What's causing my gut symptoms?

If you’ve ever experienced bloating, abdominal pain, diarrhea, constipation, or unexplained fatigue, you may have asked yourself, “What’s wrong with my gut?”

The truth is, gut symptoms can stem from a variety of causes.  The goal is to identify the root cause rather than the masking symptoms. This involves examining your entire body’s systems, diet, lifestyle, and history to understand why your gut is struggling.

Below is a guide to the most common gut issues, how we test for them, strategies to restore digestive health holistically, and then what the standard of care is.  This information can be invaluable when discussing treatment approaches with your doctor.

Profession woman in a meeting with a gut issue

Gut Terminology

• Microbiome – over 100 trillion bacteria, viruses, and yeast cells that live in the body. 

• Prebiotic- non-digestible foods that feed beneficial bacteria in the gut.

• Probiotic- Live microorganisms that improve or restore microbiota in the gut.

• Dysbiosis- when gut flora is off balance (more harmful bacteria than beneficial). Potential Causes:

  • Stress- microbes can react to stress hormones, shifting the balance of bacteria and increasing the risk of infection and leaky gut. The body may perceive excessive exercise as stress.

  • Infection, trauma, or exacerbation of chronic illness change gut flora.

  • Aging is associated with changes in gut flora.  Perhaps it’s a snowball effect of medications and diet. 

  • Antibiotics can cause yeast overgrowth negatively impacting healthy bacteria and allowing harmful bacteria to grow.   If on an antibiotic, finish the course.  Animals that we eat are also injected with antibiotics, so eating organic is essential. 

  • Medications such as non-steroidal anti-inflammatories (NSAIDS) break down the thin lining of the digestive tract  causing an inflammatory response.  

  • Alcohol disrupts gut flora. It can cause liver disease and encourage the overgrowth of harmful bacteria.

  • Poor diet has a significant effect on the microbiome (especially the western diet).

Step 1: Identify Your Gut Symptoms

Before testing, it’s essential to describe what you are experiencing clearly. Some common patterns include:

• Bloating or gas

• Abdominal pain or cramping

• Constipation

• Diarrhea

• Heartburn or reflux

• Nausea

• Unexplained weight changes

• Skin issues (acne, eczema, rosacea)

• Brain fog, fatigue, mood changes

These symptoms often overlap, which is why testing can be used pinpoint the actual cause.

Step 2:  Nutrition and the Gut

• Eat a rainbow of colors from plants

• Eat plenty of dietary fiber.  These foods provide substrates that our gut microbes ferment and metabolize into beneficial compounds for health

• Eat omega-3s and monounsaturated fats found in salmon, sardines, walnuts, avocados, and olive oil.  These support a healthy inflammatory balance in the gut. 

• Eliminate alcohol, added sugars, sugar substitutes, preservative agents, highly processed foods, and food additives. 

• Add fermented foods such as unpasteurized sauerkraut, kimchi, tempeh, and kombucha.  These foods provide benefits to the microbiome.

  
  

Step 3: Common Gut Conditions, Symptoms, Testing, and Treatment

1. Small Intestinal Bacterial Overgrowth (SIBO)

• What it is: Overgrowth of bacteria in the small intestine. The small intestines typically have little bacteria.

• Influential Factors: Motility disorders, structural issues, prior surgeries, and certain conditions like diabetes.

• Nutritional characteristics:  High carb and low fiber.  Sensitive to histamines in food (fermented, aged cheese, citrus, dried fruit, alcohol, nuts, avocado, eggplant, spinach, tomatoes, smoked fish, chocolate, and dairy). 

• Common symptoms: Bloating after meals, gas, diarrhea, constipation, and abdominal discomfort.

• How to test:

  • Lactulose or glucose breath test (measures hydrogen and methane gas production).

  • Food allergy test

  • Stool test

• Holistic treatment:

  • Short-term antimicrobial therapy (herbal or pharmaceutical).

  • Low FODMAP or specific carbohydrate diet (short term).

  • Address root causes like low stomach acid or motility issues.

  • Prokinetics to improve gut movement.

  • Stress reduction

·       Standard of Care Treatment:

• Antibiotics (e.g. rifaximin)

• Addressing underlying motility issues

  
  

2. Irritable Bowel Syndrome (IBS)

• What it is: A functional disorder of the gut with no structural damage, often linked to the gut-brain axis imbalance.

• Causes:  Dysfunction of the gut-brain axis, food intolerances, stress, changes in gut microbiota

• Influencing Factors:  Stress

• Common symptoms: Alternating diarrhea and constipation, bloating, abdominal pain, gas, and cramping.

• How to test:

  • IBS is a diagnosis of exclusion — stool studies, blood work, and imaging rule out other causes.

• Holistic treatment:

  • Stress reduction & gut-brain retraining (mindfulness, CBT, meditation).

  • Individualized diet (low FODMAP, elimination/reintroduction).

  • Optimize gut microbiome with targeted probiotics & prebiotics.

·       Standard of Care Treatments

• Fiber supplements for constipation

• Anti-diarrheal or laxative medication

• Antispasmodics, antidepressants

• Newer targeted medications for IBS-C and IBS-D

  
  

3.  Leaky Gut (Intestinal Permeability)

• What it is: Damage to the intestinal lining allowing particles to enter the bloodstream, triggering inflammation.

• Common symptoms: Food sensitivities, fatigue, joint pain, skin rashes, and autoimmune flares.

• How to test:

  • Zonulin blood test.

  • Intestinal permeability urine test (lactulose/mannitol ratio).

• Holistic treatment:

  • Remove triggers (gluten, processed foods, alcohol, NSAIDs, GMO foods, sugar, caffeine, stress).

  • Gut-healing nutrients (L-glutamine, zinc carnosine, aloe vera, collagen).

  • Balance microbiome with fiber and fermented foods.

• Standard of Care:

  • There is no disease-specific pharmaceutical treatment.  Anti-inflammatory medications are sometimes given.

    
    

4. Celiac Disease & Non-Celiac Gluten Sensitivity

• What it is: Autoimmune (celiac) or immune-reactive (non-celiac) response to gluten.

• Common symptoms: Diarrhea, nutrient deficiencies, anemia, skin rash, and brain fog.

• How to test:

  • Celiac: Anti-tTG IgA & total IgA blood test, confirmed by small bowel biopsy.

  • Non-celiac: Symptom resolution on gluten-free diet after other causes ruled out.

• Holistic treatment:

  • 100% gluten-free diet.

  • Gut healing protocol to restore nutrient absorption.

  • Correct nutrient deficiencies (iron, vitamin D, B vitamins).

• Standard of care

  • Strict life-long gluten-free diet

5. Inflammatory Bowel Disease (IBD) – Crohn’s & Ulcerative Colitis

• What it is: Autoimmune inflammation of the gut lining.

• Causes:  Autoimmune reaction, genetic factors, environmental triggers

• Common symptoms: Chronic diarrhea, abdominal pain, blood in stool, weight loss, fatigue.

• How to test:

  • Colonoscopy with biopsy.

  • Fecal calprotectin & CRP (inflammatory markers).

• Holistic treatment:

  • Anti-inflammatory diet (Mediterranean, autoimmune paleo, specific carbohydrate diet, low-residue diet).

  • Omega-3s, curcumin, and vitamin D optimization.

  • Microbiome restoration (probiotics, fecal transplant research)

  • Stress management (meditation, deep breathing, yoga) alongside medical care.

• Standard of Care Treatments:

  • Anti-inflammatory drugs (aminosalicylates, corticosteroids)

  • Immunosuppressants, biologics, JAK inhibitors

  • Surgery in severe/refractory cases

    
    

6. Candida & Other Fungal Overgrowth

• What it is: Overgrowth of yeast/fungus in the gut.

• Common symptoms: Bloating, sugar cravings, brain fog, fatigue, irritability, recurrent vaginal yeast infections, eczema, itchy ears.

• How to test:

  • Stool test for yeast overgrowth.

  • Organic acids test (OAT) for fungal markers.

• Holistic treatment:

  • Antifungal protocol (herbal or prescription).

  • Reduce refined carbohydrates & sugars (these feed fungal organisms)

  • Support detox pathways and immune function.

• Standard of Care:

  • Oral prescription anti-fungal agents for several weeks

7. Parasitic Infections

• What it is: Infection with parasites (Giardia, Blastocystis, etc.).

• Common symptoms: Diarrhea, abdominal cramping, fatigue, nutrient deficiencies.

• How to test:

  • Comprehensive stool analysis with PCR testing.

• Holistic treatment:

  • Targeted anti-parasitic treatment.

  • Replenish beneficial gut bacteria.

  • Restore gut lining integrity.

·       Standard of Care:

• Anti-parasitic drugs

  
  

8. Food Intolerances & Sensitivities

• What it is: Non-allergic immune or enzymatic reactions to foods (e.g., lactose intolerance, histamine intolerance).

• Common symptoms: Gas, bloating, diarrhea, headaches, skin rashes, abdominal pain after consuming certain foods

• How to test:

  • Elimination & reintroduction diet (gold standard).

  • Hydrogen breath test for lactose/fructose malabsorption.

  • Blood testing for IgG food reactions (controversial but sometimes applicable).

• Holistic treatment:

  • Avoid trigger foods while healing the gut.

  • Support enzyme production and gut barrier repair.

• Standard of Care Treatments:

  • Avoid certain foods and beverages (such as lactose)

    
    

9.  Gastroesophageal Reflux Disease (GERD)

• What it is:  Weakness of the lower esophageal sphincter

• Influencing Factors: obesity, certain foods, and medications

• Common symptoms:  Heartburn, chest pain, regurgitation, sore throat, belching

• How to test:

  • Upper endoscopy

  • pH monitoring

  • barium swallow

• Holistic Medicine Treatments:

  • Dietary modifications (avoiding trigger foods)

  • Weight loss

  • Elevate head of bed when sleeping (lay on wedge)

  • Stress reduction

  • Mindful eating

• Standard of Care Treatments:

  • Proton pump inhibitors (PPIs), H2 blockers

  • Antacids

  • Surgical intervention for severe cases

    
    

10. Gastritis/Peptic Ulcers

• What it is: Helicobacter pylori infection

• Influencing Factors:  excessive NSAID use, alcohol, stress

• Common symptoms:  Stomach pain, nausea, loss of appetite, vomiting, bloating, and possible bleeding.

• How to test:

  • Upper endoscopy

  • H. pylori testing (breath, stool, blood)

  • Barium swallow

• Holistic Medicine Treatments:

  • Root cause diet (removal of irritants, anti-inflammatory foods)

  • Probiotics for H. pylori

  • Gut healing nutrients (zinc carnosine, glutamine)

• Standard of Care Treatment:

  • Antibiotics for H. pylori, PPIs, antacids

  • H2 receptor blockers

    
    

Step 4: Holistic Gut Testing Toolbox

In practice, a gut workup may include:

• Comprehensive stool analysis

• SIBO breath testing

• Organic acids testing

• Food sensitivity testing (Food Elimination Diet)

• Inflammatory markers (CRP, fecal calprotectin)

• Nutrient panels

• Zonulin for intestinal permeability

Step 5: The 5R Gut Health Framework

Once you know the cause, you can follow this stepwise approach:

1. Remove – Eliminate pathogens, inflammatory foods, and toxins.

   • Food Elimination diet.

   • Avoid NSAIDs.

2. Replace – Restore digestive enzymes, stomach acid, and bile acids if needed.

   • Chew each piece of food 20 times before swallowing to improve digestion.

   • Eat digestive enzymes before meals

   • Fresh pineapple is excellent for protein digestion

   • Digestive bitters or vinegar diluted with water before meals helps with digestion

3. Reinoculate – Add beneficial bacteria with targeted probiotics & prebiotics.

   • Yogurt and fermented veggies improve microbiome (if not avoiding histamines)

   •  Add prebiotics (not if you have IBS)

4. Repair – Heal the gut lining with nutrients like L-glutamine, zinc, and omega-3s.

   • Drink bone broth

   • L-glutamine is an amino acid that feeds the gut lining

   • Drink purified aloe vera juice

   • Zinc carnosine protects organs from stress and is suitable for the gut

   • Quercetin inhibits the growth of bacteria and fungi, including strains resistant to some common treatments. 

   • Turmeric and black pepper help fight inflammation

   • Eat more prebiotics- seaweed, onions, chicory, asparagus, lentils, chickpeas, green peas, watermelon, red currants, raspberries, figs, garlic, cabbage, broccoli, Jerusalem artichokes

5. Rebalance – Address lifestyle factors: stress, sleep, movement, and emotional health.

   • Meditation

   • Exercise

   • Deep breathing

   • Yoga

Key Takeaways

• Gut symptoms often have multiple contributing factors.  It’s rarely just one thing.

• Testing allows for a targeted treatment rather than a guess. Get confirmation before making changes.

• Nutrition and lifestyle changes (stress in particular) are important

• Aims to restore whole-body balance, not just treat isolated symptoms.

• Healing your gut can have a ripple effect on your skin, hormones, mood, and overall vitality.

References

https://pmc.ncbi.nlm.nih.gov/articles/PMC6790068/pdf/nihms-1054015.pdf

https://gastro.org/press-releases/aga-issues-clinical-guidelines-outlining-drug-treatment-plans-for-patients-with-irritable-bowel-syndrome-ibs/

https://pmc.ncbi.nlm.nih.gov/articles/PMC3002524/

https://www.mayoclinic.org/diseases-conditions/inflammatory-bowel-disease/diagnosis-treatment/drc-20353320

https://my.clevelandclinic.org/health/articles/7040-gastrointestinal-diseases

https://www.urmc.rochester.edu/encyclopedia/content?ContentTypeID=85&ContentID=P00364

https://my.clevelandclinic.org/health/diseases/22724-leaky-gut-syndrome

https://pmc.ncbi.nlm.nih.gov/articles/PMC9862683/

https://www.ifm.org/gut-microbiome-health?page=0