Addressing The Root Cause Of Eczema with Functional Medicine Dermatology

Recently, I discovered a fantastic training on eczema treatment from a functional medicine dermatology perspective. If you’ve followed my journey healing from severe eczema and psoriasis, you already know I don’t believe eczema is "just a skin problem" and I'm trying to heal from the inside out. This training provided a really solid foundation for understanding the root cause of eczema and how to treat it holistically. I was especially happy to see that they went into specifics about what tests to run and how to chart a course of action based on the results.

Over the last few years, I’ve gone deep into the gut–immune–skin connection. Recently, I studied a comprehensive functional dermatology training by Dr. Greenberg that lays out a full “root-cause” blueprint for eczema treatment.

Here is the training video from Dr. Greenberg from Root Cause Dermatology:

👉 https://www.youtube.com/watch?v=QU8nWOm-wB8

This article is my notes from this training.

Core Philosophy

Functional medicine dermatology does not suppress symptoms with pharmaceuticals. The goal is to:

• Identify and treat the root cause
• Restore function to the body
• Achieve lasting clearance, not managed suppression

Pathophysiology of Eczema

What Is Eczema?

• "Atopic dermatitis" — atopic = allergic; dermatitis = skin inflammation
• Fundamentally a disease of Skin Barrier Dysfunction + deep systemic inflammation
• Not just a surface issue — the inflammation is internal and systemic

Immune Pathways Involved

Eczema is not driven by a single immune pathway. Multiple T-helper cell pathways are involved:

Key insight: Eczema has multiple subtypes (similar to breast cancer subtypes). European, Asian, African, and pediatric patient groups show different Th1/Th17 involvement profiles. Psoriasis has NO Th2 component — this is the primary distinguishing factor.

Leaky Skin: The Allergy Driver

How Leaky Skin Creates Food Allergies

• Normal intact skin prevents allergen entry — dendritic cells stay quiet
• Damaged/eczematous skin has breached barriers — allergens (dust mites, food proteins) penetrate
• Dendritic cells activate → present novel proteins to immune system → drives Th2 allergic response
• This is how eczema causes food allergies, not just the reverse

Evidence

• Food sensitization is 6x more likely in children with eczema vs. without
• Neonatal skin barrier dysfunction at birth predicts food allergies by age 2
• Children with skin barrier defects are more likely to develop asthma
• Recreated experimentally in mice: skin injury + protein exposure → eczema lesions, IgE + IgG antibodies, even anaphylaxis

The Atopic Triad / Atopic March

Eczema → Food Allergy → Asthma (both life-threatening)

• ~1/3 of children with early-onset eczema progress through this march
• Clearing eczema early can stop the atopic march — this is potentially life-saving

Food Triggers

Top 5 Food Groups Responsible for ~75% of Food-Induced Flares

1. Dairy (all mammal milk — cow, goat, sheep, camel — no exceptions)
2. Eggs
3. Wheat/Gluten
4. Soy
5. Peanuts

These can trigger via IgE (true allergy) OR IgG/IgA (food sensitivity/delayed reaction).

Practical Approach to Food

• Dairy elimination is universal — applied to 100% of eczema patients regardless of allergy test results. No eczema patient benefits from dairy.
• Elimination diet for the other 5 groups is case-by-case
• Most patients already know their triggers — don't over-engineer the food piece
• ~2/3 of eczema patients show NO sensitization to food or environmental allergens — food elimination alone won't clear them

Clinical warning: Don't get stuck on food. If dietary changes aren't getting full resolution, move on to gut investigation. Food is one lever, not the whole answer.

Notes on Gluten

• Anti-gliadin IgA elevated on stool testing = clear reason to remove gluten
• Wheat challenge study: 13/18 eczema kids flared with wheat, and all 13 had positive IgE to gliadin/gluten

Bonus: Chronic Ear Infections

• Strong clinical overlap between eczema and recurrent ear infections
• Embryologically, middle ear/eustachian tube shares origins with the digestive system
• IGG food testing in chronic ear infection patients (n=44): 70% reacted to milk, 43% to gluten, 27% egg, 7% soy — mirrors eczema triggers exactly
• Try eliminating top food allergens before considering tympanostomy tubes

The Gut-Skin Axis

Why the Gut Matters

• The gut is one of the body's largest mucocutaneous sites
• Gut dysbiosis drives systemic inflammation — the engine behind eczema
• Eczema patients consistently show altered microbiome profiles

Microbiome Findings in Eczema Patients

Lower levels of beneficial bacteria:

• Bifidobacteria
• Bacteroides
• Phyla Bacteroidetes

Higher levels of pathogenic bacteria:

• C. diff
• E. coli
• Staph aureus (also over-colonizes the skin AND nose in eczema patients)

Fungal overgrowth:

• Candida albicans — statistically significant correlation with IgE antibodies to candida in eczema patients; anti-fungal treatment improves skin

Leaky Gut in Eczema

• The majority of eczema patients have increased intestinal permeability (leaky gut)
• Positive association: more leaky gut = more severe eczema
• Mechanism: degraded mucosal barrier → gut cells exposed to bacteria/fungi/food proteins → tight junctions fail → LPS (endotoxin from gram-negative bacteria) enters bloodstream → dendritic cells activate → systemic inflammation → triggers Th1, Th17, Th2

Butyrate — Critical for Gut Integrity

Short-chain fatty acid (SCFA) produced by beneficial bacteria (Faecalibacterium prausnitzii, Clostridium butyricum, Roseburia):

• Primary fuel for enterocytes (intestinal cells)
• Calms the immune system, suppresses inflammatory cytokines
• Strengthens tight junctions
• Research: Severity of eczema inversely correlates with microbiome diversity and butyrate-producing bacteria

Key butyrate producers to assess: Faecalibacterium prausnitzii, Roseburia, Akkermansia muciniphila (mucosal barrier protector)

Two Primary "Eczema Gut Profiles"

Profile 1: Dysbiosis with Candida (Most Common)

• High Staph aureus and Streptococcus
• High Candida overgrowth
• Low/absent Akkermansia muciniphila
• Low/absent Faecalibacterium prausnitzii, Roseburia (butyrate producers)
• Low secretory IgA → leaky gut picture

Profile 2: H. pylori + Protozoa

• H. pylori present (gram-negative, LPS-producing, biofilm-forming)
• Protozoa present (Blastocystis hominis, Giardia, Endolimax nana, Dientamoeba fragilis, etc.)
• H. pylori neutralizes stomach acid via urease → impairs digestion, kills protective acidity → enables protozoa to colonize
• Creates sub-optimal digestion: pancreatic enzyme signaling disrupted, bile secretion impaired
• Triggers Th1 inflammatory pathway
• Connection to: acne, rosacea, psoriasis as well

Additional Finding: Morganella

• Morganella morganii = high histamine producer
• Elevated in gut → drives Th2 itchy response
• Treat the morganella to reduce histamine (preferred over low-histamine diets as a long-term fix)

Functional Medicine Testing Protocol

Universal Baseline Tests (Every Patient)

1. GI-MAP Stool Test (Diagnostic Solutions)

   • Bacterial profiles: H. pylori, commensal, opportunistic, pathogenic
   • Fungi/yeast (partial — supplemented by OAT)
   • Parasites, protozoa, worms, viruses
   • Fat in stool (digestive dysfunction marker)
   • Pancreatic elastase (enzyme production)
   • Short-chain fatty acids (butyrate)
   • Inflammatory markers: Calprotectin, Lactoferrin, Secretory IgA
   • Permeability markers: Zonulin

2. OAT — Organic Acids Test (Mosaic Diagnostics, urine test, ~74 metabolites)

   • Primary purpose: Yeast and fungal markers (stool testing insufficient for fungi)
   • Arabinose = marker for Candida overgrowth
   • Oxalic acid = byproduct of Candida metabolism (almost always high with Candida)
   • Additional metabolite insights across nutrient status, mitochondrial function, etc.
   • Clinical rule: Without the OAT, you're looking at half the picture

Additional Tests (As Indicated)

• Dutch Hormone Test
• Mycotoxin Testing
• Environmental Toxin Panel

Treatment Framework

Treatment Prioritization (Clinical Note)

In the classroom: treat H. pylori first (it's upstream, affects stomach acid)
In clinical practice: don't start with H. pylori — dosing is demanding (empty stomach required). Start with dysbiosis/candida to reduce inflammation and show early improvement, then address H. pylori in a subsequent plan.

Patient follow-up cadence: every 2–3 months, with updated protocols each visit.

Targeted Interventions by Finding

H. pylori:

• Mastic gum
• DGL (deglycyrrhizinated licorice)
• Berberine + Saccharomyces boulardii

Bacterial overgrowth (Staph, Strep, dysbiosis):

• Coptis (berberine-rich herb)
• Oregano oil
• Olive leaf
• Garlic
• Antimicrobial herbal blends

Fungal/Candida overgrowth:

• Rosemary
• Pau d'Arco
• Uva ursi
• Antifungal herbal blends

Protozoa/Parasites:

• Artemisia (wormwood)
• Black walnut
• Anti-parasitic herbal protocols

Leaky gut / mucosal restoration:

• Akkermansia probiotic (Pendulum brand)
• Clostridium butyricum probiotic (Pendulum brand)
• Fiber — target: 35 grams/day in adults (build up gradually)
• Prebiotics (cranberry, pomegranate-based) to encourage Faecalibacterium prausnitzii, Roseburia regrowth

General support (all patients):

• Multivitamin
• 4 core probiotics (adults)
• Anti-inflammatory foods: omega-3s (fish oil if not fish-allergic), fiber, clams

Dietary Protocol

• Remove dairy universally (100% of eczema patients)
• Elimination of top 5 food groups if indicated — not permanent, test for 4–6 weeks
• Remove gluten if anti-gliadin IgA elevated on testing
• Increase fiber, omega-3s, anti-inflammatory foods
• Nightshades: ~50% of patients report worsening — individualize

Topical Approach

Address topically in parallel with gut work, but topical alone is insufficient:

• Treat skin microbiome (Staph aureus overgrowth is almost universal on eczematous skin)
• Treat nasal colonization of Staph aureus
• Support filaggrin protein production (key for dry/leaky skin phenotype — filaggrin gene mutations common in early-onset eczema)
• Wet/oozing eczema = likely Staph aureus superinfection; may need short-term topical mupirocin or oral antibiotics (Keflex, doxycycline)

Case Study: "Tina" — Severe Adult Eczema

Presentation: 34F, eczema since infancy, severe flare x6 months, failed 5 steroids (including clobetasol — 600x strength of hydrocortisone), on montelukast, unable to work

GI-MAP Findings:

• H. pylori positive
• Akkermansia muciniphila: absent (leaky gut indicator)
• Bacteroidetes/Firmicutes overgrowth (dysbiosis)
• Morganella at E7 (high histamine producer)
• Staph aureus + Streptococcus elevated
• Blastocystis hominis (protozoa — expected given H. pylori)
• Anti-gliadin IgA: elevated → gluten must go

OAT Findings:

• Arabinose: elevated → Candida overgrowth
• Oxalic acid: elevated → confirms Candida

Treatment Plan (across multiple 2-3 month plans):

• H. pylori protocol: mastic gum, DGL, berberine
• Bacterial overgrowth: antimicrobial herbs (coptis, oregano, olive leaf, garlic)
• Anti-fungal herbs (rosemary, Pau d'Arco, uva ursi)
• Anti-parasitic herbs: artemisia, black walnut
• Akkermansia probiotic
• 4 core probiotics + multivitamin
• Fiber increase → 35g/day target
• Gluten removal
• Topical protocol (concurrent)

Outcomes:

• 2 months: Massive improvement, sleeping through the night
• 5 months: Continued clearing
• 7 months: Near complete resolution including lichenified plaques (popliteal fossa, hands, abdomen)
• Post-inflammatory pigmentation resolved with time once scratching stopped

Clinical Pearls

• "Bucket" mental model: Disease emerges when total inflammatory/toxic load overflows the body's capacity to compensate. Many inputs fill the bucket; the goal is to drain it from below.
• Probiotics alone rarely clear eczema — 2019 systematic review of 44 studies: 50/50 results. Too many variables (strain, dose, duration). Probiotics are a tool, not a solution.
• Chronic antibiotic use creates either "desert wasteland" gut (nothing surviving) or opportunistic overgrowth (C. diff, Pseudomonas). Functional medicine approach breaks the antibiotic cycle.
• Treat all pathogens found on testing, even if asymptomatic — broad-spectrum herbal protocols clean them up as a byproduct of treatment.
• Low-histamine diets = symptom control, not root cause — better to identify and eliminate the histamine-producing bacteria (e.g., Morganella). Add Mast Cell stabilization herbs (quercetin, vitamin C) while investigating root cause.
• Vaginal birth + breastfeeding = optimal microbiome seeding for infants, but C-section/formula-fed children are not predetermined for eczema — use testing to determine actual gut status.
• The skin repairs itself once the underlying drivers are cleared — hyperpigmentation and hypopigmentation resolve over time.

Key Tests to Order

Conditions Treated With This Framework

This gut-first approach applies broadly beyond eczema:

• Psoriasis (all types: guttate, palmar, scalp)
• Acne (including cystic/nodulocystic)
• Rosacea
• Seborrheic dermatitis
• Alopecia areata / hair loss
• Keratosis pilaris

All are fundamentally chronic systemic inflammatory conditions rooted in gut dysbiosis and immune dysregulation.