We often think of our stomach as just a fuel tank – we put food in, and energy comes out. But science tells us that the “gut” (your digestive system) is much more than that. It is actually the control center for your entire body. Doctors even refer to it as your “second brain.” Because of this deep connection, the state of an unhealthy gut directly influences your mental well-being, playing a significant role in managing anxiety and stress.
Inside your intestines, there are trillions of tiny living bacteria. This is called your microbiome. When these bacteria are happy, you feel great. You have energy, your skin glows and your mood is stable. Often, maintaining this balance does not require complex prescriptions, but can be achieved through effective natural remedies.
Why early detection of an unhealthy gut matters
When the delicate balance of your microbiome is disrupted (meaning the “bad” bacteria begin to outnumber the beneficial ones) the consequences ripple far beyond just your digestive tract. An unhealthy gut can cause problems that seem unrelated to your stomach, such as skin rashes, brain fog or chronic fatigue. Ignoring these underlying issues can lead to chronic health struggles and rising medication costs over time.
Many serious diseases, including diabetes, heart disease and autoimmune disorders, start in the gut. Fixing your digestion now is the best way to prevent chronic illness later. Here are 10 warning signs of an unhealthy gut to watch for.
1. Constant stomach upset
This is frequently the most immediate and persistent warning sign that your digestive system is in distress. In a truly healthy state, digestion should be a seamless, background process; you should be able to consume meals, absorb nutrients and eliminate waste without any physical discomfort or conscious effort.
However, if you find yourself regularly battling symptoms such as excessive gas, painful bloating, chronic constipation, diarrhea or recurring heartburn, your unhealthy gut is sending a clear distress signal. While an occasional stomach ache is normal, experiencing these issues on a weekly basis suggests an underlying dysfunction.
According to experts at Johns Hopkins Medicine, these chronic symptoms are often indicative of a condition known as “dysbiosis.” This medical term refers to a significant imbalance in the complex ecosystem of your gut microbiome, where harmful microbes begin to outnumber the beneficial bacteria. When this balance is disrupted, your body loses its ability to efficiently process food and eliminate toxins, leading to ongoing physical discomfort and a compromised digestive system.
2. Craving sugar all the time
Do you feel like you need a cookie or a soda after every meal? That might not be you talking. It might be your bacteria – different bacteria like different foods. Good bacteria love fiber, including that found in vegetables. Harmful bacteria and yeast love sugar.
If you have too many harmful bacteria, they can actually send chemical signals to your brain to make you crave sugar. The more sugar you eat, the more the harmful bacteria grow. It becomes a vicious cycle. A study published by the National Institutes of Health (NIH) suggests that unhealthy gut microbes can manipulate our eating behavior to serve their own survival.
3. Lack of quality sleep
It may seem counterintuitive, but your digestive system plays a critical, often overlooked role in regulating your sleep cycle. While most people assume that sleep issues are strictly neurological, the root cause frequently lies within the “second brain.” This connection centers on serotonin, a powerful neurotransmitter famously known as the “happy hormone” that is essential for regulating both mood and sleep patterns.
Contrary to popular belief, serotonin is not primarily produced in the cranial brain. Groundbreaking research from the California Institute of Technology (Caltech) reports that a staggering 90% of your body’s serotonin is actually manufactured in the gut. Consequently, the biological health of your microbiome directly influences your body’s ability to rest chemically.
If your gut is suffering from inflammation, dysbiosis or general poor health, its ability to synthesize this vital neurotransmitter is severely compromised. Without adequate serotonin production, your body struggles to regulate its natural rhythms, leading to chronic insomnia, fragmented rest or consistently poor sleep quality. Therefore, if you find yourself tossing and turning all night, the culprit may not be the stress of the day, but rather the state of your digestive tract and what you ate for dinner.
4. Sudden skin irritation
Your skin is often a mirror of what is happening inside your body. Healthcare professionals call this the “gut-skin axis.” When the gut is “leaky,” meaning toxins escape the intestines and enter the bloodstream, the body tries to clear them through the skin. This causes inflammation.
Common skin issues are linked to poor gut health. These include eczema (itchy, red, dry patches), acne (persistent breakouts, especially around the mouth and jaw) and rosacea (redness in the face). According to research published in PubMed, there is a direct link between gut inflammation and skin diseases. Adjusting your diet often clears up your skin more effectively than expensive creams.
5. New food intolerances
Developing sudden sensitivities to foods you previously enjoyed is a frustrating and significant indicator of an unhealthy gut. It is crucial to distinguish this from a food allergy; while allergies invoke an immune system response that can be life-threatening (such as anaphylactic shock from peanuts), a food intolerance is strictly a digestive issue. It doesn’t trigger the immune system, but it causes significant physical misery.
If you notice that foods like dairy, gluten or corn now leave you feeling lethargic, nauseous or suffering from gas, severe bloating and abdominal pain, your gut ecosystem is likely shifting. This phenomenon occurs because digestion is a collaborative effort between your body and the bacteria that inhabit it. Specific strains of beneficial bacteria are responsible for breaking down specific types of food.
When your microbiome diversity drops – often due to stress, diet or antibiotics – you lose the specific “worker” bacteria needed to process these complex ingredients. Without them, the food ferments rather than digests. As noted by the Cleveland Clinic, struggling to process common foods is rarely just “aging”; it is a direct symptom of poor bacterial quality and a red flag that your gut lacks the necessary diversity to function correctly.
6. Feeling anxious or down
We often say we have a “gut feeling” about things. This is medically true. The gut and the brain are connected by a large nerve called the vagus nerve. They talk to each other constantly. If your gut is inflamed, it sends “stress” signals to your brain. This can make you feel anxious, depressed or foggy.
Harvard Health explains that a troubled intestine can send signals to the brain, just as a troubled brain can send signals to the gut. Therefore, a person’s stomach or intestinal distress can be the cause or the product of anxiety, stress or depression.
7. Unintentional changes in weight
Experiencing a sudden or gradual fluctuation in weight (whether gaining or losing) without any conscious alteration to your diet, activity level or exercise routine is a confusing and significant red flag. While it is easy to blame willpower or genetics, the reality is often biological: your gut microbiome acts as a central control center for your metabolism, and when it malfunctions, the numbers on the scale can drift unpredictably.
When your gut is in a state of dysbiosis (imbalance), it disrupts critical metabolic processes. A healthy gut regulates how your body manages blood sugar, absorbs nutrients and releases the hormones that signal hunger and fullness (satiety). When this system breaks down, your body no longer processes energy efficiently. Some types of harmful bacteria actually increase the amount of calories you absorb from food, leading to weight gain. If you have bacterial overgrowth in the small intestine, it can block nutrient absorption entirely, leading to unexplained weight loss.
8. Getting sick often
If you find yourself constantly battling the sniffles, catching every flu that circulates or feeling generally run-down while others stay healthy, the culprit might be your digestive tract. While we often think of immunity as being located in the lymph nodes, a staggering 70% of your entire immune system actually resides within your gut.
This relationship is symbiotic; a healthy microbiome acts as a strict “gatekeeper” and a training ground for your body’s defenses. Beneficial bacteria communicate directly with immune cells, teaching them to effectively identify and attack dangerous invaders while ignoring harmless inputs.
However, when your gut bacteria are out of balance, this defensive wall is compromised. If your gut is in a state of dysbiosis, your immune system is forced to shift its focus inward to fight chronic inflammation in the stomach. Because your immune resources are distracted and depleted by this internal battle, they are less effective at neutralizing external threats. This leaves you significantly more vulnerable to viruses, bacteria and seasonal infections.
9. Chronic fatigue
It is crucial to distinguish between the normal tiredness felt after a busy day and the debilitating sensation of chronic fatigue. If you feel perpetually exhausted, sluggish or “heavy” regardless of how much you sleep, your digestive system may be failing to fuel your body effectively. If your intestinal villi (the tiny fingers responsible for absorption) are compromised, you may develop deficiencies in Vitamin B12, iron and magnesium, even if your diet is healthy. Without these essential fuel sources, your cells literally lack the power to function
Furthermore, a compromised gut creates a state of chronic, low-grade inflammation. Your body perceives this inflammation as an internal threat and directs a massive amount of energy toward the immune system to fight it. This metabolic “tax” depletes your reserves, leaving you physically drained and mentally foggy, no matter how many cups of coffee you drink.
10. Persistent bad breath
While society often blames bad breath on garlic, onions or poor oral hygiene, the true source of chronic halitosis frequently lies far below the gum line. If you are diligent about brushing, flossing and using mouthwash but still struggle with a persistent, unpleasant odor, the issue is likely not in your mouth – it is in your microbiome.
This condition is often a direct result of Small Intestinal Bacterial Overgrowth (SIBO) or an infection like H. pylori. When harmful bacteria populate the small intestine in large numbers, they ferment the food you eat before your body can absorb it. This fermentation process produces distinct, foul-smelling gases – such as methane or hydrogen sulfide (which smells like rotten eggs).
Unlike gas that is expelled as flatulence, these gases are absorbed through the intestinal lining directly into your bloodstream. From there, they circulate to your lungs and are eventually exhaled. Because the smell is coming from your lungs rather than your teeth, no amount of mints or brushing can mask it. It is a metabolic sign that your digestive fermentation is out of control.
What foods cause an unhealthy gut?
To heal, you must stop feeding the harmful bacteria. The biggest enemies of a healthy gut are ultra-processed foods, such as chips, fast food and boxed meals, which often contain preservatives that can kill beneficial bacteria. Dietary habits regarding sweets and drinks also play a massive role. Sugar is a major culprit, serving as a favorite food for harmful bacteria, while artificial sweeteners in diet sodas can negatively alter the composition of your microbiome.
Alcohol is similarly damaging, as drinking too much destroys the lining of the intestines and kills beneficial microbes. Also, external factors, such as medication, can have a drastic impact. While sometimes necessary for infections, antibiotics act like a nuclear bomb in the gut. They destroy the harmful germs, but unfortunately, they also eliminate the beneficial ones.
How can I fix my unhealthy gut fast?
Healing takes time, but you can start today with a few simple changes. Fermented foods are naturally rich in probiotics (live beneficial bacteria). They include yogurt (with live cultures), sauerkraut, kimchi, kefir and kombucha. Adding more fiber (or prebiotics) to your diet also helps. Plant fiber feeds your good bacteria; this includes bananas, onions and garlic, oats and apples.
It’s also recommended that you prioritize sleep, as your gut repairs itself while you sleep. Aim for seven to eight hours each night. As Dr. Justus Rabach, MD, explains, “As we age, the natural cycles slow down and don’t work as well. To counter this, lower stress, because high stress impedes digestion. Try meditation or deep breathing before meals.”
When to see a doctor about an unhealthy gut
While occasional gas is standard, some symptoms are urgent warnings. You need to see a doctor immediately if you experience diarrhea that lasts for several days or if you ever see blood in your stool. Pay attention to other physical changes as well. Severe stomach pain that persists, unintentional weight loss or difficulty swallowing are all clear signs that something is wrong.
Do not ignore these red flags. They could be symptoms of severe conditions like Crohn’s disease, ulcerative colitis or celiac disease that require professional care.
Bottom line
Your gut is far more than just a digestive system; it functions as a central control center that influences nearly every aspect of your physiology, from your emotional stability (mood) to the clarity of your complexion (skin). When this complex system is out of balance, the body often communicates through a specific set of distress signals. These include constant bloating after meals, intense and unexplainable sugar cravings, fragmented or poor-quality sleep and persistent skin irritations like eczema or acne. Fortunately, you have the power to reverse this damage and heal your microbiome through strategic dietary changes. The most effective first step is to eliminate processed sugars, which serve as a direct fuel source for harmful bacteria and yeast.
Frequently Asked Questions
How long does it take to reset your gut?
Studies show that your gut microbiome can begin to change within two to four days of changing your diet, but lasting healing can take up to six months, according to Harvard Health.
What drink heals your gut?
Bone broth is widely considered the best drink for healing because it contains collagen and amino acids (like glutamine) that help repair the intestinal lining.
What are the signs of poor gut health on the skin?
Common signs include eczema, rosacea, acne and extremely dry or flaky skin, which indicate inflammation in the body, as per PubMed.
Citations
Johns Hopkins Medicine. Your Digestive System: 5 Ways to Support Gut Health. www.hopkinsmedicine.org. Published 2025. https://www.hopkinsmedicine.org/health/wellness-and-prevention/your-digestive-system-5-ways-to-support-gut-health
Alcock J, Maley CC, Aktipis CA. Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms. BioEssays. 2014;36(10):940-949. doi:https://doi.org/10.1002/bies.201400071
Salem I, Ramser A, Isham N, Ghannoum MA. The Gut Microbiome as a Major Regulator of the Gut-Skin Axis. Frontiers in Microbiology. 2018;9(9). doi:https://doi.org/10.3389/fmicb.2018.01459
Cleveland Clinic. Food intolerance: Symptoms, causes, and treatment options. Cleveland Clinic. Published August 11, 2021. https://my.clevelandclinic.org/health/diseases/21688-food-intolerance
Harvard Health Publishing. Can gut bacteria improve your health? – Harvard Health. Harvard Health. Published October 14, 2016. https://www.health.harvard.edu/staying-healthy/can-gut-bacteria-improve-your-health