Gut & Microbiome

This module already contains one directly actionable tool — the HSI six-stage restoration sequence in Lesson 2.4. These five things make sure you use it immediately, rather than treating it as something to reference later.

1. 1

   Ask the four dysbiosis-driver questions in your next client intake

   Lesson 2.2

   Recent antibiotic use, stress load, dietary fibre pattern, and any suspected overgrowth/infection history. These four questions alone are a meaningful upgrade to a standard intake and cost nothing to add.

2. 2

   Run Identify and Investigate on one real case

   Lesson 2.4

   You don’t need to complete the full six-stage sequence to get value — just practise the first two stages from Lesson 2.4 on a real or prototype client this week: what does their history suggest, and would testing (Lesson 2.3) actually add anything, or is the picture already clear from history alone?

3. 3

   Practise saying no to over-testing

   Lesson 2.3

   Lesson 2.3’s key practical lesson — that ordering every available test is worse practice, not more thorough — is a mindset worth actively rehearsing. Next time a test feels tempting, ask: what would this result actually change about the plan?

4. 4

   Try the fibre-diversity conversation

   Lesson 2.2

   From Lesson 2.2’s SCFA content: rather than a generic "eat more fibre" message, practise explaining why — that fibre diversity feeds the bacteria that produce SCFAs, which maintain gut barrier integrity. Specific mechanism-based explanations tend to land better with clients than generic advice.

5. 5

   Start applying Reinforce-stage thinking beyond the gut

   Lesson 2.4

   Lesson 2.4’s final stage (sleep, stress, consistency) is really a preview of the Regimen/Mind domains from Module 1. Notice, this week, how often a "gut" conversation actually turns into a sleep or stress conversation — that pattern is the whole point of systems thinking.

Where to start after finishing Module 2: continue to Module 3: Integration & Application — the closing module of the Foundational Certificate, where Module 1’s HSI Method and Module 2’s gut-restoration sequence come together on one unified case, and where full “what’s next” guidance lives.

Fill this in for yourself or one real client. It builds directly on the Module 1 worksheet — use them together where possible. A fillable PDF is in the downloads below.

• The Gut-Everything Axis — diagram

  Lesson 2.1

  The gut as a hub connecting immune, nervous and endocrine systems and systemic inflammation, with the key figures (GALT ~70%, serotonin ~90–95%).

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• Gut testing modalities — comparison table

  Lesson 2.3

  Stool analysis, SIBO breath testing and permeability assessment: what each measures, strengths and limitations.

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• The HSI Gut Restoration Sequence — one-pager

  Lesson 2.4

  Identify → Investigate → Reduce burden → Rebuild → Reintroduce → Reinforce, with the evidence note.

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• Annotated case: Marcus, 52

  Lesson 2.5

  The full Lesson 2.5 worked case, each stage annotated against the HSI Method.

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• Module 2 self/client audit worksheet (fillable)

  Module 2

  Parts A–D: dysbiosis risk screen, symptom pattern, testing decision and six-stage plan. Type directly into the PDF or print.

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• Module 2 case assignment brief

  Module 2

  Leila Hart’s vignette with the submission instructions and practitioner-track referral requirement.

  Download PDF

References

1. [7]Multiple peer-reviewed sources on gut-immune and gut-brain physiology, including GALT’s role in systemic immunity and the gut microbiome as a modulator of gut-brain axis signalling (see e.g. PMC12251473, gut-brain axis and tryptophan metabolism research).
2. [8]General physiology consensus on serotonin production in the gastrointestinal tract and vagal gut-brain communication — standard, non-proprietary physiology.
3. [9]Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome — An Update. PMC7366247.
4. [10]The duodenal microbiome is altered in small intestinal bacterial overgrowth. PMC7347122.
5. [11]North American Consensus criteria for breath testing (hydrogen ≥20ppm or methane ≥10ppm by 90 minutes) — as referenced in Fecal Coprococcus, hidden behind abdominal symptoms in patients with small intestinal bacterial overgrowth. PMC11128122.
6. [12]How to test for intestinal dysbiosis — overview of stool, breath, and metabolomic testing modalities. InnerBuddies.
7. [13]Microbiome Testing overview — gut permeability and SIBO testing modalities. The Functional Gut Clinic.
8. [14]An Oral Botanical Supplement Improves Small Intestinal Bacterial Overgrowth (SIBO) and Facial Redness — example of a structured, staged intervention study design. PMC11435404. (Cited for study design/evidence example only — specific commercial products named in this study are not endorsed or referenced as recommended interventions.)
9. [15]Vighi G, Marcucci F, Sensi L, Di Cara G, Frati F. "Allergy and the gastrointestinal system." Clin Exp Immunol. 2008;153(Suppl 1):3-6 — GALT comprises approximately 70% of the immune system by weight.
10. [16]Human gut-associated lymphoid tissues (GALT): diversity, structure, and function — the intestine contains the greatest number and diversity of immune compartments and immune cells in the body. ScienceDirect, 2022.
11. [17]Bertrand PP, Bertrand RL. "Serotonin release and uptake in the gastrointestinal tract." Autonomic Neuroscience, 2010; see also Lund ML et al., Enterochromaffin Cells Are Gut Chemosensors that Couple to Sensory Neural Pathways. Cell, 2017 — approximately 90-95% of total serotonin is produced by gut enterochromaffin cells.
12. [18]Serotonin in the gut: Blessing or a curse — overview of gut-derived serotonin production and function. ScienceDirect, 2018.
13. [19]Effects of different amoxicillin treatment durations on microbiome diversity and composition in the gut — microbial composition returned to normal within 2-4 weeks in most reviewed studies. PMC9612567.
14. [20]Palleja A, et al. "Recovery of gut microbiota of healthy adults following antibiotic exposure." Nature Microbiology, 2018 — near-baseline within ~1.5 months, though some species remained undetectable in most subjects after 180 days.
15. [21]Leigh SJ, Uhlig F, Wilmes L, et al. "The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota-gut-brain axis perspective." The Journal of Physiology. 2023.
16. [22]Roles of Short-Chain Fatty Acids in Inflammatory Bowel Disease — SCFA production via fibre fermentation and role in gut barrier/colonic cell energy metabolism. PMC10609902.
17. [23]Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. "From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites." Cell. 2016;165(6):1332-1345.