Gut Issues & Functional Medicine

Digestive symptoms like bloating, constipation, diarrhea, reflux, or stomach pain are often dismissed as “normal” or blamed on stress or diet. But in functional medicine, we see gut issues as a red flag—an early warning sign that deeper imbalances are disrupting your health.

Your gut isn’t just about digestion—it’s a central hub for immunity, inflammation, hormones, detoxification, and even mood. That’s why healing the gut is one of the most important steps in restoring whole-body health.

What Are Gut Issues?

Gut issues can range from mild to debilitating, and they often show up in ways that go beyond the digestive tract. Symptoms like brain fog, fatigue, skin rashes, joint pain, anxiety, or hormone imbalances can all have roots in gut dysfunction.

Instead of masking symptoms, functional medicine works to identify what’s disrupting your gut: pathogens, food triggers, poor digestion, leaky gut, or microbiome imbalances.

Common Gut Imbalances We See

Some of the most common digestive imbalances that functional medicine addresses include:

  • Leaky Gut (Intestinal Permeability): A compromised gut lining allows toxins and food particles into the bloodstream, triggering inflammation and autoimmunity.

  • SIBO (Small Intestinal Bacterial Overgrowth): Excess bacteria in the small intestine causing bloating, pain, and food sensitivities.

  • Candida or Fungal Overgrowth: Yeast overgrowth can cause gas, sugar cravings, brain fog, and rashes.

  • Parasites or Gut Infections: Often missed on standard stool tests, chronic infections can drive symptoms for years.

  • Dysbiosis: An imbalanced microbiome that contributes to IBS, inflammation, and immune dysfunction.

  • Low Stomach Acid (Hypochlorhydria): Poor digestion, nutrient malabsorption, and bacterial overgrowth often result.

  • Pancreatic or Bile Insufficiency: Inadequate enzymes or bile impair fat digestion and create bloating or loose stools.

Signs and Symptoms of Gut Dysfunction

Gut imbalances don’t always present as obvious GI symptoms. You might notice:

  • Bloating or discomfort after meals

  • Irregular bowel movements (constipation, diarrhea, or both)

  • Reflux, burping, or heartburn

  • Gas, especially foul-smelling or excessive

  • Food sensitivities or cravings

  • Fatigue, especially after eating

  • Skin issues like acne, eczema, or rashes

  • Anxiety, depression, or irritability

  • Poor concentration or brain fog

  • Joint pain or muscle aches

  • Frequent illness or autoimmunity

Gut Health in Women

Women often experience gut issues related to:

  • Hormonal shifts during PMS, pregnancy, perimenopause, or menopause

  • Birth control use, which can disrupt microbiome balance

  • Thyroid dysfunction, commonly seen in women with IBS

  • Stress and emotional overload, which impact gut motility and secretions

  • Higher susceptibility to SIBO, candida, and UTI-bowel crossover

Gut Health in Men

Men may struggle with gut issues due to:

  • High stress and cortisol, suppressing digestion

  • Alcohol or poor dietary choices, weakening gut lining and flora

  • Sleep disruption and circadian rhythm issues

  • Silent gut inflammation, showing up as fatigue or joint pain

  • Athletic overtraining, which can impair digestion and increase permeability

What Causes Gut Dysfunction?

In functional medicine, we look at what’s contributing to gut imbalance—not just what’s wrong. Common root causes include:

  • Processed or inflammatory diets (refined sugar, gluten, seed oils)

  • Antibiotics or medications disrupting the microbiome

  • Chronic stress, which shuts down digestion and damages the gut lining

  • Hidden infections (H. pylori, parasites, candida, SIBO)

  • Food sensitivities or intolerances

  • Environmental toxins (mold, pesticides, plastics)

  • Low stomach acid or poor digestive enzyme output

  • Hormonal shifts or imbalances (especially cortisol and estrogen)

  • Poor sleep or circadian disruption

How Functional Medicine Heals the Gut

Rather than suppress symptoms, we work to identify and remove the root cause, repair the gut lining, and restore a healthy microbiome. Your personalized care plan may include:

  • Advanced stool testing, SIBO breath testing, or organic acids

  • Targeted protocols for parasites, candida, or bacterial overgrowth

  • Gut-healing diets (low-FODMAP, Paleo, or anti-inflammatory plans)

  • Removal of food triggers and support for food reintroduction

  • Digestive support: stomach acid, enzymes, and bile flow enhancers

  • Gut lining repair using nutrients like glutamine, zinc carnosine, and collagen

  • Microbiome rebalance using prebiotics, probiotics, and fiber diversity

  • Nervous system regulation (vagus nerve activation, stress tools)

  • Detox support for mold, metals, and other gut disruptors