Signs of Bad Gut Health – and What to Do About It
Is your gut trying to tell you something? Learn to recognize the signs of bad gut health and take science-backed steps to heal.
Why Gut Health Is the Foundation of Overall Wellness
Your gut is home to trillions of microbes that influence digestion, immunity, mental health, and more. When your gut is in balance, you feel energized, focused, and resilient. But when it’s off, your body starts sending signals — and you may not even realize they’re connected to your gut. Many of my patient think it is just old age (although they are in their 50s!) or familial (because they have heard similar symptoms from the elderly in their family). Usually it all boils down to not recognising that the gut is one of the MOST POWERFUL organs in the body (it’s not called the SECOND BRAIN for nothing!) and not taking care of your gut health. Additionally, symptoms of poor gut health don’t always originate from the gut. Chronic systemic inflammation stemming from an unbalanced gut can affect almost any system in the body and cause disease.
Understanding the signs of bad gut health is the first step to reclaiming your well-being.
7 Common Signs of Bad Gut Health
1. Digestive Issues
Frequent bloating, gas, constipation, diarrhea, or heartburn are classic signs of gut dysfunction. These could be caused by low stomach acid, enzyme deficiencies, dysbiosis, or conditions such as irritable bowel syndrome (IBS). You may have an occasional stomach upset after eating dubious foods. However, if you frequently experience these symptoms, it’s essential to reassess your gut health and take steps to revitalize it.
2. Weakened Immunity
Do you catch every cold or take longer to recover from illness? Since 70% of your immune system lives in your gut, imbalances can weaken your defenses.
Your gut and lungs are more connected than you might think, through what’s called the gut-lung axis. This two-way communication pathway allows gut microbes to influence immune responses in the lungs. An imbalance in gut bacteria (dysbiosis) can trigger systemic inflammation and reduce the production of protective metabolites like short-chain fatty acids, weakening the lungs’ immune defenses. Studies have shown that poor gut health is linked to increased susceptibility to respiratory infections, asthma, and even long COVID. A healthy, balanced gut microbiome plays a critical role in regulating lung immunity and maintaining respiratory resilience.
3. Fatigue and Brain Fog
A struggling gut can lead to systemic inflammation, affecting energy production and cognitive function. You may feel sluggish, forgetful, or foggy even after adequate rest.
Brain fog is a vague yet frustrating symptom that many people experience — difficulty concentrating, forgetfulness, slow thinking, and mental fatigue. Though common in clinical practice, it’s often dismissed or misunderstood because it lacks a clear medical definition. However, emerging research suggests a close connection between brain fog and gut health. Inflammation in the gut can trigger the release of immune molecules and toxins that cross the blood-brain barrier, disrupting cognitive function. An imbalanced microbiome can also affect neurotransmitter production, especially serotonin and GABA, contributing to mental sluggishness. If you’re feeling mentally cloudy, your gut may be part of the problem.
Brain fog is one of the most common and persistent symptoms reported in long COVID. While the exact causes are still being researched, one key theory suggests that gut dysbiosis is triggered by the virus. SARS-CoV-2 can disrupt the gut microbiome, leading to inflammation and a breakdown of the gut barrier (leaky gut). This allows inflammatory molecules and bacterial byproducts (like LPS) to enter the bloodstream, contributing to neuroinflammation and cognitive dysfunction. Emerging studies suggest that restoring gut health could be an important part of recovery for people experiencing post-COVID neurological symptoms.
4. Food Sensitivities
If you’re reacting to more foods than before — especially gluten, dairy, or histamine-rich items — this may be a sign of leaky gut or low microbial diversity.
Food sensitivities have seen a sharp global increase over the past few decades. In industrialized countries, studies estimate that up to 20% of the population now report some form of food intolerance — a significant rise from previous generations. Interestingly, in many traditional societies, foods such as wheat, dairy, and legumes were consumed regularly without triggering widespread health issues. What’s changed is how we eat. The modern Western diet — high in ultra-processed foods, refined sugars, emulsifiers, and additives — disrupts the gut microbiome and compromises the intestinal barrier, contributing to leaky gut and dysbiosis. Research has shown that food additives, such as polysorbates and carrageenan, can directly alter gut bacteria and increase intestinal permeability. In contrast, ancestral diets rich in whole foods, fiber, and natural fermentation supported gut diversity and tolerance. This shift from traditional to industrialized eating may help explain why food sensitivities are now more common than ever.
5. Skin Conditions
The gut-skin axis is real. Acne, eczema, rosacea, and even dandruff can be linked to gut inflammation and poor detoxification.
6. Mood Changes
Your gut and brain are in constant communication through the gut-brain axis, and the health of your microbiome directly affects your mood. The gut produces over 90% of serotonin — the “feel-good” neurotransmitter. Imbalances in gut bacteria can alter the production of serotonin, dopamine, and GABA. Several studies have found strong associations between gut dysbiosis and mental health disorders like depression and anxiety. Notably, the rise in these conditions in the Western world parallels the growing prevalence of the Standard American Diet (SAD), which is characterized by high sugar, refined carbohydrates, and processed foods, and low fiber content.
A 2019 review in Nutritional Neuroscience linked Western dietary patterns to an increased risk of depression, and Mediterranean-style diets (rich in whole foods and fiber) to better mental health. Specifically, people consuming sugar-sweetened drinks had a significantly higher incidence of depression. Supporting your gut may be one of the most under-recognized ways to support your emotional well-being.
7. Bad Breath or Coated Tongue
Persistent bad breath (halitosis) that doesn’t improve with good dental hygiene may be more than just an oral issue — it can be a sign of underlying systemic imbalances, including those in the gut. While poor oral hygiene, gum disease, or dry mouth are the most common causes, non-oral sources account for up to 10–20% of halitosis cases. These include serious medical conditions such as liver failure (fetor hepaticus), kidney disease (uremic fetor), uncontrolled diabetes (acetone breath), and gastrointestinal disorders.
Gut-related causes often stem from dysbiosis (imbalanced gut bacteria), low stomach acid (hypochlorhydria), or small intestinal bacterial overgrowth (SIBO). These conditions impair digestion and promote fermentation or putrefaction of food, leading to the production of volatile sulfur compounds (VSCs) and other gases that are exhaled through the lungs. Additionally, a coated tongue may indicate a poor microbial balance in both the mouth and the gut. In such cases, addressing the underlying gut health — not just the mouth — is essential for lasting relief.
What To Do If You Have Signs of Bad Gut Health
Here’s how you can start restoring your gut health — one step at a time:
1. Remove Irritants
- Eliminate processed foods, sugar, alcohol, and artificial additives.
- Consider an elimination diet or low FODMAP diet (short-term).
- Avoid unnecessary antibiotics and OTC meds that damage the gut lining.
2. Repair the Gut Lining
- Include healing foods like bone broth, collagen, flaxseeds, and chia.
- Add nutrients like zinc, L-glutamine, omega-3s, and vitamin D.
- Support bile flow with bitter foods like arugula, dandelion, or lemon water.
3. Repopulate with Good Bacteria
- Eat fermented foods: yogurt, kefir, sauerkraut, kimchi, miso.
- Add a high-quality, multi-strain probiotic (especially after antibiotic use).
4. Feed Your Microbiome (Prebiotics)
- Include garlic, onions, asparagus, green bananas, oats, leeks.
- Aim for 30+ different plant foods each week for microbial diversity.
5. Manage Stress
- Chronic stress harms your gut barrier and alters microbiome composition.
- Try practicing mindfulness, going on nature walks, journaling, or engaging in deep breathing.
6. Support Sleep & Gentle Movement
- Get 7–9 hours of quality sleep. Use blue light blockers at night if needed.
- Walk daily, do yoga, or stretch — movement supports digestion and motility.
When to Seek Help
If you experience persistent digestive symptoms, chronic fatigue, or unexplained inflammation despite lifestyle changes, it’s time to consult a professional. Functional medicine practitioners take a root-cause approach to health, which is particularly valuable when addressing gut issues. Instead of simply treating symptoms like bloating, fatigue, or food sensitivities, they investigate what’s driving the imbalance, such as dysbiosis, leaky gut, chronic inflammation, or environmental triggers. Through comprehensive testing (like stool analysis, food sensitivity panels, or SIBO breath tests), they can identify hidden imbalances and create a personalized healing plan. This often includes targeted nutrition, supplements, lifestyle interventions, and gut-repair protocols to restore microbial balance, support the gut lining, and regulate immune function. By addressing gut health early, functional medicine can help prevent chronic diseases, reduce inflammation, and support whole-body resilience.
Final Thoughts
If you’re noticing any of these signs of bad gut health, don’t ignore them. Your gut is incredibly responsive to care. With the right lifestyle shifts, you can support your microbiome, reduce inflammation, and feel like yourself again — from the inside out.
