Dysbiosis Explained: Causes, Testing & Treatment

Dysbiosis represents an imbalance in the gut microbiome where diversity and balance of bacterial species are disrupted. This guide covers causes, consequences, and restoration protocols.

What is Dysbiosis?

Dysbiosis occurs when the delicate balance of gut bacteria is disrupted. Beneficial bacteria decline while opportunistic or pathogenic organisms proliferate.

Types of Dysbiosis

• Loss of beneficial bacteria: Reduced Lactobacillus, Bifidobacterium species
• Loss of diversity: Fewer bacterial species overall
• Overgrowth of pathogenic bacteria: E. coli, Klebsiella, etc.
• Overgrowth of opportunistic organisms: Candida, certain proteobacteria

Common Causes

• Antibiotic use: Even single courses can disrupt microbiome for months/years
• Poor diet: High sugar, low fiber, processed foods
• Chronic stress: Affects bacterial composition and diversity
• Medications: PPIs, NSAIDs, birth control
• Low stomach acid: Allows bacteria to survive where they shouldn't
• Excessive alcohol: Directly toxic to beneficial bacteria
• Environmental toxins: Pesticides, heavy metals, chemicals
• Chronic infections: H. pylori, parasites

Symptoms

Dysbiosis can manifest in diverse ways:

• Bloating, gas, abdominal discomfort
• Diarrhea, constipation, or alternating
• Food sensitivities and intolerances
• Fatigue and brain fog
• Skin issues (acne, eczema, rashes)
• Weakened immunity (frequent infections)
• Mood issues (anxiety, depression)
• Weight gain or difficulty losing weight
• Nutrient deficiencies
• Autoimmune conditions

Testing for Dysbiosis

Comprehensive Stool Analysis is the gold standard, measuring:

• Bacterial diversity and ratios
• Beneficial bacteria levels
• Pathogenic organisms
• Inflammatory markers
• Digestive function markers
• Immune function indicators

Restoration Protocol

Phase 1: Remove

• Eliminate inflammatory foods
• Address pathogenic overgrowths with antimicrobials
• Remove toxin exposures
• Reduce stress

Phase 2: Replace

• Digestive enzymes
• Stomach acid support (if needed)
• Bile support

Phase 3: Reinoculate

• Multi-strain probiotics
• Soil-based organisms
• Spore-based probiotics
• Saccharomyces boulardii
• Prebiotic fibers (when appropriate)
• Fermented foods (if tolerated)

Phase 4: Repair

• L-glutamine, zinc carnosine, collagen
• Gut lining support supplements
• Anti-inflammatory nutrients

Phase 5: Rebalance

• Diverse whole foods diet
• Stress management
• Quality sleep
• Regular movement
• Minimize antibiotic use

Key Dietary Strategies

• Increase fiber diversity: Various prebiotic fibers feed beneficial bacteria
• Polyphenol-rich foods: Berries, green tea, dark chocolate, olive oil
• Fermented foods: When appropriate and tolerated
• Remove inflammatory foods: Seed oils, processed foods, excess sugar
• Quality proteins and fats: Support healing and satiety