Recovery and rebuild protocols 6-week protocol 11 food prescriptions

General Gut Dysbiosis 6-Week Recovery Protocol

Generalized dysbiosis (low diversity, no single dominant pathogen, multiple commensals depleted) is the most common pattern on a 16S sequencing test like Biomesight. It is also the hardest pattern to fix, because there is no single organism to target. This protocol works on three principles. Phase 1 removes the most common dysbiosis drivers (alcohol, ultra-processed food, chronic NSAID use, sleep deprivation) and starts fermented foods to deliver immediate microbial diversity. Phase 2 adds the 30 plants per week diversity target, which has the strongest evidence for raising overall gut diversity scores. Phase 3 establishes the long-term diet pattern that sustains diversity, plus adds longitudinal monitoring (retest in 12 weeks, then again at 6 months).

Who this protocol is for

Adults with low diversity on a Biomesight, Thorne, or ZOE microbiome test, especially when the report flags a shifted Bacteroidetes-to-Firmicutes ratio without naming a specific pathogen or single deficient marker.

What to expect, week by week

  1. 1 Week 1 to 2: Subtle changes. Better sleep is the most common first signal.
  2. 2 Week 3 to 4: Bowel regularity improves, post-meal energy increases.
  3. 3 Week 5 to 6: Food variety expands without symptom return.
  4. 4 Retest at 12 weeks. Diversity is the slowest-moving metric in functional medicine.

The 6-week food plan

Built from the protocol for Bacteroidetes/Firmicutes Ratio, 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
  • Target: 15 different plant species See your personalized dose
  • Mixed salad greens (4+ types) 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 Dysbiosis recovery. 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.

Upload my lab PDF

The markers behind this protocol

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

Primary driver Elevated Bacteroidetes/Firmicutes Ratio Supporting marker Low Akkermansia muciniphila Supporting marker Low Faecalibacterium prausnitzii Supporting marker Low Bifidobacterium spp. Supporting marker Low Lactobacillus spp. Supporting marker Low Total Short-Chain Fatty Acids

Common mistakes practitioners see

  • Chasing a specific organism instead of fixing the diversity deficit.
  • Eating the same 10 'healthy' foods every day (variety matters more than perfection).
  • Ignoring lifestyle drivers (sleep, alcohol, stress) that suppress diversity directly.
  • Stopping at week 6 expecting a full recovery (diversity rebuilds over months, not weeks).

When to escalate

  • New severe GI symptoms appearing during the protocol.
  • Suspected pathogen on a follow-up stool test (refer to functional medicine clinician).
  • Persistent unexplained 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

Biomesight · Upload supported Biomesight Thorne (in partnership with Onegevity) Thorne Gut Health Viome Life Sciences Viome

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