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.
Key takeaways
Phase three focuses on rebalancing the gut microbiome with researched probiotic strains, fermented foods and prebiotic foods.
Fermented foods such as sauerkraut, kimchi and kefir, and prebiotic foods such as garlic, onions, leeks and asparagus, feed beneficial microbes.
Prebiotics can worsen bloating in people with SIBO, so tracking digestion and energy during this phase matters.
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
Good options include yogurt and kefir (if dairy is tolerated), sauerkraut and kimchi (choose unpasteurized), miso and tempeh (soy-based; avoid during the elimination phase), and kombucha.
Step 3: Prebiotic foods
Prebiotic foods include chicory root and Jerusalem artichoke (inulin), garlic, onions, leeks and asparagus, and green bananas (resistant starch), as well as oats (beta-glucans) and 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 such as butyrate that help strengthen the gut lining. Supporting them helps counter the loss of microbial diversity that comes with age.
When to see a naturopathic doctor
It may be time to see a naturopathic doctor if you have ongoing bloating, gas, diarrhea or constipation, or food reactions that seem to be multiplying. The same is true if you have fatigue, skin flares or joint aches alongside gut symptoms, or if 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.
What the research shows
Prebiotic fiber has measurable effects on gut bacteria. In a 2015 randomized, double-blind crossover trial by Holscher and colleagues, 29 healthy adults took 0, 5 or 7.5 g of agave inulin a day for 21 days in each period, with a week off between periods. Bifidobacterium, a group of bacteria generally considered beneficial, rose about 3-fold at 5 g and 4-fold at 7.5 g compared with placebo, while Desulfovibrio fell by about 40%. Higher total fiber intake was linked with more butyrate, a short-chain fatty acid that feeds colon cells. The study measured bacteria and stool chemistry, not symptoms, so it shows that fiber shifts the microbiome rather than how people felt.
Probiotics are not always the right step after antibiotics. In a 2018 study by Suez and colleagues that took gut tissue samples from people and mice after a course of antibiotics, a multi-strain probiotic colonized the human gut lining more readily, but it delayed the return of each person’s own native microbes compared with letting the gut recover on its own. A transplant of the person’s own stool, banked before the antibiotics, restored the original microbiome within days. The human groups were small and the probiotic was a single product, so this does not mean all probiotics are harmful, but it supports choosing them thoughtfully.
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Questions to bring to your clinician
These questions can help you get the most out of your next visit.
Could I have SIBO, and would that change how I use probiotics and prebiotics?
Which probiotic or prebiotic foods would suit my gut in this phase?
How slowly should I introduce prebiotic fiber?
Could a probiotic supplement be helpful for me right now?
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
- Holscher HD, Bauer LL, Gourineni V, et al. Agave Inulin Supplementation Affects the Fecal Microbiota of Healthy Adults Participating in a Randomized, Double-Blind, Placebo-Controlled, Crossover Trial. J Nutr 2015. PMID: 26203099. https://pubmed.ncbi.nlm.nih.gov/26203099/
- Suez J, Zmora N, Zilberman-Schapira G, et al. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell 2018. PMID: 30193113. https://pubmed.ncbi.nlm.nih.gov/30193113/
- Savaiano DA. Lactose digestion from yogurt: mechanism and relevance. Am J Clin Nutr 2014. PMID: 24695892. https://pubmed.ncbi.nlm.nih.gov/24695892/
- McFarland LV, Evans CT, Goldstein EJC. Strain-Specificity and Disease-Specificity of Probiotic Efficacy: A Systematic Review and Meta-Analysis. Front Med (Lausanne) 2018. PMID: 29868585. https://pmc.ncbi.nlm.nih.gov/articles/PMC5949321/
- Peng L, et al. Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers. J Nutr 2009. PMID: 19625695. https://pmc.ncbi.nlm.nih.gov/articles/PMC2728689/
- Hill C, et al. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 2014. PMID: 24912386. https://pubmed.ncbi.nlm.nih.gov/24912386/
- Doron S, Snydman DR. Risk and safety of probiotics. Clin Infect Dis 2015. PMID: 25922398. https://pmc.ncbi.nlm.nih.gov/articles/PMC4490230/
- NIH Office of Dietary Supplements: Probiotics
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.
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