). 10 Signs of an Unhealthy Gut. https://www.frederickhealth.org/news/2021/july/10-signs-of-an-unhealthy-gut/

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*The statements above have not been evaluated by the FDA, and are for educational purposes only. This article is not intended to diagnose, treat, cure, or prevent any disease. This article should not be taken as medical advice. Please consult your physician before you use this information for health purposes.