Comprehensive Stool Testing: What Your Digestive Health Reveals About Your Mood

How Your Gut Affects Your Mood

If you’ve been dealing with depression, anxiety, or mental health symptoms that don’t improve the way you hoped, your digestive system may be playing a bigger role than you realize. The gut and brain communicate constantly through nerves, hormones, neurotransmitters, immune cells, and your microbiome. When something in the gut is off, mental health is often affected too.

Comprehensive stool testing helps identify issues that traditional psychiatric evaluation may miss — such as inflammation, poor digestion, nutrient malabsorption, microbial imbalance, or hidden infections. Addressing these root causes can make psychiatric treatments more effective and, in some cases, relieve symptoms that previously seemed resistant to care.

What Stool Testing Can Reveal

A complete stool analysis provides insight into four major gut areas that directly influence mood:

1. Digestive Function

If your body isn’t breaking down food well, it can’t absorb nutrients required for brain health.

Common findings:

• Low pancreatic enzymes

• Poor fat digestion

• Signs of poor protein breakdown

These issues can lead to:

• Depression or anxiety that doesn’t respond to treatment

• Fatigue and brain fog

• Vitamin D or omega-3 deficiencies

• Poor response to supplements

2. Gut Inflammation

Chronic gut inflammation can trigger inflammation in the brain.

Key markers:

• Calprotectin

• Secretory IgA

• Lactoferrin

Symptoms often include:

• Mood instability

• Cognitive fog

• Irritability

• Poor response to antidepressants

3. Microbial Balance

Your microbiome produces neurotransmitters like serotonin and GABA.

Testing shows:

• Beneficial bacteria levels

• Overgrowth of harmful bacteria

• Yeast or fungal imbalance

• Parasites

Low Lactobacillus or Bifidobacterium often correlates with:

• Anxiety

• Poor stress tolerance

• Sleep disruption

• Persistent depression

Significant yeast or harmful bacteria may cause:

• Brain fog

• Irritability

• Sugar cravings

• Mood swings

4. Immune Activity

About 70% of your immune system sits in your gut. Immune imbalance can affect mood.

High or low sIgA may show:

• Chronic stress

• Food sensitivities

• Hidden infections

How Gut Issues Show Up as Mental Health Symptoms

Low Pancreatic Enzymes

Signs:

• Depression not improving

• Fatigue

• Feeling worse after meals

• Bloating

Why it matters:
Without proper enzyme activity, you can’t absorb amino acids needed for neurotransmitters like serotonin.

Fat Malabsorption

Signs:

• Seasonal depression

• Irritability

• Poor response to omega-3s

• Memory problems

Why it matters:
Your brain needs healthy fats and vitamin D — both require good fat absorption.

Protein Digestion Problems

Signs:

• Treatment-resistant depression

• Anxiety

• Sleep issues

Why it matters:
Amino acids from protein are the raw materials for brain chemistry.

Gut Inflammation

Mild to moderate elevations can cause:

• Brain fog

• Food-triggered mood changes

• Low energy

• Stress sensitivity

More severe inflammation can mimic or worsen:

• Major depression

• Anxiety disorders

Understanding Your Microbiome

Beneficial Bacteria

Low levels often mean:

• Higher anxiety

• Poor stress resilience

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• Trouble sleeping

• Increased inflammation

Harmful Bacteria

Overgrowth can lead to:

• Mood swings

• Irritability

• Cognitive issues

• Unpredictable anxiety

Yeast Overgrowth

Common signs:

• Brain fog

• Cravings

• Mood swings

• Fatigue

Parasites

Even mild infections can contribute to:

• Chronic inflammation

• Poor nutrient absorption

• Ongoing anxiety

When Testing Is Most Helpful

Consider testing if you have:

Treatment-resistant mental health symptoms

• Depression or anxiety not improving after multiple medication trials

• Needing high doses to feel better

• Loss of medication effectiveness

Digestive issues with mood symptoms

• IBS, chronic bloating, constipation, diarrhea

• Symptoms that worsen with certain foods

Symptoms after antibiotics or infections

• Mood decline after antibiotics

• Mental health changes following stomach illness

Nutrient deficiencies that don’t correct

• Low vitamin D

• Low B vitamins

• Low omega-3s

Autoimmune or inflammatory patterns

• Ongoing fatigue

• Aches and pains

• Mood changes with inflammation

Preparing for Testing

Before the test

• Avoid antibiotics for 4 weeks (if possible)

• Keep your normal diet

• Continue psychiatric medications

• Notify your provider about supplements

How long results take

• Typically 2–3 weeks

• Interpretation appointment is essential

Using Results in Your Treatment Plan

A stool analysis doesn’t replace psychiatric care — it complements it.

Results may guide:

Targeted treatment

• Digestive enzymes

• Anti-inflammatory protocols

• Probiotics tailored to your microbiome

• Antifungals or antimicrobials when needed

• Food sensitivity or elimination guidance

Better medication response

Improving digestion and nutrient absorption often:

• Enhances antidepressant effectiveness

• Reduces side effects

• Stabilizes mood more consistently

Follow-up monitoring

• Mood tracking

• Digestive symptom changes

• Repeat labs when needed

Why This Testing Matters

For many people with treatment-resistant depression or anxiety, gut dysfunction is a major missing piece. Addressing the gut often helps:

• Improve mood

• Reduce anxiety

• Increase energy

• Improve cognition

• Enhance therapy outcomes

• Make medications work more smoothly

Comprehensive stool testing offers a clearer picture of what’s happening inside your body — and how it may be affecting your mental wellness.

Professional Support

If you’re interested in whether comprehensive stool testing may help you better understand your mental health symptoms, we can help you determine if it’s a good fit and create a personalized treatment plan based on your results.

For more information, visit www.drlewis.com.

References

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Donoso, F., Cryan, J. F., Olavarría-Ramírez, L., Nolan, Y. M., & Clarke, G. (2023). Inflammation, lifestyle factors, and the microbiome–gut–brain axis: Relevance to depression and antidepressant action. Clinical Pharmacology and Therapeutics, 113(2), 246–259. https://doi.org/10.1002/cpt.2581

Dziedzic, A., Maciak, K., Bliźniewska-Kowalska, K., et al. (2024). The power of psychobiotics in depression: A modern approach through the microbiota–gut–brain axis: A literature review. Nutrients, 16(7), 1054. https://doi.org/10.3390/nu16071054

Patel, R. A., Panche, A. N., & Harke, S. N. (2025). Gut microbiome–gut brain axis–depression: Interconnection. The World Journal of Biological Psychiatry, 26(1), 1–36. https://doi.org/10.1080/15622975.2024.2436854

Radford-Smith, D. E., & Anthony, D. C. (2023). Prebiotic and probiotic modulation of the microbiota–gut–brain axis in depression. Nutrients, 15(8), 1880. https://doi.org/10.3390/nu15081880

Radjabzadeh, D., Bosch, J. A., Uitterlinden, A. G., et al. (2022). Gut microbiome-wide association study of depressive symptoms. Nature Communications, 13(1), 7128. https://doi.org/10.1038/s41467-022-34502-3

Rathour, D., Shah, S., Khan, S., et al. (2023). Role of gut microbiota in depression: Understanding molecular pathways, recent research, and future direction. Behavioural Brain Research, 436, 114081. https://doi.org/10.1016/j.bbr.2022.114081

Sanada, K., Nakajima, S., Kurokawa, S., et al. (2020). Gut microbiota and major depressive disorder: A systematic review and meta-analysis. Journal of Affective Disorders, 266, 1–13. https://doi.org/10.1016/j.jad.2020.01.102

Sonali, S., Ray, B., Ahmed Tousif, H., et al. (2022). Mechanistic insights into the link between gut dysbiosis and major depression: An extensive review. Cells, 11(8), 1362. https://doi.org/10.3390/cells11081362

Suda, K., & Matsuda, K. (2022). How microbes affect depression: Underlying mechanisms via the gut-brain axis and the modulating role of probiotics. International Journal of Molecular Sciences, 23(3), 1172. https://doi.org/10.3390/ijms23031172