The altered landscape of the human skin microbiome in patients with primary immunodeficiencies

TLDR: Differences in microbial colonization and community stability in PID skin are examined and their understanding of host-microbiome interactions is informed, suggesting a bidirectional dialogue between skin commensals and the host organism.

Abstract: Although the relationships between microbiota, host, and disease are complex, investigators have long relied upon Koch's postulates to impute causation between microorganism and disease. However, the requirement that disease-causing microorganisms uniformly recapitulate disease in healthy individuals was compromised when Koch discovered asymptomatic carriers of Vibrio cholera and Salmonella typhi, documenting the important distinction between apparent colonization and infection. Potentially pathogenic bacteria that colonize humans are influenced not only by host factors, but also by their native microbial community. This paradigm requires that diseases of microbial origin must be investigated within the context of their microbial community, host factors, and immunity. Genome-wide surveys of the microbes inhabiting the different microenvironments of the human body (e.g., gut, skin, oral) (The Human Microbiome Project Consortium 2012), model organisms (Chung et al. 2012), and geographic regions (Yatsunenko et al. 2012) have suggested the presence of strong selective control on the microbial communities that can colonize and persist in particular environments. The identity and relative representation of microbes at a given site, the overall microbial density (bioburden) and diversity are all components that can be constrained by extrinsic or intrinsic factors, such as nutrient accessibility, temperature, oxygen, or products produced by other microbes. Innovations in sequencing technology have enabled explorations of the complexity of the vast human-associated microbiota. Recent reports have examined shifts in microbial species and communities associated with diseases as varied as atopic dermatitis, inflammatory bowel disease, colorectal cancer, obesity, and metabolic syndrome (Balter 2012). Microbes also promote human health by performing vital functions such as aiding in digestion and educating the immune system (Naik et al. 2012; Upadhyay et al. 2012). Less well understood is the role that human immunity plays in shaping resident microbial communities. Some environmental microbial communities are extremely simple, containing just a few species (e.g., acid mine drainage biofilms) (Denef et al. 2010), while others are enormously complex including hundreds of phyla, including the Guerrero Negro hypersaline mats (Harris et al. 2013), soil, or ocean. Animal-associated microbial symbioses range from monospecific association of Vibrio fischeri inhabiting the light organ of Euprymna scolopes (squid) to the modestly complex communities inhabiting the human body (Dethlefsen et al. 2007). Even at its most complex, the human system appears to be colonized by approximately 10 phyla, an order of magnitude fewer than many environmental ecosystems. An open question is the extent to which symbiotic bacteria are selected for mutualistic interactions with the human host based on the limited ecological niches of human tissues versus a more active modulation of microbial communities by the immune system. The microbiome of healthy human skin shows significant topographical variation between sebaceous, dry, and moist microenvironments. Likewise, the temporal stability of bacterial community membership and structure varies by skin site (Costello et al. 2009; Grice et al. 2009; The Human Microbiome Project Consortium 2012). These attributes differ significantly in disease states such as atopic dermatitis. Skin disease severity in atopic dermatitis patients was closely associated with marked shifts in the composition, diversity, and interpersonal and temporal variation of the resident microbial communities (Kong et al. 2012). Studying primary immunodeficiency (PID) patients provides an opportunity to evaluate the degree to which altered immunity may influence the human microbiome and how, in turn, microbiota may interact with the host to cause disease. As cutaneous immunity has been shown to be distinct from that of other organs (Jiang et al. 2012; Naik et al. 2012), we surveyed the skin microbiomes of three different groups of PID patients whose genetically defined diseases are characterized by AD-like skin disease, diminished memory T and B cells, and variable eosinophilia and elevated IgE. Importantly, despite this broad phenotypic overlap, each of these diseases has its own distinct monogenic mutations and other extracutaneous clinical manifestations: Signal transducer and activator of transcription 3 (STAT3) mutations cause autosomal dominant hyper-IgE syndrome (STAT3-HIES; Job syndrome, OMIM 243700); mutations of dedicator of cytokinesis 8 (DOCK8) cause autosomal recessive hyper IgE syndrome (DOCK8 deficiency, OMIM 611432); and mutations in WAS cause X-linked recessive Wiskott-Aldrich syndrome (WAS; OMIM 301000). STAT3-HIES arises from dominant-negative STAT3 mutations that prevent Th17 cell differentiation, abrogating CD4+ interleukin (IL)-17 production, which is important in epithelial fungal and bacterial infections as well as defensin expression (Milner et al. 2010). Clinical manifestations include recurrent staphylococcal infections, eczema, sinopulmonary infections, mucocutaneous candidiasis, and abnormalities in connective tissue, vessels, teeth, and bones, as well as an increased rate of lymphoma (Holland et al. 2007; Minegishi et al. 2007). DOCK8 deficiency more generally impairs T-cell differentiation, including Th17 cells (Engelhardt et al. 2009; Zhang et al. 2009), and is postulated to result from cytoskeletal abnormalities that may inhibit proper migration and differentiation of immune cells. In addition to recurrent sinopulmonary infections and staphylococcal skin infections, DOCK8 deficiency is associated with eczema, persistent viral infections of the skin, and a predisposition to malignancies (Renner et al. 2004). WAS results from X-linked recessive mutations in WAS. WAS has cytoskeletal abnormalities that lead to defects in T- and B-lymphocyte function via deficiencies in locomotion, signaling, and immune synapse formation (Ochs and Thrasher 2006). Clinical manifestations of WAS include eczema, thrombocytopenia, neutropenia, and a predisposition to autoimmunity and malignancy. PID patients suffer from recurrent infections caused by readily isolated common bacteria and fungi (e.g., Staphylococcus aureus and Candida albicans) as well as uncommon opportunistic pathogens. Diagnosis typically relies on culture-based analyses; however, cultivation methods are limited in their ability to investigate complex microbial communities or to detect fastidious microbiota. Culture-independent metagenomic approaches, e.g., 16S ribosomal RNA (rRNA) sequencing, greatly increase the range of detectable microbes and allow assessment of the relative abundance of members of the microbial community. The 16S rRNA gene is present in all bacteria/archaea and contains both variable regions, which enable taxonomic classification, and conserved regions, which serve as binding sites for PCR primers. Here, we present the results of a culture-independent comparative analysis, using 16S rRNA sequencing, of the skin microbiota of three groups of PID patients compared with classical AD patients and healthy controls. Our goal was to examine alterations in skin microbial communities in human immunodeficiencies as a basis for understanding the forces exerted by both the ecological niche and immune selection.