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Top 10 Signs Your Gut Health Is Out of Balance

Written by Dr. Marina Yuabova
May 10, 2025
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Gut health refers to the optimal function and balance of the digestive system—particularly the trillions of bacteria, fungi, and other microbes that make up the gut microbiome. These microorganisms aren’t just passive residents; they actively support digestion, produce essential nutrients, regulate immune responses, and even influence mood and cognitive function. When the gut is in balance, it helps the body absorb nutrients efficiently, defend against pathogens, and maintain overall well-being.
However, when the gut microbiome becomes imbalanced—due to poor diet, stress, antibiotics, or other lifestyle factors—it can lead to a wide range of symptoms that go beyond digestive discomfort. Everything from chronic fatigue to skin flare-ups may be tied back to your gut. At National Wellness Group, we help patients uncover and address the root causes of these imbalances through a holistic, personalized approach to care. In this article, we’ll explore the top 10 signs that your gut health may be out of balance, so you can identify issues early and take steps to restore harmony from the inside out.
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Persistent Bloating and Gas

While occasional bloating or gas after a large meal is normal, frequent or unexplained bloating can be a red flag for poor gut health. An imbalanced gut microbiome can disrupt proper digestion, causing food to ferment in the intestines. This fermentation produces excess gas, leading to uncomfortable bloating, pressure, and abdominal distension.
When the gut lacks enough beneficial bacteria—or is overrun by harmful microbes—it can struggle to break down certain foods efficiently. This results in a buildup of gas and slower motility, which may leave you feeling uncomfortably full even after small meals.
Key differences between occasional and chronic bloating include:

  • Occasional bloating usually follows overeating, high-sodium meals, or specific food triggers.
  • Chronic bloating occurs regularly, even with a balanced diet, and may be accompanied by other symptoms like constipation, cramps, or fatigue.
  • Gas with a foul odor may indicate fermentation issues or microbial imbalance.

If bloating and gas are persistent, it could be your gut’s way of signaling that its internal ecosystem is off-balance. Identifying and addressing the root cause—such as dysbiosis, food sensitivities, or low stomach acid—is crucial to restoring digestive comfort.

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Persistent-Bloating and Gas forming

Irregular Bowel Movements (Constipation or Diarrhea)

A healthy gut promotes regular, well-formed bowel movements. When the gut microbiome is out of balance, however, it can disrupt the body’s ability to digest and eliminate waste properly. This often results in irregular bowel habits—ranging from constipation to diarrhea—that persist over time.
Imbalanced gut flora can slow down or speed up the movement of food through the intestines. A lack of beneficial bacteria may lead to inflammation in the gut lining, poor nutrient absorption, and increased sensitivity to certain foods. These disruptions can significantly impact stool consistency and frequency.
Signs that irregular bowel movements may be linked to gut issues include:

  • Constipation: infrequent, hard, or difficult-to-pass stools due to slowed digestion or low microbial diversity.
  • Diarrhea: loose or urgent bowel movements that may signal inflammation or an overgrowth of harmful bacteria.
  • Alternating patterns: shifting between constipation and diarrhea, which is common in conditions like Irritable Bowel Syndrome (IBS).
  • Food-related symptoms: worsened digestion after eating dairy, gluten, or high-FODMAP foods, which may suggest sensitivities tied to gut dysfunction.

If you notice ongoing changes in your bowel movements without a clear dietary cause, your gut health may be compromised. Addressing microbial imbalances, improving fiber intake, and identifying trigger foods can often help restore digestive regularity.

Frequent Food Intolerances

If you find yourself reacting poorly to foods you once tolerated well, your gut health could be to blame. A compromised gut lining or imbalanced microbiome can interfere with proper digestion, making it harder for your body to process certain foods. This can lead to bloating, cramping, nausea, or fatigue shortly after eating—classic signs of food intolerance rather than a true allergy.
When the gut is inflamed or overrun with harmful bacteria, the digestive system may no longer produce enough enzymes to break down certain compounds. It can also impair nutrient absorption, meaning your body isn’t getting the fuel it needs, even from healthy meals. This creates a cycle of irritation and inflammation that worsens over time if left unaddressed.
Common food intolerances linked to poor gut health include:

  • Dairy (lactose): caused by low lactase enzyme levels or microbial imbalance in the small intestine.
  • Gluten: may trigger discomfort even in non-celiac individuals if the gut lining is damaged or inflamed.
  • High-FODMAP foods: such as garlic, onions, beans, and certain fruits, which ferment quickly and cause bloating and gas in sensitive guts.

Frequent food intolerances are often a sign that your digestive system is struggling to maintain balance. Identifying and eliminating trigger foods temporarily—while focusing on gut healing—can help reduce symptoms and gradually restore tolerance.

Unexplained Fatigue

Feeling constantly tired despite getting enough rest? Your gut could be draining your energy. The gut plays a major role in breaking down food, absorbing nutrients, and supporting metabolic function—all of which are essential for maintaining steady energy levels. When the gut is out of balance, this system falters, and fatigue can set in.
Poor gut health can lead to chronic low-grade inflammation and impaired nutrient absorption, especially of B vitamins, iron, and magnesium—nutrients vital for energy production. Even if you’re eating well, your body may not be getting what it needs to function at full capacity if your digestive system isn’t processing nutrients efficiently.
Ways gut issues can lead to fatigue include:

  • Nutrient malabsorption: resulting in deficiencies that sap energy.
  • Inflammation: taxing your immune system and causing that “drained” feeling.
  • Toxin buildup: from harmful bacteria or yeast overgrowth, which can disrupt metabolic processes.
  • Sleep disturbances: gut imbalances can interfere with melatonin and serotonin levels, affecting sleep quality.

If you’re regularly fatigued without a clear medical explanation, your gut health may be at the root of the problem. Restoring microbial balance and addressing nutrient gaps can often lead to a noticeable boost in energy.

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Skin Issues (Acne, Eczema, Rosacea)

Skin problems aren’t always skin-deep—many are rooted in the gut. The gut-skin axis refers to the connection between your digestive system and your skin’s health. When the gut microbiome is imbalanced, it can trigger systemic inflammation and allow toxins to leak into the bloodstream (a condition sometimes referred to as “leaky gut”). These internal issues often show up externally, in the form of acne, eczema, rosacea, or other chronic skin conditions.
A compromised gut can’t efficiently filter out waste or maintain proper immune regulation. As a result, your skin may try to compensate by eliminating toxins through the pores, leading to flare-ups or irritation. Additionally, inflammation originating in the gut can exacerbate immune responses in the skin, especially in people prone to eczema or rosacea.
Common ways gut issues can appear on the skin include:

  • Acne: often linked to inflammation, hormone imbalances, and poor detoxification.
  • Eczema: may flare up due to food sensitivities or immune overreaction triggered by gut imbalances.
  • Rosacea: can worsen with gut dysbiosis, especially when harmful bacteria dominate the microbiome.

If you’ve tried topical treatments with little success, it may be time to look inward. Healing your gut—through diet, probiotics, and reducing inflammatory triggers—can help calm chronic skin issues from the inside out.

Bad Breath or Unpleasant Body Odor

If you’re dealing with persistent bad breath or unusual body odor despite good hygiene, your gut might be to blame. Gut health has a direct impact on how your body processes and eliminates waste, and when the digestive system is out of balance, it can lead to the buildup of gases and toxins that cause noticeable smells—both from your mouth and skin.
An overgrowth of harmful bacteria, such as candida (a type of yeast), can disrupt the natural balance of your microbiome and contribute to halitosis (chronic bad breath) and body odor. These microbes produce foul-smelling byproducts during digestion, which can make their way into your bloodstream and exit through your lungs or sweat glands.
How gut imbalances can lead to odor issues:

  • Halitosis (bad breath): may be caused by poor digestion, candida overgrowth, or protein fermentation in the gut.
  • Body odor: toxins from dysbiosis or incomplete digestion may be excreted through the skin.
  • Metallic or sour tastes in the mouth: a sign that your body may be struggling to detox properly.

If brushing, flossing, and deodorant aren’t solving the problem, it’s worth considering whether your gut health is contributing to internal toxicity. Addressing microbial imbalances, improving digestion, and supporting liver detox pathways can help clear up the odor from the inside.

Bad Breath or Unpleasant Body Odor

Frequent Illness or Poor Immune Function

Your gut is home to roughly 70% of your immune system, making it a key player in your body’s defense against illness. The gut microbiome helps regulate immune responses, protect against harmful pathogens, and maintain a healthy barrier between your digestive tract and the rest of your body. When this balance is disrupted, your immune function can weaken—leaving you more vulnerable to infections and inflammation.

A healthy gut is rich in diverse, beneficial bacteria that train the immune system to respond appropriately. But when harmful bacteria or yeast overtake the gut, they can trigger excessive immune activity or leave your body defenseless against common viruses. Chronic inflammation in the gut can also confuse the immune system, contributing to autoimmune flare-ups and allergic responses.

Signs your gut may be weakening your immune system include:

  • Catching colds or infections frequently and taking longer than usual to recover.
  • Recurring sinus infections or sore throats that linger or return often.
  • Autoimmune symptoms worsening during times of stress or poor digestion.
  • Poor response to vaccines or supplements, suggesting absorption or immune issues.

If your body seems to get sick at the slightest trigger, it may be time to examine what’s happening in your gut. Strengthening your microbiome with probiotics, fiber-rich foods, and anti-inflammatory nutrients can go a long way toward restoring immune resilience.

Brain Fog, Anxiety, or Depression

The connection between your gut and brain is more powerful than most people realize. Often referred to as the gut-brain axis, this communication pathway allows your digestive system and central nervous system to influence each other directly. A balanced gut supports mental clarity, emotional stability, and a healthy stress response. But when the microbiome is out of sync, it can disrupt neurotransmitter production and trigger symptoms like brain fog, anxiety, or depression.

Your gut plays a critical role in producing neurotransmitters—chemical messengers like serotonin, dopamine, and GABA—that regulate mood, focus, and sleep. In fact, nearly 90% of your body’s serotonin is made in the gut. When harmful bacteria outnumber the good, it can lead to inflammation, poor nutrient absorption, and a decline in these vital chemicals, all of which negatively affect your mental health.

Signs your gut may be affecting your mood and cognition include:

  • Brain fog: difficulty concentrating, poor memory, or mental fatigue.
  • Chronic anxiety or nervousness: often accompanied by digestive discomfort or IBS.
  • Low mood or mild depression: despite no clear external cause.
  • Sleep issues: due to disrupted melatonin and serotonin production.

If you’re struggling with mental clarity or emotional well-being, your gut could be playing a hidden role. Supporting your microbiome with a balanced diet, probiotics, and stress-reduction practices may help restore both mental and digestive balance.

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Sudden Weight Changes

Unexplained weight gain or loss can be a sign that your gut health is out of balance. Your digestive system does more than just break down food—it also helps regulate metabolism, manage hunger signals, and influence how your body stores fat. When your gut microbiome is disrupted, these systems can go haywire, leading to fluctuations in weight that don’t align with your diet or lifestyle.

An overgrowth of harmful bacteria can contribute to chronic inflammation, which has been linked to insulin resistance and fat storage, especially around the midsection. At the same time, gut imbalances can interfere with the production of hormones like leptin and ghrelin, which control hunger and fullness. On the flip side, poor nutrient absorption and gut inflammation can cause unintended weight loss, especially if your body struggles to extract calories and nutrients from food.

Ways gut health impacts your weight include:

  • Unexplained weight gain: due to inflammation, slower metabolism, or overproduction of hunger hormones.
  • Unintentional weight loss: caused by poor absorption of nutrients, chronic diarrhea, or microbial overgrowth.
  • Increased cravings: especially for sugar or processed foods, driven by imbalanced gut bacteria.
  • Difficulty losing or maintaining weight: despite calorie control and regular exercise.

If your weight is shifting without a clear reason, it may not be about willpower—it may be about your gut. Addressing microbial imbalances can help bring your metabolism and appetite signals back into alignment.

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Sugar Cravings

Intense or frequent sugar cravings can be more than just a matter of habit—they’re often a sign that your gut is out of balance. Certain harmful microbes in the gut, like candida yeast and some strains of bad bacteria, thrive on sugar. When these organisms multiply, they can manipulate your cravings, pushing you to consume more sugar to feed their growth.

This creates a vicious cycle: the more sugar you eat, the more these microbes grow, and the stronger your cravings become. As they dominate your gut, they also interfere with blood sugar regulation and nutrient absorption, which can lead to energy crashes shortly after eating. These crashes often prompt another sugary snack for a quick energy boost, further feeding the imbalance.

Signs your sugar cravings may be gut-related:

  • Constant cravings for sweets or refined carbs, even after meals.
  • Low energy or brain fog that lifts temporarily after eating sugar.
  • Worsening bloating or digestive discomfort after consuming sugary foods.
  • Recurring yeast infections or signs of candida overgrowth (like white tongue coating or skin issues).

If your sugar cravings feel out of control, it may be time to address the underlying gut imbalance. Reducing added sugars, increasing fiber, and introducing probiotics can help starve harmful microbes and restore a healthier microbiome—leading to fewer cravings and more stable energy.

What to Do If You Notice These Signs

If you’re experiencing several of the symptoms discussed—like bloating, fatigue, brain fog, or skin flare-ups—it’s likely your gut health needs attention. Fortunately, you don’t have to overhaul everything at once. Small, consistent changes can make a big difference in rebalancing your gut microbiome and improving overall wellness.

Start by adjusting your diet to support healthy digestion. A gut-friendly eating plan includes plenty of fiber, which feeds beneficial bacteria and helps regulate bowel movements, and fermented foods like yogurt, kefir, kimchi, and sauerkraut, which introduce helpful probiotics into the system. Avoid heavily processed foods, excess sugar, and artificial sweeteners, which can fuel harmful bacteria and yeast.

Gut-friendly steps to take:

  • Eat fiber-rich foods: such as leafy greens, oats, legumes, chia seeds, and berries.
  • Incorporate fermented foods: like kimchi, miso, tempeh, and unsweetened yogurt.
  • Take a high-quality probiotic supplement and eat prebiotic foods (e.g., garlic, onions, bananas) to nourish good bacteria.
  • Manage stress: Chronic stress affects gut function and microbiome diversity. Try meditation, exercise, or breathwork.
  • Stay hydrated: Water supports digestion and regular elimination.

If your symptoms persist or worsen, it’s wise to consult a healthcare provider. A functional medicine doctor or gastroenterologist can evaluate your gut health through stool tests, blood work, or food sensitivity testing to provide personalized recommendations. Addressing gut health early can prevent more serious health issues down the line—and help you feel better from the inside out.

Your gut plays a vital role in nearly every aspect of your health—from digestion and immunity to mood and energy levels. If you’re experiencing symptoms like bloating, fatigue, skin issues, or frequent illness, it could be a sign that your gut is out of balance. At National Wellness Group, we help patients recognize these signs early and guide them toward personalized, gut-friendly solutions. Simple changes—like increasing fiber and fermented foods, managing stress, and incorporating probiotics—can restore balance and support long-term wellness from the inside out.

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