Quick answer: Flora Fix is the third phase of the Leaky Gut Protocol. It focuses on restoring a healthy gut microbiome with probiotic supplements when appropriate, fermented foods and prebiotic fibers that feed beneficial bacteria. Track how you feel as you go: prebiotics can worsen symptoms for people with SIBO, so adjust with your provider.
The goal of Phase 3
Rebalance the gut microbiome. Background: microbial diversity and dysbiosis.
Step 1: Probiotic supplements
Look for products with researched strains, often from the Lactobacillus and Bifidobacterium families. Strains studied for gut health include Lactobacillus plantarum, Lactobacillus acidophilus, Bifidobacterium lactis, Bifidobacterium bifidum and breve, Streptococcus thermophilus (helps digest lactose) and the beneficial yeast Saccharomyces boulardii. Effects are strain-specific, so ask your provider which fits you.
Step 2: Probiotic-rich foods
- Yogurt and kefir (if dairy is tolerated)
- Sauerkraut and kimchi (choose unpasteurized)
- Miso and tempeh (soy-based; avoid during the elimination phase)
- Kombucha
Step 3: Prebiotic foods
- Chicory root and Jerusalem artichoke (inulin)
- Garlic, onions, leeks and asparagus
- Green bananas (resistant starch)
- Oats (beta-glucans)
- Apples (pectin)
Step 4: Monitor progress
Track digestion, energy and overall health. Prebiotics can worsen bloating in people with small intestinal bacterial overgrowth (SIBO). If symptoms flare, talk with your provider. Next phase: Phase 4: Cellular Rebuilding.
The microbiome and healthy aging
Beneficial microbes produce short-chain fatty acids that calm inflammation and support the gut lining. Supporting them helps counter the loss of microbial diversity that comes with age.
When to see a naturopathic doctor
- Ongoing bloating, gas, diarrhea or constipation
- Food reactions that seem to be multiplying
- Fatigue, skin flares or joint aches alongside gut symptoms
- You want a personalized gut plan instead of guessing
See a medical provider promptly for blood in your stool, black stools, unexplained weight loss, persistent vomiting, severe abdominal pain, fever, or trouble swallowing.
Want help finding the root of your gut symptoms?
A free 15-minute consultation with Dr. Kneessi. No cost, no obligation. In-office in Odenton, MD or by telehealth.
Frequently asked questions
Which probiotic is best for leaky gut?
Effects are strain-specific. Discuss options with your provider.
What is the difference between probiotics and prebiotics?
Probiotics are live beneficial microbes; prebiotics are fibers that feed them.
Can probiotics make symptoms worse?
Some people feel temporary bloating. Prebiotics may worsen SIBO symptoms.
Are probiotics safe?
Generally safe for healthy people; people who are immunocompromised should ask their doctor first.
Sources
This article is for educational purposes only and is not medical advice. It does not replace an individual evaluation. Talk with your healthcare provider before starting supplements or changing medications, especially if you are pregnant, nursing, or managing a health condition.
Free: The 28-Day Longevity Reset
A simple day-by-day email guide to sleep, movement, food, and daily habits that support healthy aging. It’s free, and you can unsubscribe anytime.
Get the free guide
