# Skin Barrier Function and the Microbiome

## Overview

The skin barrier is a complex, multi-layered defense system. The "brick-and-mortar" model of the stratum corneum provides the physical and chemical scaffold, while the cutaneous microbiome represents a dynamic biologic barrier that interacts with both pathogens and the host immune system. Disruption of either component is central to the pathogenesis of atopic dermatitis, ichthyoses, and infectious dermatoses.

## The Brick-and-Mortar Model

### Corneocytes (Bricks)

The corneocytes are terminally differentiated, anucleate keratinocytes that form the structural units of the stratum corneum. Each corneocyte is filled with keratin macrofibrils aggregated by filaggrin and enclosed by the cornified envelope — a tough shell composed of involucrin, loricrin, and small proline-rich proteins, all cross-linked by the enzyme transglutaminase 1 (TGM1). The outermost surface of each corneocyte is coated with omega-hydroxy ceramides covalently bonded to the cornified envelope, creating what is called the corneocyte lipid envelope.

### Intercellular Lipid Lamellae (Mortar)

Between the corneocytes, three essential lipid classes are arranged in roughly equimolar ratio:

| Lipid Class | Proportion | Role |
|---|---|---|
| Ceramides | ~50% | Most critical for barrier integrity |
| Cholesterol | ~25% | Structural component of lamellar bilayers |
| Free fatty acids | ~15% | Maintain acid mantle and bilayer organization |

These lipids are the most critical for barrier integrity. These lipids are organized into ordered lamellar bilayers with both long and short periodicity phases, and they are secreted from lamellar bodies at the junction between the stratum granulosum and stratum corneum. Processing of these lipids into their active forms requires an acidic pH and specific enzymes: beta-glucocerebrosidase converts glucosylceramides to ceramides, acid sphingomyelinase generates ceramides from sphingomyelin, and secretory phospholipase A2 releases free fatty acids.

### Desquamation

The shedding of corneocytes from the skin surface is a tightly controlled process governed by kallikrein-related peptidases (KLKs), particularly KLK5 and KLK7. These serine proteases degrade the corneodesmosomes — the modified desmosomes containing desmoglein-1 and corneodesmosin — that hold corneocytes together. KLK activity is pH-dependent and optimal at neutral pH, which means it increases when the skin surface becomes less acidic. The key restraint on KLK activity is LEKTI, a serine protease inhibitor encoded by the SPINK5 gene. Mutations in SPINK5 cause Netherton syndrome, a dramatic illustration of what happens when protease activity goes unchecked: severe barrier failure, ichthyosis linearis circumflexa, atopy, and markedly elevated IgE.

## Filaggrin: Keystone of the Barrier

### Biology

Filaggrin is encoded by the FLG gene on chromosome 1q21, within a cluster of barrier-related genes known as the epidermal differentiation complex. It is initially synthesized as a massive precursor protein called profilaggrin (over 400 kDa), which is stored in the keratohyalin granules of the granular layer. During terminal differentiation, profilaggrin is proteolytically processed into 10 to 12 individual filaggrin monomers. These monomers aggregate keratin intermediate filaments, which is what causes corneocytes to flatten into their characteristic shape. Filaggrin is then itself degraded into free amino acids, collectively known as natural moisturizing factor (NMF).

### Filaggrin Breakdown Products

The breakdown of filaggrin yields several metabolites with important functions. Pyrrolidone carboxylic acid (PCA) acts as a humectant, drawing water into the stratum corneum. Urocanic acid (UCA) absorbs ultraviolet radiation and contributes to the acidic pH of the skin surface. Together, these metabolites maintain stratum corneum hydration and help sustain the acid mantle.

### Filaggrin and Atopic Dermatitis

Loss-of-function mutations in FLG (most commonly R501X and 2282del4) are found in approximately 30 to 50 percent of patients with moderate-to-severe atopic dermatitis, making them the strongest known genetic risk factor for AD. These same mutations also predispose to ichthyosis vulgaris, which is inherited in a semi-dominant pattern. Carriers have increased risk of allergic sensitization, asthma, and peanut allergy. However, not all AD patients carry FLG mutations — Th2 cytokines such as IL-4 and IL-13 can independently downregulate filaggrin expression, which is one reason dupilumab (which blocks both cytokines) can restore barrier function even in patients without genetic filaggrin deficiency. Notably, FLG mutation carriers have higher transepidermal water loss (TEWL) even in clinically uninvolved skin, indicating an intrinsic, whole-body barrier defect.

## The Cutaneous Microbiome

### Composition and Topography

The skin surface harbors approximately one million bacteria per square centimeter, drawn from four major phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The composition of the microbiome varies dramatically by body site.

| Body Site Type | Examples | Dominant Organisms |
|---|---|---|
| Sebaceous | Face, chest, back | Cutibacterium acnes |
| Moist | Axillae, groin, antecubital fossae | Staphylococcus, Corynebacterium |
| Dry | Forearms, legs | Betaproteobacteria, Flavobacteriales (most diverse) |
| Sebaceous (fungal) | Face, scalp | Malassezia species |
| Follicular | Hair follicles | Demodex mites (D. folliculorum, D. brevis) |

Sebaceous areas like the face, chest, and back are dominated by Cutibacterium acnes. Moist sites such as the axillae, groin, and antecubital fossae favor Staphylococcus and Corynebacterium species. Dry sites like the forearms and legs support the most diverse communities, including Betaproteobacteria and Flavobacteriales. Fungal communities on sebaceous sites are dominated by Malassezia species, and Demodex mites (D. folliculorum and D. brevis) are normal commensals within hair follicles.

### Commensals and Colonization Resistance

Commensal bacteria contribute to "colonization resistance" — the ability to prevent pathogenic organisms from gaining a foothold. Staphylococcus epidermidis is a particularly important commensal: it produces antimicrobial peptides (lantibiotics) that are active against S. aureus, stimulates keratinocyte production of antimicrobial peptides, and modulates T cell immunity by inducing IL-17A. Cutibacterium acnes metabolizes sebum triglycerides into free fatty acids that lower skin pH, although strain-level variation determines whether a given C. acnes population behaves as a commensal or contributes to acne (ribotype III strains are particularly associated with acne vulgaris). Roseomonas mucosa, another commensal, has shown promise in pilot studies for improving atopic dermatitis when applied topically.

### Microbiome in Atopic Dermatitis

During AD flares, the skin microbiome undergoes a dramatic collapse in diversity, with Staphylococcus aureus colonizing over 90 percent of lesional skin. S. aureus drives disease through multiple mechanisms: superantigen production (SEA, SEB) that drives polyclonal T cell activation, delta-toxin that triggers mast cell degranulation, biofilm formation that resists clearance, and protease-mediated barrier disruption. Meanwhile, protective coagulase-negative staphylococci like S. epidermidis and S. hominis are reduced during flares. When flares resolve, restoration of microbial diversity correlates with clinical improvement — a pattern sometimes described as the "dysbiosis-flare cycle."

### Microbiome-Targeted Therapies

Several microbiome-directed approaches are under investigation, though none has yet been validated by large randomized trials. Topical bacteriotherapy, in which commensal organisms like S. hominis, S. epidermidis, or R. mucosa are transplanted onto AD skin, has shown promise in small pilot studies by reducing S. aureus colonization and AD severity. Prebiotics and postbiotics are being incorporated into skin care formulations. Endolysin-based approaches use engineered bacteriophage-derived enzymes to selectively target S. aureus cell walls. Antimicrobial peptide therapies are also under investigation. The central controversy is whether manipulating the microbiome can produce durable disease modification or merely offers transient symptomatic relief.

## Transepidermal Water Loss (TEWL)

### Measurement and Significance

TEWL is the gold standard objective measure of barrier function, quantified using open or closed chamber evaporimeters. Normal TEWL on forearm skin is 5 to 10 grams per square meter per hour; elevated values indicate a compromised barrier. TEWL is increased even in uninvolved AD skin, suggesting an intrinsic barrier defect rather than one purely driven by inflammation. Neonates have higher TEWL than adults, with barrier maturation occurring over the first weeks of life.

### Clinical Applications

Emollient therapy, the foundation of AD management, works in part by reducing TEWL. Barrier repair creams containing ceramides, cholesterol, and free fatty acids in physiologic ratios have shown superior barrier restoration compared to simpler emollients. The BEEP trial (Barrier Enhancement for Eczema Prevention) tested whether applying emollients from birth could prevent AD in high-risk infants; initial positive signals were not confirmed in larger studies, leaving the preventive role of early emollient use uncertain.

## pH and the Acid Mantle

Normal skin surface pH ranges from 4.5 to 5.5, maintained by filaggrin breakdown products (urocanic acid, PCA), free fatty acids from sebum and lipid processing, and lactic acid from eccrine sweat. This acidic pH is essential for several reasons: it drives the lipid-processing enzymes (beta-glucocerebrosidase, acid sphingomyelinase) that generate barrier ceramides, it restrains serine protease (KLK) activity to prevent premature desquamation, it supports antimicrobial defense, and it maintains the commensal microbiome. In atopic dermatitis, skin pH is elevated to roughly 5.5 to 6.5, which promotes KLK activity and accelerates barrier degradation. Alkaline soaps further raise skin pH, which is why pH-neutral or mildly acidic cleansers are preferred in patients with compromised barriers.

<image>Detailed illustration of the "brick-and-mortar" model of the stratum corneum, showing flattened corneocytes (bricks) with keratin filaments inside and cornified envelope surrounding them, and intercellular lipid lamellae (mortar) arranged in ordered bilayers between the corneocytes. Label ceramides, cholesterol, and free fatty acids within the lamellae. Show lamellar bodies being secreted at the granular-corneum interface. Include a magnified inset of the cornified envelope structure.</image>

<image>Comparative illustration of normal skin microbiome versus atopic dermatitis flare. Left panel shows diverse microbial communities with S. epidermidis, Cutibacterium, and Corynebacterium in balance. Right panel shows dramatic S. aureus overgrowth with loss of diversity, S. aureus biofilm on damaged epidermis, superantigen release stimulating T cells, and delta-toxin activating mast cells. Use color coding to distinguish bacterial species.</image>

<image>Diagram showing the filaggrin processing pathway: profilaggrin in keratohyalin granules is cleaved into filaggrin monomers that aggregate keratin filaments, then further degraded into natural moisturizing factor components (pyrrolidone carboxylic acid, urocanic acid, free amino acids). Show the consequence of FLG loss-of-function mutation: reduced NMF, increased TEWL, elevated skin pH, and impaired barrier leading to allergen penetration and S. aureus colonization.</image>

## Clinical Pearls

Filaggrin loss-of-function mutations are found in approximately 30 to 50 percent of moderate-to-severe AD patients, but Th2 cytokines (IL-4, IL-13) also suppress filaggrin expression — which is why dupilumab can restore barrier function even in patients without FLG mutations. The skin microbiome in AD undergoes a "dysbiosis-flare cycle" in which S. aureus dominance triggers inflammation, further damages the barrier, and promotes additional S. aureus growth. Dilute bleach baths (0.005 percent sodium hypochlorite) reduce S. aureus colonization and may improve AD severity, though RCT evidence remains mixed. Barrier repair creams with a physiologic lipid ratio (ceramides to cholesterol to fatty acids at 3:1:1) are more effective than petrolatum-based emollients for long-term barrier restoration. Netherton syndrome (SPINK5 mutation) demonstrates the catastrophic consequence of unrestrained protease activity: severe barrier failure, ichthyosis, atopy, and elevated IgE. Neonatal skin barrier is immature, placing premature infants at particular risk for barrier failure, infection, and percutaneous absorption of topical agents. The BEEP and PEBBLES trials failed to show that prophylactic emollient application from birth prevents AD development, challenging the "outside-in" hypothesis of AD prevention.

## References
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- Nakatsuji T, et al. Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis. Sci Transl Med. 2017;9(378):eaah4680.