Skin and Gut Microbiome

Introduction

Interest in the human microbiome and its role in both normal human physiology and in disease has grown dramatically in recent years. Our understanding of the composition and abundance of organisms in the human body has increased as more precise techniques have been developed. No longer viewed as bystanders, commensal organisms are now understood to play vital physiologic roles, including nutrient metabolism, vitamin synthesis, barrier protection, and immune system development. Dysbiosis, a term used to describe imbalance in the healthy microbiome, can lead to increased inflammation and is associated with disease states. This chapter will explore the composition of the healthy microbiome and the changes that occur in dysbiosis and its impact on atopic dermatitis.

Microbiome

The human microbiome refers to the genetic material (collection of all genomes) of the community of organisms, including bacteria, fungi, and viruses, that inhabit the body both inside and out. This adds significant genetic information to the human body, as the amount of nonhuman cells is estimated to be in the trillions and accounts for at least as many human cells, and potentially even 10-fold more ( ). The majority of microbes reside in the intestinal tract, followed next by the skin ( ).

Use of sequencing techniques has led to a better understanding of the composition of the microbiome. These sequencing techniques can either be directed toward a specific genetic target or the genome as a whole ( ). For bacteria, 16 S ribosomal RNA (rRNA) sequencing targets a conserved and yet highly variable region of bacterial genomes, allowing for increased detection of microbes compared to traditional culture techniques ( ). For fungi, sequencing of ribosomal internal transcribed spacer (ITS) allows for identification to the species level ( ).

Whole genome (shotgun) sequencing, a technique used to analyze all genomic material in a given sample, has helped to further classify skin microbes. Compared to 16 S rRNA and ITS sequencing, this technique confers the additional benefits of identifying viral genes, classifying bacterial species to the strain level, and quantifying relative abundances at the kingdom level ( ). Using these techniques, the overall composition of the skin demonstrates highest abundance of bacteria, followed by viruses and lastly fungi (~4%), though site-specific compositional differences exist ( ). Nineteen different phyla of bacteria have been identified on the skin, with the four predominant phyla among these being Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes, with the most abundant genera being Corynebacteria, Propionibacteria , and Staphylococci ( ). The most abundant viruses are bacteriophages (viruses that target bacteria), and the predominant fungal genus is Malassezia ( ).

The predominant species found on human skin evolves over time, dependent upon various environmental and physiologic factors. As infants, the microbiome is first influenced by delivery method. Vaginal delivery results in colonization by common vaginal bacteria ( Lactobacillus, Prevotella, Sneathia ), while delivery through cesarean section leads to colonization with common skin bacteria ( Staphylococcus, Corynebacterium, Propionibacterium ) ( ). Regardless of delivery method, this colonization is temporary, with diversification by body site occurring by 6 weeks of age ( ). In prepubescence, the microbiome shifts to an abundance of Firmicutes (including Streptococcaceae ), Bacteroidetes, and Proteobacteria, while changes in hormone levels at puberty result in increased sebum production and subsequent expansion of Propionibacterium, Cornyebacterium , and Malassezia ( ).

Beyond these age-related changes, multiple additional environmental factors have been shown to influence the skin microbiome, including pH, gender, ethnicity, geography, and ultraviolet (UV) exposure ( Table 6.1 ). Healthy skin exhibits a lower skin pH (in the acidic range of 4–6), allowing for the growth of select bacteria (coagulase-negative Staphylococcus, Corynebacteria), while inhibiting pathogenic strains ( Staphylococcus aureus and Streptococcus pyogenes ) ( ). Gender differences also influence the skin microbiome, likely due to inherent differences in hormone, sebum, and sweat production as well as differences in skin surface pH ( ). Numerous studies have also shown variations in the skin microbiome of patients with different ethnic and geographic backgrounds, which likely result from differences in diet and lifestyle among studied populations ( ). For example, Propionibacteriaceae , Staphylococcaceae , and Streptococceacea are more abundant on adult hands in the United States, while Rhodobacteraceae and Nocardioidaceae , bacteria commonly found in soil and aquatic environments, are more abundant on adults’ hands in Tanzania ( ). UV light has an immunomodulatory influence on skin and can decrease skin S. aureus levels ( ). Though influenced by many factors, once established, an individual’s skin microbiome remains stable over time ( ). Factors that influence skin microbiome are listed in Table 6.1 .

Skin microbial communities also vary based on body location, which can be categorized by areas that are moist, dry, or sebaceous. Moist areas include the axillae, nostrils, antecubital and popliteal fossae, interdigital web spaces, inguinal creases, plantar heels, and umbilicus (skin creases). These areas tend to have greater abundance of Corynebacterium and Staphylococcus— microorganisms that thrive in environments with higher temperature and humidity. Dry areas include the forearms, palms, and buttocks. These areas tend to have more mixed populations, with an abundance of β-Proteobacteria and Flavobacteriales. Sebaceous areas include the glabella, alar crease, inside and behind the ear, occiput, upper chest, and back; these areas have the lowest amount of diversity, attributed to the anoxic and lipid-rich environment. Sebaceous areas are dominated by Propionibacteria , though Staphylococci are also present ( ). Like bacteria, viruses tend to be less diverse at sebaceous sites ( ). While Malassezia is the predominant fungus on the majority of skin surfaces, increased fungal diversity is seen on parts of the foot ( ).

In its normal state, the skin microbiome is in a healthy homeostasis and consists primarily of commensal organisms, or those conferring benefit without causing harm, and transient microbes ( ). This homeostasis is maintained by a combination of protective mechanisms inherent to the skin, as well as contributions from a diverse resident bacterial population. Keratinocytes produce numerous antimicrobial peptides (AMPs), including cathelicidin and β-defensin, that protect the skin barrier through multiple mechanisms, including direct attack on microbes and eliciting a host response ( ).

Similar to innate host defense, commensal bacteria ( Staphylococcus epidermidis being the most widely studied) also contribute to this balance through multiple mechanisms. Directly, S. epidermidis can produce peptides that inhibit growth of pathogenic organisms such as S. aureus , without disrupting other commensals ( ). Indirectly, S. epidermidis is capable of eliciting an immune response targeting pathogens through activation of toll-like receptors ( ). S. epidermidis has also been shown to inhibit the formation of S. aureus biofilms ( ).

Regulatory T cells (Tregs), a subset of CD4+ T cells, play an important role in immune regulation and maintain-ing homeostasis through promotion of tolerance to self-antigens. A greater number of regulatory T cells are present in infancy ( ), and exposure to commensal bacteria on the skin early on in life plays a significant role in establishing this tolerance ( ). Specifically, in the skin, the early presence of S. epidermidis is detected by antigen-presenting cells, presented to T cells that express the matching antigen receptor, which results in the expansion of a population of regulatory T cells that allows for tolerance to the organism ( ). As a result, subsequent detection of S. epidermidis does not trigger inflammation (immune tolerance), but instead results in the induction of cytokine interleukin 1a (IL1a), which in turn acts as host defense, an example of immune-commensal crosstalk ( ). Early exposure is necessary for this commensal tolerance to occur ( ). Since regulatory T cells play a key role in self-tolerance, dysfunctional or decreased number of Tregs are seen with autoimmune conditions ( ).

Skin dysbiosis

Dysbiosis refers to a disruption of the microbiome and a shift away from homeostasis, and is seen in disease states such as atopic dermatitis. A study published in 1989 highlighted epidemiologic data that correlated increases in the incidence of atopic dermatitis with improved personal cleanliness and smaller family sizes (with subsequent decreases in sibling contact), suggesting that a disruption in microbial exposure may contribute to atopic dermatitis ( ). This idea became known as the hygiene hypothesis. In support of this hypothesis were subsequent data that showed that exposure of children to microbial products (endotoxin) through their environment was protective against the development of atopic disease ( ).

Risk factors of skin dysbiosis

Patients with atopic dermatitis are at increased risk for dysbiosis through skin barrier dysfunction ( Table 6.2 ). Extrinsically, as flares drive itch, scratching physically breeches the barrier. Intrinsic factors include the higher skin pH seen in these patients, which results in altered synthesis of protective lipids that creates an environment conducive to pathogen growth, including Staphylococcus and Candida ( ). Loss-of-function mutations in filaggrin, a protein with multiple roles important to skin barrier function, including pH regulation and maintaining hydration, is a major risk factor for the development of atopic dermatitis and is present in nearly half of patients ( ).

Patients with atopic dermatitis also produce fewer antimicrobial peptides, such as cathelicidin and β-defensins, predisposing individuals to increased S. aureus colonization ( ). Antibiotics, commonly used as part of the treatment for atopic dermatitis, may be an additional contributor to dysbiosis through nonselective elimination of both beneficial and pathogenic bacteria ( ). Together, these factors contribute to a state of dysbiosis by altering the skin’s natural defenses and allowing allergens and microbes to enter the skin (a state also known as leaky skin), ultimately resulting in inflammation ( ).