Recovery and rebuild protocols 6-week protocol 11 food prescriptions

Post-Antibiotic Gut Recovery 6-Week Protocol

A course of broad-spectrum antibiotics can shift the gut microbiome for months, sometimes years. The classic post-antibiotic patterns are depleted Bifidobacterium and Lactobacillus, opportunistic Candida overgrowth, and low Faecalibacterium prausnitzii leading to low SCFA and inflammation. This protocol is designed for the 6-to-12-week window after an antibiotic course, which is when intervention has the highest leverage. Phase 1 starts Saccharomyces boulardii (the probiotic with the strongest post-antibiotic evidence) and a multi-strain Lactobacillus and Bifidobacterium combination. Phase 2 introduces prebiotic fibers gradually to feed the recovering commensals, plus fermented foods for ongoing strain diversity. Phase 3 establishes the long-term diet that sustains the recovery without ongoing supplementation.

Who this protocol is for

Adults within 12 weeks of finishing a broad-spectrum antibiotic course (especially clindamycin, ciprofloxacin, amoxicillin-clavulanate), or anyone with persistent gut symptoms tracing back to a previous antibiotic course.

What to expect, week by week

  1. 1 Week 1 to 2: Bowel regularity starts to normalize. Gas and bloating may temporarily increase as fiber comes in.
  2. 2 Week 3 to 4: Energy stabilizes. Yeast symptoms (if present) drop noticeably.
  3. 3 Week 5 to 6: Mood and sleep improve as the gut-brain axis recovers.
  4. 4 If stool tested at the start: retest at 12 weeks to confirm recovery.

The 6-week food plan

Built from the protocol for Bifidobacterium spp., the primary marker behind this condition. Phase 1 is partially visible. The full plan with exact quantities unlocks when you upload your stool test PDF.

Phase 1 Weeks 1 & 2 · Remove and Reduce
  • Bifidobacterium multi-strain probiotic See your personalized dose
  • Galacto-oligosaccharide (GOS) powder See your personalized dose
Phase 2 Weeks 3 & 4 · Seed and Feed Locked
Phase 3 Weeks 5 & 6 · Build and Sustain Locked

Unlock the full personalized version

This is the off-the-shelf protocol for Post-antibiotic protocol. Upload your stool test PDF and we will build the version that handles your specific marker pattern (most people have 4 to 7 abnormal markers, not just one), with conflicts resolved and a grocery list ready to send to Instacart or Kroger.

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The markers behind this protocol

The primary driver is Bifidobacterium spp.. Click through for what the result means in detail. Supporting markers below often co-occur and inform the full protocol.

Primary driver Low Bifidobacterium spp. Supporting marker Low Lactobacillus spp. Supporting marker Elevated Candida species Supporting marker Low Faecalibacterium prausnitzii Supporting marker Low Secretory IgA

Common mistakes practitioners see

  • Starting probiotics during the antibiotic course (some strains interfere with absorption; Saccharomyces boulardii is the exception).
  • Stopping probiotics too early (the post-antibiotic window is 6 to 12 weeks for the highest yield).
  • Going straight to high-dose prebiotics in week 1 (causes gas, derails compliance).
  • Ignoring the underlying infection that prompted the antibiotic (recurrence undoes the recovery).

When to escalate

  • Severe watery diarrhea (test for C. difficile, especially in older adults or recent hospitalization).
  • Fever and chills returning.
  • Blood in stool.
  • Rapid weight loss.

These signs mean stop the protocol and see a clinician. The protocol is not designed to manage acute or severe disease.

Tests that produce the markers driving this protocol

Diagnostic Solutions Laboratory · Upload supported GI-MAP Genova Diagnostics · Upload supported Genova GI-Effects Biomesight · Upload supported Biomesight

Frequently asked questions

Do I need to do the full 6 weeks?
Yes. Symptom changes show up within 2 to 3 weeks for most people, but the underlying microbiome shift takes the full duration. Stopping at week 2 because you feel better is the single most common reason protocols fail.
Can I do this protocol without a stool test?
You can run the off-the-shelf version of this protocol without a test. The trade-off: you lose the personalization that addresses your other markers. Most people on a stool test have 4 to 7 abnormal markers, not just one. The personalized version sequences interventions based on which combinations are present.
What if I have multiple findings on my test?
Almost everyone does. Upload your full PDF instead of running this single-condition protocol. The personalized output handles marker conflicts (for example, fiber that helps one marker can worsen another) and sequences phases in the right order across all of them.
When should I retest?
8 to 12 weeks after starting the protocol is the validated retest window for most stool tests. Earlier than that, the markers have not had time to change. Later than that, you lose the ability to attribute changes to the protocol vs. drift.
Should I work with a practitioner alongside this?
For protocols involving parasites, H. pylori, or significant inflammation (Calprotectin above 120 µg/g), yes. For dysbiosis, low diversity, or low SCFA findings, dietary protocols can be self-directed for most people. The 'when to escalate' section above lists the specific signs that mean stop and see a clinician.

Get the version built for your full report

This protocol assumes a single primary driver. Most stool tests show 4 to 7 abnormal markers. Upload your PDF and get the version that handles all of them, in the right order.

Upload your lab PDF