The role of gut flora in mental health and neurological disease is fascinating.
Recent studies confirm the function of Enteric Nervous System and the Central Nervous System is modulated by the gut bacteria.  In fact, all  autoimmune and neurological disease, and most mood disorder show condition-specific changes in the microbium.  Essentially an imbalanced natural host bacteria is part of the functional medicine puzzle that keeps the condition from improving and makes remissions unattainable.

Clinical Observations:
Gastrointestinal symptoms associated with Autoimmune disease, Mood disorders, and Neurological disease. Chronic constipation, diarrhea, or recurrent bloating. Aggravation or improvement of existing symptoms after antibiotic prescription.
Naturopathic Integrative Mental Health Approach

Functional Diagnosis:
Complete stool bacteriology and culture for expected healthy gut flora and possible pathological and commensal bacteria.  Urine Organic Acid testing looking at the byproducts of bacterial metabolism. Specific Food Allergy Testing.

Treatment Protocols:
Individualized diet and lifestyle counseling focused on identified microbial alteration.
Orthomollecular medicine: high dose botanical and nutraceutical preparations with the focus of overcrowding the pathogenic overgrowth and balancing the microbium.