Dr. Paul Deglmann
Meghan Feir Walker
When your stomach is regularly tight and bloated, gas is rumbling, and constipation or diarrhea frequently affects you, it’s easy to tell you’re facing some digestive troubles. However, not every ailment is as easy to tie back to gut health. Other problems can be caused by digestive distress, including insomnia, mood changes, and other health problems. In this article, we’re covering our top 10 signs of an unhealthy gut to help you understand how connected the body is and what you can do to improve your own digestive health.
Our top 10 signs of an unhealthy gut:
1. Persistent digestive issues
While bloating, gas, constipation, or diarrhea are some of the most obvious red flags of gut health being off, other symptoms commonly affect people with digestive issues.
This can include:
- Bloating
- Gas
- Constipation
- Diarrhea
- Abdominal pain
- Acid reflux
- Heartburn
- Indigestion
- Nausea
- More
These symptoms are frequently caused by imbalances in gut bacteria.
With a healthy gut/microbiome, we should be able to eat a healthy diet, digest the food well, absorb the nutrients from our food, positively impact our healthy gut bacteria, and have consistent/healthy bowel movements on a daily basis. When the gut is unhealthy, there are several steps along the way where problems can occur.

2. Food intolerances or sensitivities
Have more foods been causing symptoms lately? Your gut health is probably the culprit.
Poor gut lining integrity can cause your immune system to overreact to various foods, environmental particles, and more.
When the lining or barrier of the gut breaks down, this can lead to “leaky gut” and passage of undigested food proteins into the bloodstream. This can also cause an increase in immune activation, which can lead to food intolerances, food sensitivities, food allergies, and other symptoms.
A food intolerance is a reaction to a food due to difficulty digesting the food or a specific component of the food (e.g., lactose intolerance).
A food sensitivity is a delayed immune response that occurs after eating a food that can lead to digestive symptoms or symptoms beyond the gut, such as wheezing, sinus issues, headaches, skin rashes, joint pain and many other problems.
A food allergy occurs when your immune system mistakes something (such as a certain type of food) as a threat, causing a severe reaction. Food allergies can also cause symptoms such as wheezing, throat tightness, sinus issues, headaches, and many other problems, but they can also lead to life-threatening symptoms like anaphylaxis in severe cases.
3. Skin flare-ups or acne
The root cause of skin issues often resides in the gut. Whether you’re suffering from acne, eczema, rosacea, psoriasis, other types of dermatitis, welts, and more, these issues are often caused by gut problems.
Dysbiosis or an imbalance of the microbiome can lead to inflammation of the skin. There is a direct connection between the gut and the skin called the “gut-skin axis.” If dysbiosis and inflammation are present in the gut, this can trigger your immune system, often manifesting as skin issues.
This is why many patients see a reflection of their gut health through the appearance of their skin.
4. Weakened immune system
Always catching colds, other viruses, and infections? Your gut undoubtedly needs extra support.
An unhealthy gut can cause the immune system to weaken or make an already weakened immune system even less robust. This can increase your susceptibility to getting sick and cause your body to take longer to repair. The gut directly impacts the immune system because 70-80% of your immune system resides in your gut.
The immune system also controls the inflammatory response. If the gut is unhealthy, inflammation is more likely to occur. When your body is dealing with chronic inflammation, it’s less equipped to ward off additional problems like viruses and infections.
5. Unexplained fatigue
Your energy levels are often directly tied to your gut health.
Poor gut health can lead to mitochondrial dysfunction. Mitochondria are the organelles in your cells that make energy. They are considered the powerhouse of the cell. If the mitochondria are negatively impacted, less ATP or energy is manufactured.
Poor gut health can also lead to poor digestion and poor absorption of nutrients in the small intestine, leading to nutritional deficiencies. Nutritional deficiencies can cause significant fatigue.

6. Frequent mood changes or anxiety
Since the gut makes an estimated 90% of the body’s total neurotransmitters, such as serotonin, an unhealthy gut clearly decreases the production of the body’s neurotransmitters, leading to mood changes and impacting mental health.
There’s no question that the gut-brain connection affects mental health. This is why they say the gut is the second brain. The gut significantly impacts brain health.
7. Sugar cravings and blood sugar swings
Do you have an insatiable sweet tooth? You can probably blame the state of your microbiome for that.
If you have dysbiosis in the gut due to something like candida or bacterial overgrowth, you will probably have intense sugar cravings and blood sugar swings. The yeast and opportunistic bacteria thrive off sugar and cause the body to crave it more. The more you feed these microbes sugar, the more they grow and thrive, and the more they tell your body to feed it increasing amounts of sugar. It’s a vicious cycle.
8. Trouble sleeping or frequent waking
Poor gut health can disrupt your natural sleep rhythm.
Many people don’t realize that the melatonin production in the gut is over 400 times that of the melatonin production in the brain. If the gut is inflamed or out of balance, this can lead to lower melatonin production and cause difficulty sleeping.
Gut inflammation can also drive cortisol levels too high, which is our body’s stress hormone. This, too, can lead to sleep issues.
Another common reason for sleep disturbances is the digestive symptoms themselves. These uncomfortable symptoms, constipation, diarrhea, trapped gas, acid reflux, and other issues, can make it difficult to fall asleep, stay asleep, and get quality sleep.
9. Unintentional weight changes
If you’re having trouble losing or gaining weight and can’t figure out why, both can be signs of microbiome imbalances.
The health of your microbiome has a huge impact on metabolism and body weight. If out of balance, this can be a big reason why you may gain weight easily or have difficulty losing weight.
The opposite problem can also occur, where poor gut health can make it difficult for you to gain weight. Sometimes, a decrease in absorption of nutrients (vitamins, minerals, amino acids, essential fats, etc.) can lead to weight loss or difficulty gaining weight.

10. Bad breath or white-coated tongue
Oral health reflects gut health. Chronic bad breath (that occurs regularly, not just when you eat garlic) is an indicator that something is awry in the gut.
There are several things that can contribute to bad breath, like poor oral hygiene and dehydration, but low stomach acid and candida overgrowth can also be contributing factors.
Poor gut health can also lead to a white-coated tongue. If the white-coated tongue is due to something like candida or fungal overgrowth, this is referred to as oral thrush.
How to tell if your gut is unhealthy
- Persistent digestive issues
- Food intolerances or sensitivities
- Skin flare-ups or acne
- Weakened immune system
- Unexplained fatigue
- Frequent mood changes or anxiety
- Sugar cravings and blood sugar swings
- Trouble sleeping or frequent waking
- Unintentional weight changes
- Bad breath or white-coated tongue
Besides these signs and symptoms, at RHS, we review each patient’s history and testing results to help answer questions regarding the patient’s gut health.
Here are some of the tests we use to thoroughly evaluate gut health:
- Food testing (genetic predisposition for gluten sensitivity, food allergy panels, food sensitivity panels)
- Stool/microbiome testing
- Organic Acids Testing (OAT)
- Nutritional deficiencies
- Adrenal/cortisol testing
- Blood sugar testing
How to fix an unhealthy gut
Step 1: Remove gut irritants
Eliminate ultra-processed foods, sugar, alcohol, and inflammatory seed oils. Use NSAIDs and antibiotics only when truly necessary, as overuse can cause harm, but always consult your healthcare provider to determine what’s right for you.
Step 2: Provide digestive support, if needed
Whether you need to take betaine HCl for stomach acid support, digestive enzymes to break down food more effectively, or other digestive support, ask your healthcare practitioner which may be right for you.
Step 3: Repair the gut lining
Be mindful of what you eat when your gut is in a compromised state. Eat whole, organic, anti-inflammatory foods whenever possible.
For some people, gut-soothing nutrients like L-glutamine, collagen, zinc carnosine, and others can also help repair the lining of the gut.
Step 4: Remove any overgrowth of bacteria, yeast, and/or parasites
Through testing, you can get a better picture of what your microbiome is currently battling. These imbalances can include an overgrowth of yeast, parasites, or bacteria (including H. Pylori). After discovering more information about your gut health, you should work on addressing these issues with your doctor.
Step 5: Repopulate with beneficial bacteria
After problems have been addressed, it’s time to repopulate your gut with beneficial bacteria it may be lacking.
Eating foods rich in prebiotics and probiotics or taking them in supplement form are great ways to add to your microbiome diversity. Whether you’re incorporating fermented foods like sauerkraut, kefir, kimchi, or other foods rich in probiotics or taking probiotics in supplement form, make sure you are taking quality products.
Step 6: Rebalance lifestyle factors
To help your body heal and stay healthy, be sure to practice healthy lifestyle habits. Eat healthy food, drink clean water, breathe clean air, exercise/move your body daily, get daily sunshine, get good/restful sleep, and practice good stress-management strategies
Can you detox your gut?
While the body detoxes naturally, being subjected to too many toxins over time can overwhelm organs and cause congestion, often resulting in slower and clogged detox pathways.
You can support the detoxification process by eating fiber-rich foods that help bind toxins, eating a healthy diet, drinking plenty of purified water (not in plastic bottles), getting regular movement, sweating regularly (whether through exercise or sauna use), and taking liver-supporting herbs like milk thistle and dandelion.
Discuss detox plans with your practitioner first to make sure your plans are safe and appropriate for your unique case.
A healthy gut is foundational
In functional medicine, almost every practitioner starts with addressing the gut first because we believe the gut is the primary root cause of many symptoms and conditions.
Hippocrates is famously quoted as saying, “All disease begins in the gut.” Even then, physicians like him realized how important gut health is to the entire body. This is why we encourage you to pay attention to your health, listen to what your body is trying to tell you, and be proactive before or when symptoms arise.
At RHS, we offer a personalized approach for a helpful and effective path to healing. If you’re ready to learn more about your gut health and the RHS approach, schedule your free 15-minute consultation with Dr. Paul. After running through your health history and symptoms, we test and look at your test results before making a specific protocol with specific dietary and lifestyle recommendations.
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