The Autoimmune Root Cause Clinical Toolkit

Six practitioner-ready resources that take you from a complex autoimmune presentation to a clear root-cause picture, a confident management plan, and safe co-prescribing alongside medical care.

Autoimmune cases are rarely simple. By the time a patient reaches you, there's usually a long history behind the diagnosis — infections, stress, exposures, medications, diet — and a list of prescriptions you have to work safely around. The hard part isn't the textbook pathophysiology. It's knowing what's actually driving this person's disease, in what order to address it, and how to support them without colliding with the medications they're already on.

That's the work this toolkit was built for. It turns a sprawling, intimidating case into a structured process you can repeat with confidence, every time.

Why autoimmune cases need a root-cause approach

Symptom suppression is the easy path, and it's where many cases stall. Lasting progress comes from addressing the terrain underneath — what I think of as the four drivers of autoimmunity: inflammation, dysbiosis, immune dysregulation and intestinal permeability. But terrain is only useful if you can systematically uncover it. Which infections, exposures and early-life events primed this immune system? Which medications are helping, and which herbs or nutrients might dangerously interact with them? Without a framework, those questions get answered inconsistently, or missed.

Every resource here was built to make that assessment systematic, and to make your management both effective and safe.

What you're getting

The Autoimmune Root Cause Clinical Toolkit is a complete clinical resource library — six professionally produced guides and tools that work together across the whole arc of a case: assess, understand, treat, and co-prescribe safely. Buy once, download instantly, and use them in your practice for as long as you practise.

Inside the toolkit

1. The Autoimmune Root Cause Assessment Guide

The flagship, and worth the price on its own. This in-depth practitioner guide systematically works through the major contributors to autoimmune onset and progression, turning the vague question of "what's driving this?" into a structured, repeatable assessment. Across twenty-seven guided questions, it covers:

• Infections — past gastroenteritis, identified enteric pathogens, and chronic viral burden (EBV, CMV, COVID, HSV).
• Lifestyle factors — early-life and current stress and trauma, exercise, and sleep.
• Environmental exposure — mercury, heavy metals, hazardous chemicals and mould.
• Personal and early-life history — childhood microbial exposure, birth and feeding, and dietary history.
• Family history and inherited predisposition.
• Medication and supplement history — antibiotics, NSAIDs, PPIs and corticosteroids.
• Dietary intake — food reactions, sodium, arachidonic acid and fibre.
• Vitamin D — status, history and relevant genetics.

For each area you get the exact questions to ask, a clinical interpretation explaining why it matters mechanistically, and a clear management pathway — the testing, nutrients, herbs and lifestyle interventions to consider. It's the difference between chasing symptoms and resolving the terrain.

2. Autoimmune Root Cause Questionnaire

A ready-to-use intake tool that captures the full root-cause history before the patient even sits down. It does the heavy lifting of the assessment for you, so your consult time goes to interpreting and planning rather than gathering.

3. The Autoimmune Pathology Guide

A clear reference to the mechanisms behind autoimmune presentations — loss of self-tolerance, molecular mimicry, immune dysregulation and barrier dysfunction. It keeps your clinical reasoning grounded and helps you explain the "why" to patients with authority.

4. Autoimmune Management Nutrition & Lifestyle Recommendations

Practical, ready-to-apply dietary and lifestyle guidance built on an anti-inflammatory Mediterranean foundation, so you can translate your root-cause findings straight into a plan a patient can realistically follow.

5. Autoimmune Supplement Protocols

Considered supplement and dosing protocols for autoimmune presentations — taking the guesswork out of what to recommend, in what form, and at what stage.

6. Medication Interactions & Co-Prescribing Cheat Sheet

The piece you won't find anywhere else. A fast, structured clinical reference to the medications your autoimmune patients are most likely to be taking — more than thirty, across every major class:

• Biologics — adalimumab (Humira), etanercept (Enbrel), infliximab (Remicade), rituximab, ustekinumab (Stelara) and more.
• DMARDs — methotrexate, hydroxychloroquine (Plaquenil), sulfasalazine, azathioprine, mycophenolate.
• Glucocorticoids and NSAIDs — prednisolone, ibuprofen, naproxen, celecoxib.
• Targeted synthetics and JAK inhibitors — apremilast (Otezla), tofacitinib (Xeljanz).
• MS therapies — dimethyl fumarate (Tecfidera), fingolimod (Gilenya), ocrelizumab (Ocrevus) and others.
• Low-dose naltrexone, thyroid, acid-control, cardiovascular and bone-protective agents.

For each medication you get the typical dosage, the conditions it's used for, its mechanism of action, its interactions with herbs and nutrients, and the clinical considerations for co-prescribing. It lets you support patients alongside their medical care with confidence — spotting herb–drug and nutrient–drug interactions before they become a problem, and collaborating safely with the prescribing doctor.

What this does for your practice

• Hours back, every week. The assessment, interpretation and protocols are already done.
• Confidence in complex cases. A systematic root-cause framework behind every recommendation.
• Safer prescribing. Know the herb– and nutrient–drug interactions before you add a single supplement.
• Polish in front of patients. A professional intake questionnaire that elevates the way your practice runs.
• Consistency. One trusted framework across every autoimmune case you take on.

Who this is for

Naturopaths, clinical nutritionists, herbalists, integrative GPs and any qualified practitioner managing autoimmune cases — rheumatoid arthritis, lupus, Hashimoto's, psoriasis and psoriatic arthritis, multiple sclerosis, inflammatory bowel disease and beyond.

It is a clinical resource for practitioners. The medication cheat sheet supports safe co-prescribing alongside a patient's existing care; it is not prescribing guidance, and it is not patient education.

These resources are the same you'll find in the Autoimmune Mentoring Program.