Is Your Gut a Mess?

Your gut is often called the “second brain” of your body, and for a good reason. It plays a crucial role not just in digestion, but also in immunity, mental health, energy levels, and even skin health. Yet, millions of people live with gut issues bloating, gas, constipation, diarrhea, food sensitivities, fatigue, and brain fog—without ever understanding the root cause. Often, these symptoms are dismissed as “normal” or just part of getting older.

The truth is, many gut problems are caused by underlying imbalances that can be identified and addressed with the right testing. Here are seven important tests that can help you understand what’s really happening in your digestive system and guide you toward better health.

1. Comprehensive Stool Test

A comprehensive stool test is one of the most important tools for understanding your gut. It goes far beyond checking if you’re “regular.” This test analyzes:

  • Microbiome composition: Helps identify the balance of good and bad bacteria in your gut.
  • Bacterial and fungal overgrowths: Detects overgrowths that can cause bloating, gas, and digestive issues.
  • Parasites and viruses: Identifies infections that may go unnoticed.
  • Digestive efficiency: Looks at enzyme activity and undigested food particles to assess nutrient absorption.
  • Metabolites like butyrate: Helps determine gut health and anti-inflammatory function.
  • Inflammation, immunity, and detox markers: Provides insight into gut-related immune activity and toxin processing.

Research shows that disruptions in the microbiome can contribute to constipation, diarrhea, gas, bloating, fatigue, and even food sensitivities. By pinpointing these imbalances, a stool test provides a roadmap for targeted treatment.

2. Gut Lining Tests

Your gut lining acts as a protective barrier, preventing harmful substances from entering your bloodstream. When this lining becomes too permeable—a condition often called “leaky gut”—it can trigger a range of symptoms:

  • Food reactions
  • Skin problems such as eczema or acne
  • Joint pain
  • Fatigue
  • Histamine intolerance
  • Autoimmune reactions

Common markers used to test gut permeability include:

  • Zonulin (plasma or stool) – regulates tight junctions in the gut lining.
  • DAO enzyme – indicates histamine metabolism issues.
  • LPS IgA/IgG/IgM – measures immune reactivity to endotoxins.

Testing the gut lining helps uncover hidden inflammation that may be contributing to chronic health issues and guides strategies to restore gut barrier function.

3. Breath Tests

Breath tests are a simple and non-invasive way to detect gas levels produced by bacteria in your small intestine, often indicating Small Intestinal Bacterial Overgrowth (SIBO). These tests measure gases such as:

  • Hydrogen
  • Methane
  • Hydrogen sulfide

Symptoms commonly associated with SIBO include bloating, gas, abdominal pain, diarrhea, constipation, brain fog, and sometimes skin issues. Most breath tests measure only hydrogen and methane, but newer tests also include hydrogen sulfide, offering a more complete picture. Detecting SIBO is crucial for addressing persistent digestive issues.

4. Organic Acids Test (OAT)

The Organic Acids Test is a urine test that examines metabolic byproducts to reveal imbalances in gut bacteria, yeast/fungal overgrowths, and downstream effects on the body. This test can assess:

  • Bacterial and fungal overgrowths
  • Mitochondrial function – energy production at the cellular level
  • Neurotransmitter function – influencing mood, sleep, and cognitive performance
  • Nutrient status – including vitamins, minerals, and antioxidants

Imbalances in these areas can contribute to fatigue, brain fog, mood swings, skin issues, and digestive disturbances. The OAT test gives a window into the body’s metabolic health, linking gut health to overall wellness.

5. Blood Work

Blood tests are essential for getting a full-body overview of your health, and they can reveal markers that affect gut function. Common panels include:

  • CBC, CMP, and lipid profiles – check overall health, liver, and kidney function
  • Thyroid markers (TSH, Free T3/T4, rT3, antibodies) – thyroid dysfunction can impact digestion
  • Liver panel – important for detoxification
  • Hormones (sex hormones, cortisol, DHEA) – influence gut motility, inflammation, and energy
  • C-reactive protein (CRP) – a marker of systemic inflammation
  • Iron studies (iron, ferritin, transferrin, TIBC) – deficiencies can affect gut lining and microbiome balance

Blood work provides insight into systemic issues that may be contributing to gut symptoms and helps practitioners design targeted treatment plans.

6. Hair Mineral Analysis

Hair mineral analysis measures long-term mineral levels and exposure to toxic metals. This test evaluates:

  • Essential minerals – iron, magnesium, zinc, selenium, and others important for enzyme function, gut motility, and overall gut health
  • Toxic metals – mercury, lead, arsenic, aluminum, and more, which can disrupt the microbiome, gut lining, and detoxification pathways

Minerals and heavy metals play a key role in the gut’s enzymatic and structural functions. By understanding mineral deficiencies or toxic exposures, this test helps create a comprehensive gut health strategy.

7. Mycotoxin Testing

Mycotoxins are toxic compounds produced by molds that can accumulate in the body and negatively affect gut health. Common mycotoxins tested include:

  • Ochratoxin A
  • Aflatoxin
  • Gliotoxin

These toxins can suppress immunity, disrupt detoxification, damage the gut lining, and throw off the balance of your microbiome. Testing for mycotoxins is particularly useful for people with chronic digestive issues, unexplained fatigue, or immune problems.