Heidi H. Kong

The Close and Personal Biome Fortunately, our skin is readily accessible for ecological studies of the microbial communities that influence health and disease states. Grice et al. (p. 1190 ) present a metagenomic survey of body sites from 10 healthy human individuals sampled over time. Although, altogether 18 phyla were discovered, only a few predominated. The most diverse communities were found on the forearm and the least behind the ear, but between people the microorganisms living behind the knees, in the elbow, and behind the ear were most similar. This finding might have some bearing on the common occurrence of atopic dermatitis in these zones, although no similar relationship was discerned between skin microbial flora and psoriasis.

Atopic dermatitis (AD) has long been associated with Staphylococcus aureus skin colonization or infection and is typically managed with regimens that include antimicrobial therapies. However, the role of microbial communities in the pathogenesis of AD is incompletely characterized. To assess the relationship between skin microbiota and disease progression, 16S ribosomal RNA bacterial gene sequencing was performed on DNA obtained directly from serial skin sampling of children with AD. The composition of bacterial communities was analyzed during AD disease states to identify characteristics associated with AD flares and improvement post-treatment. We found that microbial community structures at sites of disease predilection were dramatically different in AD patients compared with controls. Microbial diversity during AD flares was dependent on the presence or absence of recent AD treatments, with even intermittent treatment linked to greater bacterial diversity than no recent treatment. Treatment-associated changes in skin bacterial diversity suggest that AD treatments diversify skin bacteria preceding improvements in disease activity. In AD, the proportion of Staphylococcus sequences, particularly S. aureus, was greater during disease flares than at baseline or post-treatment, and correlated with worsened disease severity. Representation of the skin commensal S. epidermidis also significantly increased during flares. Increases in Streptococcus, Propionibacterium, and Corynebacterium species were observed following therapy. These findings reveal linkages between microbial communities and inflammatory diseases such as AD, and demonstrate that as compared with culture-based studies, higher resolution examination of microbiota associated with human disease provides novel insights into global shifts of bacteria relevant to disease progression and treatment.

Intestinal commensal bacteria induce protective and regulatory responses that maintain host-microbial mutualism. However, the contribution of tissue-resident commensals to immunity and inflammation at other barrier sites has not been addressed. We found that in mice, the skin microbiota have an autonomous role in controlling the local inflammatory milieu and tuning resident T lymphocyte function. Protective immunity to a cutaneous pathogen was found to be critically dependent on the skin microbiota but not the gut microbiota. Furthermore, skin commensals tuned the function of local T cells in a manner dependent on signaling downstream of the interleukin-1 receptor. These findings underscore the importance of the microbiota as a distinctive feature of tissue compartmentalization, and provide insight into mechanisms of immune system regulation by resident commensal niches in health and disease.

The varied topography of human skin offers a unique opportunity to study how the body's microenvironments influence the functional and taxonomic composition of microbial communities. Phylogenetic marker gene-based studies have identified many bacteria and fungi that colonize distinct skin niches. Here metagenomic analyses of diverse body sites in healthy humans demonstrate that local biogeography and strong individuality define the skin microbiome. We developed a relational analysis of bacterial, fungal and viral communities, which showed not only site specificity but also individual signatures. We further identified strain-level variation of dominant species as heterogeneous and multiphyletic. Reference-free analyses captured the uncharacterized metagenome through the development of a multi-kingdom gene catalogue, which was used to uncover genetic signatures of species lacking reference genomes. This work is foundational for human disease studies investigating inter-kingdom interactions, metabolic changes and strain tracking, and defines the dual influence of biogeography and individuality on microbial composition and function.

The many layers and structures of the skin serve as elaborate hosts to microbes, including a diversity of commensal and pathogenic bacteria that contribute to both human health and disease. To determine the complexity and identity of the microbes inhabiting the skin, we sequenced bacterial 16S small-subunit ribosomal RNA genes isolated from the inner elbow of five healthy human subjects. This analysis revealed 113 operational taxonomic units (OTUs; "phylotypes") at the level of 97% similarity that belong to six bacterial divisions. To survey all depths of the skin, we sampled using three methods: swab, scrape, and punch biopsy. Proteobacteria dominated the skin microbiota at all depths of sampling. Interpersonal variation is approximately equal to intrapersonal variation when considering bacterial community membership and structure. Finally, we report strong similarities in the complexity and identity of mouse and human skin microbiota. This study of healthy human skin microbiota will serve to direct future research addressing the role of skin microbiota in health and disease, and metagenomic projects addressing the complex physiological interactions between the skin and the microbes that inhabit this environment.

Biogeography and individuality shape the structural and functional composition of the human skin microbiome. To explore these factors' contribution to skin microbial community stability, we generated metagenomic sequence data from longitudinal samples collected over months and years. Analyzing these samples using a multi-kingdom, reference-based approach, we found that despite the skin's exposure to the external environment, its bacterial, fungal, and viral communities were largely stable over time. Site, individuality, and phylogeny were all determinants of stability. Foot sites exhibited the most variability; individuals differed in stability; and transience was a particular characteristic of eukaryotic viruses, which showed little site-specificity in colonization. Strain and single-nucleotide variant-level analysis showed that individuals maintain, rather than reacquire, prevalent microbes from the environment. Longitudinal stability of skin microbial communities generates hypotheses about colonization resistance and empowers clinical studies exploring alterations observed in disease states.

We observed a syndrome of intermittent fevers, early-onset lacunar strokes and other neurovascular manifestations, livedoid rash, hepatosplenomegaly, and systemic vasculopathy in three unrelated patients. We suspected a genetic cause because the disorder presented in early childhood.

The skin represents the primary interface between the host and the environment. This organ is also home to trillions of microorganisms that play an important role in tissue homeostasis and local immunity. Skin microbial communities are highly diverse and can be remodelled over time or in response to environmental challenges. How, in the context of this complexity, individual commensal microorganisms may differentially modulate skin immunity and the consequences of these responses for tissue physiology remains unclear. Here we show that defined commensals dominantly affect skin immunity and identify the cellular mediators involved in this specification. In particular, colonization with Staphylococcus epidermidis induces IL-17A(+) CD8(+) T cells that home to the epidermis, enhance innate barrier immunity and limit pathogen invasion. Commensal-specific T-cell responses result from the coordinated action of skin-resident dendritic cell subsets and are not associated with inflammation, revealing that tissue-resident cells are poised to sense and respond to alterations in microbial communities. This interaction may represent an evolutionary means by which the skin immune system uses fluctuating commensal signals to calibrate barrier immunity and provide heterologous protection against invasive pathogens. These findings reveal that the skin immune landscape is a highly dynamic environment that can be rapidly and specifically remodelled by encounters with defined commensals, findings that have profound implications for our understanding of tissue-specific immunity and pathologies.

Genomic and functional analyses of staphylococcal strain specificity reveal roles for microbes in human atopic dermatitis pathogenesis.

As an interface with the environment, the skin is a complex ecosystem colonized by many microorganisms that coexist in an established balance. The cutaneous microbiome inhibits colonization with pathogens, such as Staphylococcus aureus, and is a crucial component for function of the epidermal barrier. Moreover, crosstalk between commensals and the immune system is now recognized because microorganisms can modulate both innate and adaptive immune responses. Host-commensal interactions also have an effect on the developing immune system in infants and, subsequently, the occurrence of diseases, such as asthma and atopic dermatitis (AD). Later in life, the cutaneous microbiome contributes to the development and course of skin disease. Accordingly, in patients with AD, a decrease in microbiome diversity correlates with disease severity and increased colonization with pathogenic bacteria, such as S aureus. Early clinical studies suggest that topical application of commensal organisms (eg, Staphylococcus hominis or Roseomonas mucosa) reduces AD severity, which supports an important role for commensals in decreasing S aureus colonization in patients with AD. Advancing knowledge of the cutaneous microbiome and its function in modulating the course of skin disorders, such as AD, might result in novel therapeutic strategies.

The multitargeted kinase inhibitors (MKIs) sorafenib and sunitinib have shown benefit in patients with renal cell carcinoma, hepatocellular carcinoma (sorafenib), and gastrointestinal stromal tumor (sunitinib). Their efficacy in other malignancies is currently being investigated because of their broad range of activity. The effectiveness of these drugs is somewhat diminished by the development of a variety of toxicities, most notably hand-foot skin reaction (HFSR). Although HFSR does not appear to directly affect survival, it can impact quality of life and lead to MKI dose modification or interruption, potentially limiting the antitumor effect. Currently, no standard guidelines exist for the prevention and management of MKI-associated HFSR. To address this issue, an international, interdisciplinary panel of experts gathered in January 2008 to discuss and evaluate the best-practice management of these reactions. Based on these proceedings, recommendations for the management of HFSR have been provided to offer patients the best possible quality of life while taking these drugs and to optimize the patient benefit associated with MKI therapy.

Characterization of the topographical and temporal diversity of the microbial collective (microbiome) hosted by healthy human skin established a reference for studying disease-causing microbiomes. Physiologic changes occur in the skin as humans mature from infancy to adulthood. Thus, characterizations of adult microbiomes might have limitations when considering pediatric disorders such as atopic dermatitis (AD) or issues such as sites of microbial carriage. The objective of this study was to determine if microbial communities at several body sites in children differed significantly from adults.Using 16S-rRNA gene sequencing technology, we characterized and compared the bacterial communities of four body sites in relation to Tanner stage of human development. Body sites sampled included skin sites characteristically involved in AD (antecubital/popliteal fossae), a control skin site (volar forearm), and the nares. Twenty-eight healthy individuals aged from 2 to 40 years were evaluated at the outpatient dermatology clinic in the National Institutes of Health's Clinical Center. Exclusion criteria included the use of systemic antibiotics within 6 months, current/prior chronic skin disorders, asthma, allergic rhinitis, or other chronic medical conditions.Bacterial communities in the nares of children (Tanner developmental stage 1) differed strikingly from adults (Tanner developmental stage 5). Firmicutes (Streptococcaceae), Bacteroidetes, and Proteobacteria (β, γ) were overrepresented in Tanner 1 compared to Tanner 5 individuals, where Corynebacteriaceae and Propionibacteriaceae predominated. While bacterial communities were significantly different between the two groups in all sites, the most marked microbial shifts were observed in the nares, a site that can harbor pathogenic species, including Staphylococcus aureus and Streptococcus pneumonia.Significant shifts in the microbiota associated with progressive sexual maturation as measured by Tanner staging suggest that puberty-dependent shifts in the skin and nares microbiomes may have significant implications regarding prevention and treatment of pediatric disorders involving microbial pathogens and colonization.

Trillions of bacteria, fungi, viruses, archaea, and small arthropods colonize the skin surface, collectively comprising the skin microbiome. Generations of researchers have classified these microbes as transient versus resident, beneficial versus pathogenic, and collaborators versus adversaries. Culturing and direct sequencing of microbial inhabitants identified distinct populations present at skin surface sites. Herein, we explore the history of this field, describe findings from the current molecular sequencing era, and consider the future of investigating how microbes and antimicrobial therapy contribute to human health.

Disease flares of established atopic dermatitis (AD) are generally associated with a low-diversity skin microbiota and Staphylococcus aureus dominance. The temporal transition of the skin microbiome between early infancy and the dysbiosis of established AD is unknown.We randomly selected 50 children from the Cork Babies After SCOPE: Evaluating the Longitudinal Impact Using Neurological and Nutritional Endpoints (BASELINE) longitudinal birth cohort for microbiome sampling at 3 points in the first 6 months of life at 4 skin sites relevant to AD: the antecubital and popliteal fossae, nasal tip, and cheek. We identified 10 infants with AD and compared them with 10 randomly selected control infants with no AD. We performed bacterial 16S ribosomal RNA sequencing and analysis directly from clinical samples.Bacterial community structures and diversity shifted over time, suggesting that age strongly affects the skin microbiome in infants. Unlike established AD, these patients with infantile AD did not have noticeably dysbiotic communities before or with disease and were not colonized by S aureus. In comparing patients and control subjects, infants who had affected skin at month 12 had statistically significant differences in bacterial communities on the antecubital fossa at month 2 compared with infants who were unaffected at month 12. In particular, commensal staphylococci were significantly less abundant in infants affected at month 12, suggesting that this genus might protect against the later development of AD.This study suggests that 12-month-old infants with AD were not colonized with S aureus before having AD. Additional studies are needed to confirm whether colonization with commensal staphylococci modulates skin immunity and attenuates development of AD.

While landmark studies have shown that microbiota activate and educate host immunity, how immune systems shape microbiomes and contribute to disease is incompletely characterized. Primary immunodeficiency (PID) patients suffer recurrent microbial infections, providing a unique opportunity to address this issue. To investigate the potential influence of host immunity on the skin microbiome, we examined skin microbiomes in patients with rare monogenic PIDs: hyper-IgE (STAT3-deficient), Wiskott-Aldrich, and dedicator of cytokinesis 8 syndromes. While specific immunologic defects differ, a shared hallmark is atopic dermatitis (AD)-like eczema. We compared bacterial and fungal skin microbiomes (41 PID, 13 AD, 49 healthy controls) at four clinically relevant sites representing the major skin microenvironments. PID skin displayed increased ecological permissiveness with altered population structures, decreased site specificity and temporal stability, and colonization with microbial species not observed in controls, including Clostridium species and Serratia marcescens. Elevated fungal diversity and increased representation of opportunistic fungi (Candida, Aspergillus) supported increased PID skin permissiveness, suggesting that skin may serve as a reservoir for the recurrent fungal infections observed in these patients. The overarching theme of increased ecological permissiveness in PID skin was counterbalanced by the maintenance of a phylum barrier in which colonization remained restricted to typical human-associated phyla. Clinical parameters, including markers of disease severity, were positively correlated with prevalence of Staphylococcus, Corynebacterium, and other less abundant taxa. This study examines differences in microbial colonization and community stability in PID skin and informs our understanding of host-microbiome interactions, suggesting a bidirectional dialogue between skin commensals and the host organism.

Recent advances in DNA sequencing methodology have facilitated studies of human skin microbes that circumvent difficulties in isolating and characterizing fastidious microbes. Sequence-based approaches have identified a greater diversity of cutaneous bacteria than studies using traditional cultivation techniques. However, improved sequencing technologies and analytical methods are needed to study all skin microbes, including bacteria, archaea, fungi, viruses and mites, and how they interact with each other and their human hosts. This review discusses current skin microbiome research, with a primary focus on bacteria, and the challenges facing investigators striving to understand how skin microorganisms contribute to health and disease.

Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a rare primary immunodeficiency disorder typically caused by homozygous AIRE mutations. It classically presents with chronic mucocutaneous candidiasis and autoimmunity that primarily targets endocrine tissues; hypoparathyroidism and adrenal insufficiency are most common. Developing any two of these classic triad manifestations establishes the diagnosis. Although widely recognized in Europe, where nonendocrine autoimmune manifestations are uncommon, APECED is less defined in patients from the Western Hemisphere. We enrolled 35 consecutive American APECED patients (33 from the US) in a prospective observational natural history study and systematically examined their genetic, clinical, autoantibody, and immunological characteristics. Most patients were compound heterozygous; the most common AIRE mutation was c.967_979del13. All but one patient had anti-IFN-ω autoantibodies, including 4 of 5 patients without biallelic AIRE mutations. Urticarial eruption, hepatitis, gastritis, intestinal dysfunction, pneumonitis, and Sjögren's-like syndrome, uncommon entities in European APECED cohorts, affected 40%-80% of American cases. Development of a classic diagnostic dyad was delayed at mean 7.38 years. Eighty percent of patients developed a median of 3 non-triad manifestations before a diagnostic dyad. Only 20% of patients had their first two manifestations among the classic triad. Urticarial eruption, intestinal dysfunction, and enamel hypoplasia were prominent among early manifestations. Patients exhibited expanded peripheral CD4+ T cells and CD21loCD38lo B lymphocytes. In summary, American APECED patients develop a diverse syndrome, with dramatic enrichment in organ-specific nonendocrine manifestations starting early in life, compared with European patients. Incorporation of these new manifestations into American diagnostic criteria would accelerate diagnosis by approximately 4 years and potentially prevent life-threatening endocrine complications.

Growing interest in microbial contributions to human health and disease has increasingly led investigators to examine the microbiome in both healthy skin and cutaneous disorders, including acne, psoriasis, and atopic dermatitis. The need for common language, effective study design, and validated methods is critical for high-quality standardized research. Features, unique to skin, pose particular challenges when conducting microbiome research. This review discusses microbiome research standards and highlights important factors to consider, including clinical study design, skin sampling, sample processing, DNA sequencing, control inclusion, and data analysis. Growing interest in microbial contributions to human health and disease has increasingly led investigators to examine the microbiome in both healthy skin and cutaneous disorders, including acne, psoriasis, and atopic dermatitis. The need for common language, effective study design, and validated methods is critical for high-quality standardized research. Features, unique to skin, pose particular challenges when conducting microbiome research. This review discusses microbiome research standards and highlights important factors to consider, including clinical study design, skin sampling, sample processing, DNA sequencing, control inclusion, and data analysis.

Immune cells and epithelium form sophisticated barrier systems in symbiotic relationships with microbiota. Evidence suggests that immune cells can sense microbes through intact barriers, but regulation of microbial commensalism remain largely unexplored. Here, we uncovered spatial compartmentalization of skin-resident innate lymphoid cells (ILCs) and modulation of sebaceous glands by a subset of RORγt+ ILCs residing within hair follicles in close proximity to sebaceous glands. Their persistence in skin required IL-7 and thymic stromal lymphopoietin, and localization was dependent on the chemokine receptor CCR6. ILC subsets expressed TNF receptor ligands, which limited sebocyte growth by repressing Notch signaling pathway. Consequently, loss of ILCs resulted in sebaceous hyperplasia with increased production of antimicrobial lipids and restricted commensalism of Gram-positive bacterial communities. Thus, epithelia-derived signals maintain skin-resident ILCs that regulate microbial commensalism through sebaceous gland-mediated tuning of the barrier surface, highlighting an immune-epithelia circuitry that facilitates host-microbe symbiosis.

Atopic dermatitis (AD) affects up to 20% of children worldwide and is an increasing public health problem, particularly in developed countries. Although AD in infants and young children can resolve, there is a well-recognized increased risk of sequential progression from AD to other atopic diseases, including food allergy (FA), allergic rhinitis, allergic asthma, and allergic rhinoconjunctivitis, a process referred to as the atopic march. The mechanisms underlying the development of AD and subsequent progression to other atopic comorbidities, particularly FA, are incompletely understood and the subject of intense investigation. Other major research objectives are the development of effective strategies to prevent AD and FA, as well as therapeutic interventions to inhibit the atopic march. In 2017, the Division of Allergy, Immunology, and Transplantation of the National Institute of Allergy and Infectious Diseases sponsored a workshop to discuss current understanding and important advances in these research areas and to identify gaps in knowledge and future research directions. International and national experts in the field were joined by representatives from several National Institutes of Health institutes. Summaries of workshop presentations, key conclusions, and recommendations are presented herein.

Drug-induced hypersensitivity syndrome/drug reaction with eosinophilia and systemic symptoms (DiHS/DRESS) is a potentially fatal multiorgan inflammatory disease associated with herpesvirus reactivation and subsequent onset of autoimmune diseases1–4. Pathophysiology remains elusive and therapeutic options are limited. Cases refractory to corticosteroid therapy pose a clinical challenge1,5 and approximately 30% of patients with DiHS/DRESS develop complications, including infections and inflammatory and autoimmune diseases1,2,5. Progress in single-cell RNA sequencing (scRNA-seq) provides an opportunity to dissect human disease pathophysiology at unprecedented resolutions6, particularly in diseases lacking animal models, such as DiHS/DRESS. We performed scRNA-seq on skin and blood from a patient with refractory DiHS/DRESS, identifying the JAK–STAT signaling pathway as a potential target. We further showed that central memory CD4+ T cells were enriched with DNA from human herpesvirus 6b. Intervention via tofacitinib enabled disease control and tapering of other immunosuppressive agents. Tofacitinib, as well as antiviral agents, suppressed culprit-induced T cell proliferation in vitro, further supporting the roles of the JAK–STAT pathway and herpesviruses in mediating the adverse drug reaction. Thus, scRNA-seq analyses guided successful therapeutic intervention in the patient with refractory DiHS/DRESS. scRNA-seq may improve our understanding of complicated human disease pathophysiology and provide an alternative approach in personalized medicine. Single-cell RNA sequencing facilitates successful therapeutic treatment of a patient with a rare and severe drug-induced inflammatory skin reaction.

Candida auris is a fungal pathogen of high concern due to its ability to cause healthcare-associated infections and outbreaks, its resistance to antimicrobials and disinfectants and its persistence on human skin and in the inanimate environment. To inform surveillance and future mitigation strategies, we defined the extent of skin colonization and explored the microbiome associated with C. auris colonization. We collected swab specimens and clinical data at three times points between January and April 2019 from 57 residents (up to ten body sites each) of a ventilator-capable skilled nursing facility with endemic C. auris and routine chlorhexidine gluconate (CHG) bathing. Integrating microbial-genomic and epidemiologic data revealed occult C. auris colonization of multiple body sites not targeted commonly for screening. High concentrations of CHG were associated with suppression of C. auris growth but not with deleterious perturbation of commensal microbes. Modeling human mycobiome dynamics provided insight into underlying alterations to the skin fungal community as a possible modifiable risk factor for acquisition and persistence of C. auris. Failure to detect the extensive, disparate niches of C. auris colonization may reduce the effectiveness of infection-prevention measures that target colonized residents, highlighting the importance of universal strategies to reduce C. auris transmission.

While Staphylococcus epidermidis is commonly isolated from healthy human skin, it is also the most frequent cause of nosocomial infections on indwelling medical devices. Despite its importance, few genome sequences existed and the most frequent hospital-associated lineage, ST2, had not been fully sequenced. We cultivated 71 commensal S. epidermidis isolates from 15 skin sites and compared them with 28 nosocomial isolates from venous catheters and blood cultures. We produced 21 commensal and 9 nosocomial draft genomes, and annotated and compared their gene content, phylogenetic relatedness and biochemical functions. The commensal strains had an open pan-genome with 80% core genes and 20% variable genes. The variable genome was characterized by an overabundance of transposable elements, transcription factors and transporters. Biochemical diversity, as assayed by antibiotic resistance and in vitro biofilm formation, demonstrated the varied phenotypic consequences of this genomic diversity. The nosocomial isolates exhibited both large-scale rearrangements and single-nucleotide variation. We showed that S. epidermidis genomes separate into two phylogenetic groups, one consisting only of commensals. The formate dehydrogenase gene, present only in commensals, is a discriminatory marker between the two groups. Commensal skin S. epidermidis have an open pan-genome and show considerable diversity between isolates, even when derived from a single individual or body site. For ST2, the most common nosocomial lineage, we detect variation between three independent isolates sequenced. Finally, phylogenetic analyses revealed a previously unrecognized group of S. epidermidis strains characterized by reduced virulence and formate dehydrogenase, which we propose as a clinical molecular marker.

Background Outbreaks of antibiotic-resistant bacterial infections emphasize the importance of surveillance of potentially pathogenic bacteria. Genomic sequencing of clinical microbiological specimens expands our capacity to study cultivable, fastidious and uncultivable members of the bacterial community. Herein, we compared the primary data collected by the NIH’s Human Microbiome Project (HMP) with published epidemiological surveillance data of Staphylococcus aureus. Methods The HMP’s initial dataset contained microbial survey data from five body regions (skin, nares, oral cavity, gut and vagina) of 242 healthy volunteers. A significant component of the HMP dataset was deep sequencing of the 16S ribosomal RNA gene, which contains variable regions enabling taxonomic classification. Since species-level identification is essential in clinical microbiology, we built a reference database and used phylogenetic placement followed by most recent common ancestor classification to look at the species distribution for Staphylococcus, Klebsiella and Enterococcus. Main Results We show that selecting the accurate region of the 16S rRNA gene to sequence is analogous to carefully selecting culture conditions to distinguish closely related bacterial species. Analysis of the HMP data showed that Staphylococcus aureus was present in the nares of 36% of healthy volunteers, consistent with culture-based epidemiological data. Klebsiella pneumoniae and Enterococcus faecalis were found less frequently, but across many habitats. Conclusions This work demonstrates that large 16S rRNA survey studies can be used to support epidemiological goals in the context of an increasing awareness that microbes flourish and compete within a larger bacterial community. This study demonstrates how genomic techniques and information could be critically important to trace microbial evolution and implement hospital infection control.

Sorafenib, a vascular endothelial growth factor (VEGF) receptor-2 and RAF kinase inhibitor, commonly causes skin toxicity. We retrospectively analyzed dermatologic toxicity in patients receiving combined antiangiogenic therapy involving sorafenib and bevacizumab.Castration-resistant prostate cancer and metastatic non-small cell lung cancer patients were accrued to phase II studies, receiving sorafenib 400 mg twice daily. A phase I study explored sorafenib 200 to 400 mg twice daily with bevacizumab 5 to 10 mg/kg every 2 weeks in patients with advanced solid tumors. The probability of development of maximum grade of dermatologic toxicity as a function of the cumulative dose of sorafenib was determined. Additional analyses compared extent of toxicity, pharmacokinetics, and patient risk factors.Ninety-six patients were enrolled: 54 received sorafenib and 42 received bevacizumab/sorafenib. Hand-foot skin reaction (HFSR) was observed in 50 of 96 (52%) patients. Grade 2 to 3 HFSR developed in 16 of 54 (30%) sorafenib patients and 24 of 42 (57%) bevacizumab/sorafenib patients (P=0.012) and was associated with cumulative sorafenib exposure (P=0.0008). Twenty-four of 42 phase I patients randomized to start with bevacizumab had increased risk of grade 2 to 3 HFSR than those starting with sorafenib (P=0.013) after adjusting for association between HFSR risk and hypertension (P=0.01), which was the only toxicity associated with HFSR. There was no association between HFSR and baseline history of neuropathy, prior taxane/platinum treatment, or systemic sorafenib levels.Sorafenib-related HFSR is associated with increasing cumulative sorafenib dose. HFSR is increased in patients treated with bevacizumab/sorafenib combination anti-VEGF therapy, and this finding is not explained by pharmacokinetic interaction between the two agents. Our results suggest that the pathophysiology of HFSR may be related to VEGF inhibition.

The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics of the microbial communities that populate diverse habitats. Over the past decade, these advances have yielded an avalanche of metagenomic data. The current stage of "van Leeuwenhoek"-like cataloguing, as well as functional analyses, will likely accelerate as DNA and RNA sequencing, plus protein and metabolic profiling capacities and computational tools, continue to improve. However, it is time to consider: what's next for microbiome research? The short pieces included here briefly consider the challenges and opportunities awaiting microbiome research.

Understanding the skin mycobiome (fungal communities) is important because both commensal and pathogenic fungi can drive cutaneous disease depending on host status and body sites, including the scalp, feet, and groin. Interestingly, age may also affect skin fungal infections as certain dermatophytoses (i.e., tinea capitis) are more frequent in children than adults. We previously described the skin mycobiomes in healthy adults, showing lipophilic fungi Malassezia predominate in most skin sites. Because children have less sebaceous skin before puberty, we compared the fungal communities of primary clinical samples from healthy children and adults, based on sequencing of a fungal phylogenetic marker. Although Malassezia predominated on the trunk, head, and arm skin of adults (age 18-39), children (age < 14) had more diverse fungal communities, for example, Eurotiomycetes, which includes common dermatophytes. Species-level classification showed that Malassezia globosa predominated in children. Collectively, our findings indicate that prepubertal skin is colonized by diverse fungi, whereas adult skin is predominantly obligatory lipophilic Malassezia, suggesting that fungal communities on skin profoundly shift during puberty. Mycobiome shifts during puberty are likely due to alterations in sebaceous gland activation and sebum composition. This study provides a foundational framework for studies investigating interactions between fungi, skin, and pediatric dermatophytosis.

Severe atopic conditions associated with elevated serum IgE are heterogeneous with few known causes. Nearly every patient with autosomal-dominant hyper-IgE syndrome (AD-HIES) due to signal transducer and activator of transcription 3 (STAT3) mutations has a history of eczematous dermatitis and elevated IgE; however, clinical atopy has never been systematically studied.Understanding of genetic determinants of allergic disease may lead to novel therapies in controlling allergic disease.We conducted clinical evaluation of the rates of food allergies and anaphylaxis in patients with AD-HIES, a cohort of patients with no STAT3 mutation but with similar histories of elevated IgE and atopic dermatitis, and healthy volunteers with no history of atopy. Morphine skin prick testing, ImmunoCAP assays for allergen-specific IgE, and basophil activation were measured. A model of systemic anaphylaxis was studied in transgenic mice carrying an AD-HIES mutation. STAT3 was silenced in LAD2 and primary human mast cells to study the role of STAT3 in signaling and degranulation after IgE cross-linking.Food allergies and anaphylaxis were markedly diminished in patients with AD-HIES compared with a cohort of patients with no STAT3 mutation but with similar histories of elevated IgE and atopic dermatitis. Morphine skin prick testing and basophil activation were diminished in patients with AD-HIES, whereas mice carrying an AD-HIES mutation were hyporesponsive to systemic anaphylaxis models. Rapid mast cell STAT3 serine727 phosphorylation was noted after IgE cross-linking, and inhibition of STAT3 signaling in mast cells lead to impaired FcεRI-mediated proximal and distal signaling, as well as reduced degranulation.This study serves as an example for how mutations in specific atopic pathways can lead to discrete allergic phenotypes, encompassing increased risk of some phenotypes but a relative protection from others.

Human microbiome studies have revealed the intricate interplay of host immunity and bacterial communities to achieve homeostatic balance. Healthy skin microbial communities are dominated by bacteria with low viral representation1–3, mainly bacteriophage. Specific eukaryotic viruses have been implicated in both common and rare skin diseases, but cataloging skin viral communities has been limited. Alterations in host immunity provide an opportunity to expand our understanding of microbial–host interactions. Primary immunodeficient patients manifest with various viral, bacterial, fungal, and parasitic infections, including skin infections4. Dedicator of cytokinesis 8 (DOCK8) deficiency is a rare primary human immunodeficiency characterized by recurrent cutaneous and systemic infections, as well as atopy and cancer susceptibility5. DOCK8, encoding a guanine nucleotide exchange factor highly expressed in lymphocytes, regulates actin cytoskeleton, which is critical for migration through collagen-dense tissues such as skin6. Analyzing deep metagenomic sequencing data from DOCK8-deficient skin samples demonstrated a notable increase in eukaryotic viral representation and diversity compared with healthy volunteers. De novo assembly approaches identified hundreds of novel human papillomavirus genomes, illuminating microbial dark matter. Expansion of the skin virome in DOCK8-deficient patients underscores the importance of immune surveillance in controlling eukaryotic viral colonization and infection. Skin from individuals with a rare immunodeficiency harbors more eukaryotic viruses than healthy skin, highlighting the role of immune surveillance in modulating the skin microbiome.

Background Emollients are a mainstay of treatment in atopic dermatitis (AD), a disease distinguished by skin bacterial dysbiosis. However, changes in skin microbiota when emollients are used as a potential AD preventative measure in infants remain incompletely characterized. Results We compared skin barrier parameters, AD development, and bacterial 16S ribosomal RNA gene sequences of cheek, dorsal and volar forearm samples from 6-month-old infants with a family history of atopy randomized to receive emollients (n = 11) or no emollients (controls, n = 12). The emollient group had a lower skin pH than the control group. The number of bacterial taxa in the emollient group was higher than in the control group at all sites. The Streptococcus salivarius proportion was higher in the emollient versus control groups at all sites. S. salivarius proportion appeared higher in infants without AD compared to infants with AD. A decrease in S. salivarius abundance was further identified in a separate larger population of older children demonstrating an inverse correlation between AD severity at sampling sites and S. salivarius proportions. Conclusions The decreased skin pH and the increased proportion of S. salivarius after long-term emollient use in infants at risk for developing AD may contribute to the preventative effects of emollients in high-risk infants.

Cutimycin, a thiopeptide antibiotic produced by the skin commensal Cutibacterium acnes , reduces Staphylococcus colonization of human skin hair follicles.

Skin constantly encounters external elements, including microbes. Culture-based studies have identified fungi present on human skin and have linked some species with certain skin diseases. Moreover, modern medical treatments, especially immunosuppressants, have increased the population at risk for cutaneous and invasive fungal infections, emphasizing the need to understand skin fungal communities in health and disease. A major hurdle for studying fungal flora at a community level has been the heterogeneous culture conditions required by skin fungi. Recent advances in DNA sequencing technologies have dramatically expanded our knowledge of the skin microbiome through culture-free methods. This review discusses historical and recent research on skin fungal communities – the mycobiome – in health and disease, and challenges associated with sequencing-based mycobiome research.

Skin serves as a protective barrier and also harbors numerous microorganisms collectively comprising the skin microbiome. As a result of recent advances in sequencing (next-generation sequencing), our understanding of microbial communities on skin has advanced substantially. In particular, the 16S ribosomal RNA gene sequencing technique has played an important role in efforts to identify the global communities of bacteria in healthy individuals and patients with various disorders in multiple topographical regions over the skin surface. Here, we describe basic principles, study design, and a workflow of 16S ribosomal RNA gene sequencing methodology, primarily for investigators who are not familiar with this approach. This article will also discuss some applications and challenges of 16S ribosomal RNA sequencing as well as directions for future development.

Human skin functions as a physical barrier to foreign pathogen invasion and houses numerous commensals. Shifts in the human skin microbiome have been associated with conditions ranging from acne to atopic dermatitis. Previous metagenomic investigations into the role of the skin microbiome in health or disease have found that much of the sequenced data do not match reference genomes, making it difficult to interpret metagenomic datasets. We combined bacterial cultivation and metagenomic sequencing to assemble the Skin Microbial Genome Collection (SMGC), which comprises 622 prokaryotic species derived from 7,535 metagenome-assembled genomes and 251 isolate genomes. The metagenomic datasets that we generated were combined with publicly available skin metagenomic datasets to identify members and functions of the human skin microbiome. The SMGC collection includes 174 newly identified bacterial species and 12 newly identified bacterial genera, including the abundant genus 'Candidatus Pellibacterium', which has been newly associated with the skin. The SMGC increases the characterized set of known skin bacteria by 26%. We validated the SMGC metagenome-assembled genomes by comparing them with sequenced isolates obtained from the same samples. We also recovered 12 eukaryotic species and assembled thousands of viral sequences, including newly identified clades of jumbo phages. The SMGC enables classification of a median of 85% of skin metagenomic sequences and provides a comprehensive view of skin microbiome diversity, derived primarily from samples obtained in North America.

Vitamin A deficiency increases susceptibility to skin infection. However, the mechanisms by which vitamin A regulates skin immunity remain unclear. Here, we show that resistin-like molecule α (RELMα), a small secreted cysteine-rich protein, is expressed by epidermal keratinocytes and sebocytes and serves as an antimicrobial protein that is required for vitamin-A-dependent resistance to skin infection. RELMα was induced by microbiota colonization of the murine skin, was bactericidal in vitro, and was protected against bacterial infection of the skin in vivo. RELMα expression required dietary vitamin A and was induced by the therapeutic vitamin A analog isotretinoin, which protected against skin infection in a RELMα-dependent manner. The RELM family member Resistin was expressed in human skin, was induced by vitamin A analogs, and killed skin bacteria, indicating a conserved function for RELM proteins in skin innate immunity. Our findings provide insight into how vitamin A promotes resistance to skin infection.

5004 Background: HLRCC is a familial cancer syndrome associated with a type 2 papillary RCC (pRCC) variant. HLRCC is caused by germline mutations in the gene for the Krebs cycle enzyme fumarate hydratase (FH). FH inactivation results in VHL-independent upregulation of hypoxia inducible factor, a reliance on aerobic glycolysis, and activation of the NRF2 pathway, features also shared by some sporadic pRCC tumors. We hypothesized that the metabolic alterations underlying these tumors would be susceptible to targeted therapy with a combination of bevacizumab and erlotinib. Methods: Patients with advanced pRCC were eligible to enroll on this phase II study. To enrich for patients with FH deficiency, those with 1) HLRCC and 2) sporadic pRCC were enrolled into parallel, independent cohorts. All patients received bevacizumab 10 mg/kg IV every 2 weeks and erlotinib 150 mg orally daily. Patients who had received no more than two agents targeting the VEGFR pathway were included. Patients remained on treatment until unacceptable toxicity or progression. The primary endpoint was overall response rate (ORR); secondary endpoints were progression free survival (PFS) and duration of response. Results: A total of 83 patients with pRCC, including 42 in the HLRCC cohort and 41 in the sporadic cohort were enrolled on study. The majority of patients were IMDC intermediate risk (53/83, 64%) and 27 (33%) had at least one prior treatment. The ORR was 51% (42/83; 95% CI, 40 – 61) in all patients, 64% (27/42; 95% CI, 49 – 77) in the HLRCC cohort, and 37% (15/41; 95% CI, 24 – 52) in the sporadic cohort. The median PFS was 14.2 months (95% CI, 11.4 – 18.6) in all patients, 21.1 months (95% CI, 15.6 – 26.6) in the HLRCC cohort, and 8.7 months (95% CI, 6.4 – 12.6) in the sporadic cohort. The majority of treatment related adverse events (TRAEs) were grade 1 or 2 with the most common being acneiform rash (92%), diarrhea (77%), proteinuria (71%), and dry skin (61%). Grade ≥3 TRAEs occurred in 47% of patients, including hypertension (34%) and proteinuria (13%), with one patient (1.2%) with a grade 5 GI hemorrhage possibly related to bevacizumab. Conclusions: The combination of bevacizumab and erlotinib is well tolerated and is associated with encouraging activity in advanced pRCC, particularly in patients with FH deficient tumors. This is the first and largest prospective study in HLRCC and provides the basis for considering bevacizumab and erlotinib as a preferred option in a patient population that has no widely accepted standard. Clinical trial information: NCT01130519 .

The gut microbiota potentially plays an important role in the immunologic education of the host during early infancy.We sought to determine how the infant gut microbiota evolve during infancy, particularly in relation to hygiene-related environmental factors, atopic disorders, and a randomized introduction of allergenic solids.A total of 1303 exclusively breast-fed infants were enrolled in a dietary randomized controlled trial (Enquiring About Tolerance study) from 3 months of age. In this nested longitudinal study, fecal samples were collected at baseline, with additional sampling of selected cases and controls at 6 and 12 months to study the evolution of their gut microbiota, using 16S ribosomal RNA gene-targeted amplicon sequencing.In the 288 baseline samples from exclusively breast-fed infant at 3 months, the gut microbiota was highly heterogeneous, forming 3 distinct clusters: Bifidobacterium-rich, Bacteroides-rich, and Escherichia/Shigella-rich. Mode of delivery was the major discriminating factor. Increased Clostridium sensu stricto relative abundance at 3 months was associated with presence of atopic dermatitis on examination at age 3 and 12 months. From the selected cases and controls with longitudinal samples (n = 70), transition to Bacteroides-rich communities and influx of adult-specific microbes were observed during the first year of life. The introduction of allergenic solids promoted a significant increase in Shannon diversity and representation of specific microbes, such as genera belonging to Prevotellaceae and Proteobacteria (eg, Escherichia/Shigella), as compared with infants recommended to exclusively breast-feed.Specific gut microbiota characteristics of samples from 3-month-old breast-fed infants were associated with cesarean birth, and greater Clostridium sensu stricto abundance was associated with atopic dermatitis. The randomized introduction of allergenic solids from age 3 months alongside breast-feeding was associated with differential dynamics of maturation of the gut microbial communities.

Previous cross-sectional studies have shown that skin microbiomes in adults are distinct from those in children. However, the human skin microbiome in individuals as they sexually mature has not been studied as extensively. We performed a prospective, longitudinal study to investigate the puberty-associated shifts in skin microbiota. A total of 12 healthy children were evaluated every 6-18 months for up to 6 years. Using 16S ribosomal RNA (V1-V3) and internal transcribed spacer 1 amplicon sequencing analyzed with Divisive Amplicon Denoising Algorithm 2, we characterized the bacterial and fungal communities of five different skin and nares sites. We identified significant alterations in the composition of skin microbial communities, transitioning toward a more adult microbiome, during puberty. The microbial shifts were associated with Tanner stages (classification method for the degree of sexual maturation) and showed noticeable sex-specific differences. Over time, female children demonstrated a predominance of Cutibacterium with decreasing diversity. Among fungi, Malassezia predominated at most skin sites in more sexually mature subjects, which was more pronounced in female children. The higher relative abundances of these lipophilic taxa-C. acnes and M. restricta-were strongly associated with serum sex hormone concentrations with known influence on sebaceous gland activity. Taken together, our results support the relationship between sexual maturation, skin physiology, and the skin microbiome.

Atopic dermatitis (AD) is a multifactorial, chronic relapsing disease associated with genetic and environmental factors. Among skin microbes, Staphylococcus aureus and Staphylococcus epidermidis are associated with AD, but how genetic variability and staphylococcal strains shape the disease remains unclear. We investigated the skin microbiome of an AD cohort (n = 54) as part of a prospective natural history study using shotgun metagenomic and whole genome sequencing, which we analyzed alongside publicly available data (n = 473). AD status and global geographical regions exhibited associations with strains and genomic loci of S. aureus and S. epidermidis. In addition, antibiotic prescribing patterns and within-household transmission between siblings shaped colonizing strains. Comparative genomics determined that S. aureus AD strains were enriched in virulence factors, whereas S. epidermidis AD strains varied in genes involved in interspecies interactions and metabolism. In both species, staphylococcal interspecies genetic transfer shaped gene content. These findings reflect the staphylococcal genomic diversity and dynamics associated with AD.

To the Editor: Sorafenib (BAY 43-9006; Nexavar) is one of the new-generation oral small-molecule antineoplastic agents targeting multiple kinases and is approved for use in the treatment of metastatic renal cell carcinoma. There are currently more than 50 National Institutes of Health–sponsored clinical trials investigating sorafenib for the treatment of other solid cancers.1

Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant "genomes" are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT) sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation.The species comprising a microbial community are often difficult to deconvolute due to technical limitations inherent to most short-read sequencing technologies. Here, we leverage new advances in sequencing technology, single-molecule sequencing, to significantly improve reconstruction of a complex human skin microbial community. With this long-read technology, we were able to reconstruct and annotate a closed, high-quality genome of a previously uncharacterized skin species. We demonstrate that hybrid approaches with short-read technology are sufficiently powerful to reconstruct even single-nucleotide polymorphism level variation of species in this a community.

Next-generation sequencing provides the opportunity to practice predictive medicine based on identified variants. Putative loss-of-function (pLOF) variants are common in genomes and understanding their contribution to disease is critical for predictive medicine. To this end, we characterized the consequences of pLOF variants in an exome cohort by iterative phenotyping. Exome data were generated on 951 participants from the ClinSeq cohort and filtered for pLOF variants in genes likely to cause a phenotype in heterozygotes. 103 of 951 exomes had such a pLOF variant and 79 participants were evaluated. Of those 79, 34 had findings or family histories that could be attributed to the variant (28 variants in 18 genes), 2 had indeterminate findings (2 variants in 2 genes), and 43 had no findings or a negative family history for the trait (34 variants in 28 genes). The presence of a phenotype was correlated with two mutation attributes: prior report of pathogenicity for the variant (p = 0.0001) and prior report of other mutations in the same exon (p = 0.0001). We conclude that 1/30 unselected individuals harbor a pLOF mutation associated with a phenotype either in themselves or their family. This is more common than has been assumed and has implications for the setting of prior probabilities of affection status for predictive medicine.

Atopic dermatitis (AD) is associated with epidermal barrier defects, dysbiosis, and skin injury caused by scratching. In particular, the barrier-defective epidermis in patients with AD with loss-of-function filaggrin mutations has increased IL-1α and IL-1β levels, but the mechanisms by which IL-1α, IL-1β, or both are induced and whether they contribute to the aberrant skin inflammation in patients with AD is unknown.We sought to determine the mechanisms through which skin injury, dysbiosis, and increased epidermal IL-1α and IL-1β levels contribute to development of skin inflammation in a mouse model of injury-induced skin inflammation in filaggrin-deficient mice without the matted mutation (ft/ft mice).Skin injury of wild-type, ft/ft, and myeloid differentiation primary response gene-88-deficient ft/ft mice was performed, and ensuing skin inflammation was evaluated by using digital photography, histologic analysis, and flow cytometry. IL-1α and IL-1β protein expression was measured by means of ELISA and visualized by using immunofluorescence and immunoelectron microscopy. Composition of the skin microbiome was determined by using 16S rDNA sequencing.Skin injury of ft/ft mice induced chronic skin inflammation involving dysbiosis-driven intracellular IL-1α release from keratinocytes. IL-1α was necessary and sufficient for skin inflammation in vivo and secreted from keratinocytes by various stimuli in vitro. Topical antibiotics or cohousing of ft/ft mice with unaffected wild-type mice to alter or intermix skin microbiota, respectively, resolved the skin inflammation and restored keratinocyte intracellular IL-1α localization.Taken together, skin injury, dysbiosis, and filaggrin deficiency triggered keratinocyte intracellular IL-1α release that was sufficient to drive chronic skin inflammation, which has implications for AD pathogenesis and potential therapeutic targets.

Studies in patients with genetic defects can provide unique insights regarding the role of specific genes and pathways in humans. Patients with defects in the Th17/IL-17 axis, such as patients harboring loss-of-function STAT3 mutations (autosomal-dominant hyper IgE syndrome; AD-HIES) present with recurrent oral fungal infections. Our studies aimed to comprehensively evaluate consequences of STAT3 deficiency on the oral commensal microbiome. We characterized fungal and bacterial communities in AD-HIES in the presence and absence of oral fungal infection compared with healthy volunteers. Analyses of oral mucosal fungal communities in AD-HIES revealed severe dysbiosis with dominance of Candida albicans (C. albicans) in actively infected patients and minimal representation of health-associated fungi and/or opportunists. Bacterial communities also displayed dysbiosis in AD-HIES, particularly in the setting of active Candida infection. Active candidiasis was associated with decreased microbial diversity and enrichment of the streptococci Streptococcus oralis (S. oralis) and S. mutans, suggesting an interkingdom interaction of C. albicans with oral streptococci. Increased abundance of S. mutans was consistent with susceptibility to dental caries in AD-HIES. Collectively, our findings illustrate a critical role for STAT3/Th17 in the containment of C. albicans as a commensal organism and an overall contribution in the establishment of fungal and bacterial oral commensal communities.

Hidradenitis suppurativa (HS) is a prevalent and debilitating inflammatory skin disease characterized by painful and recurrent nodules and abscesses, malodorous purulent drainage, and disfiguring sinus tract and scar formation involving intertriginous body sites. Microorganisms have been implicated in HS pathogenesis, and broad-spectrum antimicrobial therapy is one of the mainstays of HS management. However, bacteria have been identified in only ∼50% of HS lesions using conventional culture-based methods, and no consistent organism has been cultured from HS lesions (Brook and Frazier, 1999; Gener et al., 2009; Jemec, 2003; Join-Lambert et al., 2011; Leach et al., 1979).

Hair follicles (HFs) function as hubs for stem cells, immune cells, and commensal microbes, which must be tightly regulated during homeostasis and transient inflammation. Here we found that transmembrane endopeptidase ADAM10 expression in upper HFs was crucial for regulating the skin microbiota and protecting HFs and their stem cell niche from inflammatory destruction. Ablation of the ADAM10-Notch signaling axis impaired the innate epithelial barrier and enabled Corynebacterium species to predominate the microbiome. Dysbiosis triggered group 2 innate lymphoid cell-mediated inflammation in an interleukin-7 (IL-7) receptor-, S1P receptor 1-, and CCR6-dependent manner, leading to pyroptotic cell death of HFs and irreversible alopecia. Double-stranded RNA-induced ablation models indicated that the ADAM10-Notch signaling axis bolsters epithelial innate immunity by promoting β-defensin-6 expression downstream of type I interferon responses. Thus, ADAM10-Notch signaling axis-mediated regulation of host-microbial symbiosis crucially protects HFs from inflammatory destruction, which has implications for strategies to sustain tissue integrity during chronic inflammation.

Atopic dermatitis (AD) is a multifactorial, heterogeneous disease characterized by epidermal barrier dysfunction, immune system dysregulation, and skin microbiome alterations. Skin microbiome studies in AD have demonstrated that disease flares are associated with microbial shifts, particularly Staphylococcus aureus predominance. AD-associated S. aureus strains differ from those in healthy individuals across various genomic loci, including virulence factors, adhesion proteins, and proinflammatory molecules-which may contribute to complex microbiome barrier-immune system interactions in AD. Different microbially based treatments for AD have been explored, and their future therapeutic successes will depend on a deeper understanding of the potential microbial contributions to the disease.

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We performed allogeneic hematopoietic stem cell transplantation in 6 patients with mutations in the dedicator-of-cytokinesis-8 (DOCK8) gene using a myeloablative conditioning regimen consisting of busulfan 3.2 mg/kg/day i.v. for 4 days and fludarabine 40 mg/m(2)/day for 4 days. Three patients received allografts from matched related donors and 3 patients from matched unrelated donors. Two patients received peripheral blood stem cells and 4 patients bone marrow hematopoietic stem cells. Tacrolimus and short-course methotrexate on days 1, 3, 6, and 11 were used for graft-versus-host-disease (GVHD) prophylaxis. All 6 patients are alive at a median follow-up of 22.5 months (range, 14 to 35). All patients achieved rapid and high levels of donor engraftment and complete reversal of the clinical and immunologic phenotype. Adverse events consisted of acute skin GVHD in 2 patients and post-transplant pulmonary infiltrates in a patient with extensive bronchiectasis pretransplant. Thus, a uniform myeloablative conditioning regimen followed by allogeneic hematopoietic stem cell transplantation in DOCK8 deficiency results in reconstitution of immunologic function and reversal of the clinical phenotype with a low incidence of regimen-related toxicity.

Building upon the knowledge garnered from investigations utilizing traditional culturing methods, advances in sequencing technologies have catalyzed a revolution in studying human-associated microbes: bacteria, fungi and viruses. Skin microbiome research in healthy individuals and patients with dermatologic disorders has provided insights into the complexity and biogeography of human skin microbes. The continual developments in sequencing and analyses will provide increasingly sophisticated tools to interrogate human-associated microbes, ultimately to improve our understanding of health and disease.

<h2>Abstract</h2> Dedicator-of-cytokinesis 8 (DOCK8) deficiency, a primary immunodeficiency disease, can be reversed by allogeneic hematopoietic stem cell transplantation (HSCT); however, there are few reports describing the use of alternative donor sources for HSCT in DOCK8 deficiency. We describe HSCT for patients with DOCK8 deficiency who lack a matched related or unrelated donor using bone marrow from haploidentical related donors and post-transplantation cyclophosphamide (PT/Cy) for graft-versus-host disease (GVHD) prophylaxis. Seven patients with DOCK8 deficiency (median age, 20 years; range, 7 to 25 years) received a haploidentical related donor HSCT. The conditioning regimen included 2 days of low-dose cyclophosphamide, 5 days of fludarabine, 3 days of busulfan, and 200 cGy total body irradiation. GVHD prophylaxis consisted of PT/Cy 50 mg/kg/day on days +3 and +4 and tacrolimus and mycophenolate mofetil starting at day +5. The median times to neutrophil and platelet engraftment were 15 and 19 days, respectively. All patients attained >90% donor engraftment by day +30. Four subjects developed acute GVHD (1 with maximum grade 3). No patient developed chronic GVHD. With a median follow-up time of 20.6 months (range, 9.5 to 31.7 months), 6 of 7 patients are alive and disease free. Haploidentical related donor HSCT with PT/Cy represents an effective therapeutic approach for patients with DOCK8 deficiency who lack a matched related or unrelated donor.

The use of genomic sequencing to investigate microbes has expanded, yet it has also raised questions regarding optimal approaches to studying the skin microbiome. Meisel et al. show that while whole genome shotgun metagenomic sequences were most similar to expected microbial profiles, sequencing of the hypervariable regions V1-V3 of the 16S ribosomal RNA gene had greater accuracy than sequencing of the hypervariable region V4 in determining genus and species level classifications of prominent skin bacteria.

Human papillomavirus (HPV) infections underlie a wide spectrum of both benign and malignant epithelial diseases. In this report, we describe the case of a young man who had encephalitis caused by herpes simplex virus during adolescence and currently presented with multiple recurrent skin and mucosal lesions caused by HPV. The patient was found to have a pathogenic germline mutation in the X-linked interleukin-2 receptor subunit gamma gene (IL2RG), which was somatically reverted in T cells but not in natural killer (NK) cells. Allogeneic hematopoietic-cell transplantation led to restoration of NK cytotoxicity, with normalization of the skin microbiome and persistent remission of all HPV-related diseases. NK cytotoxicity appears to play a role in containing HPV colonization and the ensuing HPV-related hyperplastic or dysplastic lesions. (Funded by the National Institutes of Health and the Herbert Irving Comprehensive Cancer Center Flow Cytometry Shared Resources.).

Cancer immunotherapy has significantly improved patient survival. Yet, half of patients do not respond to immunotherapy. Gut microbiomes have been linked to clinical responsiveness of melanoma patients on immunotherapies; however, different taxa have been associated with response status with implicated taxa inconsistent between studies. We used a tumor-agnostic approach to find common gut microbiome features of response among immunotherapy patients with different advanced stage cancers. A combined meta-analysis of 16S rRNA gene sequencing data from our mixed tumor cohort and three published immunotherapy gut microbiome datasets from different melanoma patient cohorts found certain gut bacterial taxa correlated with immunotherapy response status regardless of tumor type. Using multivariate selbal analysis, we identified two separate groups of bacterial genera associated with responders versus non-responders. Statistical models of gut microbiome community features showed robust prediction accuracy of immunotherapy response in amplicon sequencing datasets and in cross-sequencing platform validation with shotgun metagenomic datasets. Results suggest baseline gut microbiome features may be predictive of clinical outcomes in oncology patients on immunotherapies, and some of these features may be generalizable across different tumor types, patient cohorts, and sequencing platforms. Findings demonstrate how machine learning models can reveal microbiome-immunotherapy interactions that may ultimately improve cancer patient outcomes.

Abstract: Pemphigus vulgaris is an uncommon autoimmune blistering skin disorder that is particularly rare in children. Immunosuppressive treatment can be challenging. Rituximab (anti‐CD20 monoclonal antibody) has been used to treat autoimmune disorders by depletion of CD20 B cells. Successful rituximab therapy has been reported in adults with refractory pemphigus vulgaris. We present a girl with childhood pemphigus vulgaris unresponsive to treatment with azathioprine, mycophenolate mofetil, plasmapheresis, and intravenous immunoglobulin with systemic prednisone who responded to treatment with rituximab. She had a corresponding decline in circulating antibodies against desmoglein 1 and 3 and a decline in diphtheria and tetanus‐specific antibody titers.

This Viewpoint discusses the challenges and successes of the application of microbiome science to human health and highlights the need for basic mechanistic research informed by clinical questions to advance the field.

Cutaneous T-cell lymphomas (CTCLs) are a heterogeneous group of lymphoid malignancies derived from skin-homing T cells. Mycosis fungoides (MF) is the most common form of CTCL, and Sezary syndrome (SS) is an aggressive variant with varying levels of clonal lymphocytes in the blood. The variable presentation and lack of definitive diagnostic markers make CTCL diagnosis challenging. Although the biology of these malignancies is not fully understood, some microbes, particularly viruses, have been hypothesized to play roles in malignant T-cell transformation in CTCL (Berger et al., 2002; Mirvish et al., 2013; van der Loo et al., 1979).

Candida auris is a human pathogen of high concern due to its extensive antifungal drug resistance and high mortality rates associated with invasive infections. Candida auris skin colonization and persistence on environmental surfaces make this pathogen difficult to control once it enters a health care facility. Residents in long-term care hospitals and nursing homes are especially vulnerable.

To the Editor: We read with interest the article by Robert et al1Robert C. Mateus C. Spatz A. Wechsler J. Escudier B. Dermatologic symptoms associated with the multikinase inhibitor sorafenib.J Am Acad Dermatol. 2009; 60: 299-305Abstract Full Text Full Text PDF PubMed Scopus (137) Google Scholar in the February 2009 issue of the Journal. The frequency of sorafenib-associated dermatologic side effects and their impact on quality of life highlight the important role of dermatologists in caring for these patients. We wish to share our experience with oncology patients receiving sorafenib at the National Cancer Institute. We found skin changes similar to those described by the authors in addition to some not included in their report. Sixty-five patients on sorafenib therapy for solid tumors were evaluated in our dermatology clinic between August 2005 and December 2007. Twenty-four individuals were examined at baseline and followed for the development of dermatologic side effects (prospective cohort) and 41 individuals were examined after developing cutaneous lesions (consultation cohort). The cutaneous adverse effects discussed by the authors were similarly encountered in both of our cohorts: hand-foot skin reaction (HFSR; 63% prospective cohort and 78% consultation cohort, respectively), facial/scalp erythema/dysesthesias (63% and 68%), nail changes (33% and 32%), alopecia (21% and 39%), rash/exanthems (21% and 10%), cysts (8% and 27%), eruptive keratoacanthomas (4% and 7%), and eruptive nevi2Kong H.H. Sibaud V. Chanco Turner M.L. Fojo T. Hornyak T.J. Chevreau C. Sorafenib-induced eruptive melanocytic lesions.Arch Dermatol. 2008; 144: 820-822Crossref PubMed Scopus (71) Google Scholar (0% and 2%). In comparison with the review by Robert et al,1Robert C. Mateus C. Spatz A. Wechsler J. Escudier B. Dermatologic symptoms associated with the multikinase inhibitor sorafenib.J Am Acad Dermatol. 2009; 60: 299-305Abstract Full Text Full Text PDF PubMed Scopus (137) Google Scholar our cohorts had a much higher incidence of HFSR.3Azad N.S. Aragon-Ching J.B. Dahut W.L. Gutierrez M. Figg W.D. Jain L. et al.Hand-foot skin reaction increases with cumulative sorafenib dose and with combination anti-VEGF therapy.Clin Cancer Res. 2009; 15: 1411-1416Crossref PubMed Scopus (127) Google Scholar Dermatologic adverse effects identified in our patients but not reported in Robert's review include the development of a generalized keratosis pilaris (KP)-like eruption (21% prospective cohort and 41% consultation cohort, respectively); stomatitis (17% and 22%), inflamed seborrheic keratoses (13% and 10%), and leukocytoclastic vasculitis4Chung N.M. Gutierrez M. Turner M.L. Leukocytoclastic vasculitis masquerading as hand-foot syndrome in a patient treated with sorafenib.Arch Dermatol. 2006; 142: 1510-1511PubMed Google Scholar (0% and 2%). The histology of the generalized KP-like eruption was typical for keratosis pilaris (Fig 1). The findings of a KP-like eruption, eruptive keratoacanthomas, and multiple cysts support the hypothesis that sorafenib causes alterations in the keratinocyte differentiation/proliferation pathways. While some of the exanthematous eruptions experienced by our patients clinically resembled erythema multiforme (EM), multiple biopsies revealed only mild superficial perivascular lymphocytic infiltrates with no evidence of basal vacuolization or necrotic keratinocytes as would be expected in EM. A previously reported patient, who presented with EM-like lesions, was demonstrated to have leukocytoclastic vasculitis on histologic examinaton. We recommend biopsies from these skin lesions for more precise diagnoses. Sorafenib was successfully reinitiated at reduced doses after temporary rest periods despite these eruptions. We concur with the assessments of Robert et al1Robert C. Mateus C. Spatz A. Wechsler J. Escudier B. Dermatologic symptoms associated with the multikinase inhibitor sorafenib.J Am Acad Dermatol. 2009; 60: 299-305Abstract Full Text Full Text PDF PubMed Scopus (137) Google Scholar and Autier et al5Autier J. Escudier B. Wechsler J. Spatz A. Robert C. Prospective study of the cutaneous adverse effects of sorafenib, a novel multikinase inhibitor.Arch Dermatol. 2008; 144: 886-892Crossref PubMed Scopus (200) Google Scholar that the dermatologic side effects of sorafenib are often manageable with topical therapies and/or dose modifications. Increased awareness within the dermatologic community of the diversity, frequency, and treatment of sorafenib-induced cutaneous adverse reactions will be helpful to patients who require chronic therapy with this medication for their cancers. Dermatologic symptoms associated with the multikinase inhibitor sorafenibJournal of the American Academy of DermatologyVol. 60Issue 2PreviewThe multikinase inhibitor sorafenib (Nexavar) is associated with a relatively high incidence of dermatologic symptoms. Full-Text PDF

Photosensitivity has been reported in patients who were treated with vandetanib (ZD6474), an inhibitor of epidermal growth factor receptor, vascular endothelial growth factor receptor, and the RET (rearranged during transfection) kinases.We describe the occurrence of cutaneous hyperpigmentation after photosensitivity in 2 patients who were treated with vandetanib. The pigmentation patterns were variable within and between patients. Biopsy specimens from different sites revealed variability in Perls and Fontana staining patterns.These 2 cases highlight the unusual occurrence of cutaneous hyperpigmentation after vandetanib-associated photosensitivity, a reaction that demonstrates that medications are important causes of acquired photosensitivity and hyperpigmentation. Aggressive photoprotection may facilitate the resolution of diffuse hyperpigmentation. Dermatologists should endeavor to identify and report novel cutaneous adverse effects as new targeted therapies are developed.

Growing interest in host-fungal interactions has implications for human health and disease

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Dermatology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Dermatology journal

Study Objective. To determine if excretion of sorafenib in sweat is associated with hand‐foot skin reaction in patients receiving sorafenib. Design. Prospective pilot study. Setting. Outpatient clinic of a cancer research institution. Patients. Two patients who were receiving sorafenib and developed a hand‐foot skin reaction of at least grade 1 and two healthy subjects (controls). Intervention. Sweat production was stimulated in both the patients with hand‐foot skin reaction and the healthy subjects by means of pilocarpine iontophoresis. Measurements and Main Results. Sweat samples were collected from the patients with hand‐foot skin reaction and from the healthy subjects. Using liquid chromatography‐tandem mass spectrometry, sorafenib concentrations were measured in the sweat samples. Sweat samples from the healthy subjects were spiked with known concentrations of sorafenib to determine the lower limit of quantification of the assay, which was determined to be 5 ng/ml. Sorafenib concentrations in the samples from the patients with hand‐foot skin reaction were undetectable based on the assay's sensitivity. Conclusion. Our results suggest that hand‐foot skin reaction in patients receiving sorafenib is not associated with excretion of sorafenib in sweat. Further studies are needed to understand the mechanism of hand‐foot skin reaction, a treatment‐limiting adverse effect of multikinase inhibitors.

A conference entitled ‘Human microbiome science: Vision for the future’ was organized in Bethesda, MD from July 24 to 26, 2013. The event brought together experts in the field of human microbiome research and aimed at providing a comprehensive overview of the state of microbiome research, but more importantly to identify and discuss gaps, challenges and opportunities in this nascent field. This report summarizes the presentations but also describes what is needed for human microbiome research to move forward and deliver medical translational applications.

Advances in genomics have significantly expanded our ability to examine human microbes. These studies on the human microbiome are elucidating the integral relationships that hosts have with their m...

The National Cancer Institute (NCI) sponsored a 2-day workshop, “Next Steps in Studying the Human Microbiome and Health in Prospective Studies,” in Bethesda, Maryland, May 16–17, 2017. The workshop brought together researchers in the field to discuss the challenges of conducting microbiome studies, including study design, collection and processing of samples, bioinformatics and statistical methods, publishing results, and ensuring reproducibility of published results. The presenters emphasized the great potential of microbiome research in understanding the etiology of cancer. This report summarizes the workshop and presents practical suggestions for conducting microbiome studies, from workshop presenters, moderators, and participants.

Resident microbes in skin and gut predominantly impact local immune cell function during homeostasis. However, colitis-associated neutrophilic skin disorders suggest possible breakdown of this compartmentalization with disease. Using a model wherein neonatal skin colonization by Staphylococcus epidermidis facilitates generation of commensal-specific tolerance and CD4+ regulatory T cells (Tregs), we ask whether this response is perturbed by gut inflammation. Chemically induced colitis is accompanied by intestinal expansion of S. epidermidis and reduces gut-draining lymph node (dLN) commensal-specific Tregs. It also results in reduced commensal-specific Tregs in skin and skin-dLNs and increased skin neutrophils. Increased CD4+ circulation between gut and skin dLN suggests that the altered cutaneous response is initiated in the colon, and resistance to colitis-induced effects in Cd4creIl1r1fl/fl mice implicate interleukin (IL)-1 in mediating the altered commensal-specific response. These findings provide mechanistic insight into observed connections between inflammatory skin and intestinal diseases.

Human skin hosts a diversity of microbiota. Advances in sequencing and analytical methods have increasingly illuminated the importance of the finest resolution in understanding the genetic diversity of the skin microbiota, highlighting strain-level differences and their functional implications. Such genetic diversity, which exists within an individual and is strongly individual specific underscores the difficulty in elucidating functionality. Integrated investigations of the microbial strain diversity through sequencing and culture-based approaches with host immunology and physiology will be critical in expanding our understanding of the roles of the skin microbiome.

Background Different wavelengths of ultraviolet (UV) light cause skin damage through different mechanisms. Minimal erythema dose (MED) is usually used to clinically evaluate skin sensitivity to ultraviolet radiation by inducing skin erythema using ultraviolet B (UVB) or ultraviolet A (UVA) + UVB. Aims In this study, we detected changes in the blood flow at the MED erythema caused by UVB and UVA + UVB radiation through optical coherence tomography (OCT) to explain the role of different bands of ultraviolet rays in erythema induction. Methods Two MED irradiation areas on the subjects' back were irradiated with UVB alone or UVA + UVB (UVA: UVB = 8:1). The absolute energy of UVB remained the same in UVB and UVA+UVB. At 24 h after the irradiation, the changes in the blood flow in the MED area were detected using OCT. Results Compared with the blank control, the maximum blood flow depth, blood flow peak, and total blood flow of UVB-MED and UVA+UVB-MED were significantly increased. Notably, the maximum blood flow depth and blood flow peak of UVB-MED were higher than UVA+UVB-MED. There was no significant difference in total blood perfusion between UVA+UVB-MED and UVB-MED. Under the same UVB energy, the skin erythema caused by UVA + UVB was weaker than UVB alone. Conclusions The analysis of local blood flow by OCT showed that the peak and maximum depth of local blood flow caused by UVB alone were significantly higher than UVA + UVB.

Monochromosome transfers of selected chromosomes into a nasopharyngeal carcinoma (NPC) cell line were performed to determine if tumor suppressing activity for NPC mapped to chromosomes 9, 11, and 17. Current information from cytogenetic and molecular allelotyping studies indicate that these chromosomes may harbor potential tumor suppressor genes vital to NPC. The present results show the importance of CDKN2A on chromosome 9 in NPC development. There was no functional suppression of tumor development in nude mice with microcell hybrids harboring the newly transferred chromosome 9 containing an interstitial deletion at 9p21, whereas transfection of CDKN2A into the NPC HONE1 cells resulted in obvious growth suppression. Whereas intact chromosome 17 transfers into HONE1 cells showed no functional suppression of tumor formation, chromosome 11 was able to do so. Molecular analysis of chromosome 11 tumor segregants indicated that at least two tumor suppressive regions mapping to 11q13 and 11q22-23 may be critical for the development of NPC.

Helminth infections and allergic diseases are characterized by increases in IgE and type 2 cytokines such as IL-4. Despite their common immunopathogenesis, epidemiologic studies reveal an inverse relationship between the prevalence rates of these diseases1Cooper P.J. Interactions between helminth parasites and allergy.Curr Opin Allergy Clin Immunol. 2009; 9: 29-37Crossref PubMed Scopus (171) Google Scholar, 2Fallon P.G. Mangan N.E. Suppression of TH2-type allergic reactions by helminth infection.Nat Rev Immunol. 2007; 7: 220-230Crossref PubMed Scopus (158) Google Scholar and a number of animal experiments have demonstrated that helminth infections can actively protect against the development of allergy.2Fallon P.G. Mangan N.E. Suppression of TH2-type allergic reactions by helminth infection.Nat Rev Immunol. 2007; 7: 220-230Crossref PubMed Scopus (158) Google Scholar While several mechanisms have been proposed, the pathophysiology underlying this phenomenon remains unclear.2Fallon P.G. Mangan N.E. Suppression of TH2-type allergic reactions by helminth infection.Nat Rev Immunol. 2007; 7: 220-230Crossref PubMed Scopus (158) Google Scholar Recently, we demonstrated that chronic helminth infections suppress basophil responsiveness to IgE-mediated activation in mice.3Larson D. Hübner M.P. Torrero M.N. Morris C.P. Brankin A. Swierczewski B.E. et al.Chronic helminth infection reduces basophil responsiveness in an IL-10-dependent manner.J Immunol. 2012; 188: 4188-4199Crossref PubMed Scopus (46) Google Scholar This phenomenon may be a principal mechanism underlying helminth-mediated protection against allergy because basophils are increasingly being recognized as functionally important in allergic diseases. Basophils participate in the effector phase of allergic responses by releasing acute inflammatory mediators such as histamine after IgE-mediated activation. Through the release of IL-4, they also play a prominent role amplifying the type 2 responses that drive allergic diseases.4Falcone F.H. Knol E.F. Gibbs B.F. The role of basophils in the pathogenesis of allergic disease.Clin Exp Allergy. 2011; 41: 939-947Crossref PubMed Scopus (47) Google Scholar, 5Sokol C.L. Medzhitov R. Emerging functions of basophils in protective and allergic immune responses.Mucosal Immunol. 2010; 3: 129-137Abstract Full Text Full Text PDF PubMed Scopus (51) Google Scholar Given the many differences between murine and human basophils,5Sokol C.L. Medzhitov R. Emerging functions of basophils in protective and allergic immune responses.Mucosal Immunol. 2010; 3: 129-137Abstract Full Text Full Text PDF PubMed Scopus (51) Google Scholar, 6Lee J.J. McGarry M.P. When is a mouse basophil not a basophil?.Blood. 2007; 109: 859-861Crossref PubMed Scopus (52) Google Scholar in this study we sought to determine whether basophil suppression occurs in human beings infected with helminths. To evaluate this, we compared basophil histamine release in helminth-infected children before and after anthelmintic treatment. Studies were approved by the institutional review boards at the Universidad San Francisco de Quito, Ecuador, and at the Uniformed Services University. Parasitologic examinations were conducted on stool samples from 28 children aged 8 to 14 years in a rural community in Esmeraldas province, Ecuador. Ascaris lumbricoides and Trichuris trichiura eggs were found in the stool of all children, and Hymenolepis nana eggs were found in the stool of 2 children. Blood from children was collected in heparinized tubes and centrifuged. After centrifugation, plasma was carefully removed and blood cells were washed twice with PBS. Blood cells were resuspended to the original volume by using PBS, diluted with Histamine Release Buffer (Beckman Coulter, Inc, Indianapolis, Ind), and stimulated for 30 minutes with seven 4-fold concentrations of anti-IgE (0.0005–2 μg/mL, Sigma-Aldrich, St Louis, Mo) and ionomycin (5 μg/mL, Calbiochem, San Diego, Calif). Stimulated blood was centrifuged for 10 minutes at 400g, supernatant was acylated, and histamine levels determined by using a competitive histamine ELISA (Beckman Coulter, Inc). The percentage of total histamine released was calculated by dividing the amount of histamine released into the supernatant by the amount of histamine in a lysed aliquot of blood. Infected children were then treated orally with 3 daily 800 mg doses of albendazole and a single dose of ivermectin at 0.2 mg/kg. Two weeks after therapy, histamine release from blood basophils was measured again from 22 of the treated children by using identical stimulation conditions. To enable paired comparisons, samples only from the 22 children who provided blood before and after treatment were utilized in analyses. The 2-week time point was chosen because human basophil lifespan is estimated to be 2 to 14 days.7MacGLashan D. Xia H.Z. Schwartz L.B. Gong J. IgE-regulated loss, not IgE-regulated synthesis, controls expression of FcepsilonR1 in human basophils.J Leukoc Biol. 2001; 70: 207-218Crossref PubMed Google Scholar Efforts were made to standardize blood processing, and basophil activation studies were conducted on average 4.5 hours after blood draw. When sufficient plasma was available, samples were analyzed for circulating total IgE levels by using a human IgE ELISA kit (Immunology Consultants Laboratory, Inc, Portland, Ore). Two-tailed Wilcoxon signed ranked test was used to determine statistical significance between paired samples. GraphPad Prism version 4.03 was used for all statistical analyses. To evaluate whether helminth infections play a role in suppressing basophil function, histamine release from basophils of infected children was measured 2 weeks after anthelmintic therapy. As seen in Fig 1, substantial increases in basophil activation in response to IgE-mediated activation developed in endemic children after their infections were treated. Two weeks after treatment, basophils of endemic children released more of their total histamine in response to 0.031, 0.125, and 0.5 μg/mL anti-IgE (mean percentage of total histamine release, pretreatment 32.8%, 45.0%, and 42.1% vs posttreatment 46.9%, 63.3%, and 57.7%, respectively; P = .014, P = .002, and P = .0007; Fig 1, A). These differences did not appear to be due to treatment-induced alterations in basophil IgE levels because no changes in circulating IgE levels were observed before and after treatment (Fig 1, B). To assess basophil responsiveness to non–IgE-mediated activation, histamine release was measured in response to ionomycin. As seen in Fig 2, A, anthelmintic treatment resulted in significantly greater basophil histamine release after ionomycin stimulation (mean percentage of total histamine release, pretreatment 53.2% vs posttreatment 76.2%; P = .0005). Of note, basal basophil histamine release was observed to be significantly lower posttreatment (mean concentration of spontaneous histamine release, pretreatment 8.4 nM vs posttreatment 2.1 nM; P = .002; Fig 2, B), perhaps due to less ongoing activation of these cells in the absence of helminth infection. This phenomenon likely did not account for the observed increases in anti-IgE and ionomycin-mediated basophil activation posttreatment, because we did not subtract out basal histamine release when calculating percentages of total histamine released. In addition, analysis of individuals with equivalent baseline histamine release pre- and posttreatment exhibited the same changes as analysis of all individuals (data not shown). These findings suggest that the ability of basophils to respond to both IgE-dependent and IgE-independent activation is suppressed during human intestinal helminth infection. This suppression appears to require the continuous presence of helminths because basophil histamine release increases within 2 weeks of the elimination of helminths. While the mechanism of basophil suppression requires further study, it could have important clinical consequences. First, as basophils have been shown to be important for protection against intestinal helminth infections in some murine models,8Ohnmacht C. Schwartz C. Panzer M. Schiedewitz I. Naumann R. Voehringer D. Basophils orchestrate chronic allergic dermatitis and protective immunity against helminths.Immunity. 2010; 33: 364-374Abstract Full Text Full Text PDF PubMed Scopus (286) Google Scholar basophil suppression may help worms to survive in hosts. Second, because basophils function as effector cells of allergy and are involved in the development of type 2 immune responses, reduced basophil functionality may be a mechanism by which helminths protect against allergic diseases. The participation of study mothers and children in the Esmeraldas province of Ecuador is gratefully acknowledged.

Cancer immunotherapies are showing promising clinical results in a variety of malignancies. Monitoring the immune as well as the tumor response following these therapies has led to significant advancements in the field. Moreover, the identification and assessment of both predictive and prognostic biomarkers has become a key component to advancing these therapies. Thus, it is critical to develop systematic approaches to monitor the immune response and to interpret the data obtained from these assays. In order to address these issues and make recommendations to the field, the Society for Immunotherapy of Cancer reconvened the Immune Biomarkers Task Force. As a part of this Task Force, Working Group 3 (WG3) consisting of multidisciplinary experts from industry, academia, and government focused on the systematic assessment of immune regulation and modulation. In this review, the tumor microenvironment, microbiome, bone marrow, and adoptively transferred T cells will be used as examples to discuss the type and timing of sample collection. In addition, potential types of measurements, assays, and analyses will be discussed for each sample. Specifically, these recommendations will focus on the unique collection and assay requirements for the analysis of various samples as well as the high-throughput assays to evaluate potential biomarkers.

ABSTRACT: Effective highly active antiretroviral therapy (HAART) has increased survival in patients infected with the human immunodeficiency virus (HIV). However, HAART is not without toxicities. Cutaneous adverse reactions from antiretroviral agents have become increasingly important to recognize as the population of patients surviving with HIV infection grows. Dermatologists play an important role in managing these cutaneous effects of HAART therapy in HIV patients. This article reviews cutaneous adverse effects from nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors, protease inhibitors, and fusion inhibitors, as well as separately addresses lipodystrophy, and immune reconstitution.

Based on molecular, morphological and cytological studies the previously monotypic genus Deinostigma W.T.Wang & Z.Y.Li has been expanded to include several species previously ascribed to Primulina Hance. Deinostigma now comprises seven species, including one previously placed in synonymy. The new combinations Deinostigma cicatricosa (W.T.Wang) D.J.Middleton & Mich.Moller, Deinostigma cycnostyla (B.L.Burtt) D.J.Middleton & H.J.Atkins, Deinostigma cyrtocarpa (D.Fang & L.Zeng) Mich.Moller & H.J.Atkins, Deinostigma eberhardtii (Pellegr.) D.J.Middleton & H.J.Atkins, Deinostigma minutihamata (D.Wood) D.J.Middleton & H.J.Atkins and Deinostigma tamiana (B.L.Burtt) D.J.Middleton & H.J.Atkins are made. Deinostigma eberhardtii is lectotypified. The genus is defined by a combination of an alternate leaf arrangement, hooked hairs on many plant parts, flowers with the pedicel inserted at an angle and off-centre on the receptacle, and, where known, a somatic chromosome number (2n) of < 36. This new circumscription of the genus expands its distribution from Vietnam into South China.

Hidradenitis suppurativa has been previously defined as a “chronic, inflammatory, recurrent, debilitating skin disease” of the hair follicle that typically presents postpuberty with “painful, deep-seated, inflamed lesions in apocrine gland-bearing areas of the body,” particularly the axillary, inguinal, and anogenital regions (Paus et al., 2008). Although the precise molecular pathogenesis remains unknown, some patients with familial hidradenitis suppurativa (acne inversa, OMIM. Johns Hopkins University, Baltimore, MD.

Dedicator of cytokinesis 8 (DOCK8) gene mutations are responsible for a combined immunodeficiency characterized by atopy, sinopulmonary infections, and DNA viral infections including varicella zoster, herpes simplex 1 and 2 (HSV 1 and 2), human papilloma virus and molluscum contagiosum, and Epstein-Barr virus (EBV)-driven lymphomas (reviewed in Aydin et al1). In that study of 136 patients with DOCK8 deficiency, the median survival at 20 years was 47%, and the event-free survival at 20 years was 18%.

Chronic Obstructive Pulmonary Disease (COPD) is a chronic respiratory disease characterized by a slow progression and caused by the inhalation of harmful particulate matter. Cigarette smoke and air pollutants are the primary contributing factors. Currently, the pathogenesis of COPD remains incompletely understood. The PI3K/Akt signaling pathway has recently emerged as a critical regulator of inflammation and oxidative stress response in COPD, playing a pivotal role in the disease's progression and treatment. This paper reviews the association between the PI3K/Akt pathway and COPD, examines effective PI3K/Akt inhibitors and novel anti-COPD agents, aiming to identify new therapeutic targets for clinical intervention in this disease.

POEMS Syndrome is a constellation of findings including Polyneuropathy, Organomegaly, Endocrinopathy, Monoclonal plasma cell disorder, and Skin changes. Calciphylaxis, a microangiopathy involving vascular calcification and thrombotic occlusions, occurs rarely in POEMS. We present a case of prominent calciphylaxis that antedated the diagnosis of POEMS. The patient presented with extensive ecchymoses progressing to necrotic lesions in the setting of acute renal injury. Previously, she had chronic slowly progressive polyneuropathy, splenomegaly, hypothyroidism, amenorrhea, and ascites. Calciphylaxis was diagnosed on skin biopsy, and POEMS was diagnosed based upon clinical findings plus a bone marrow biopsy showing 15% lambda chain restricted plasma cells. Treatment for the calciphylaxis was supportive with fluids, tissue debridement, wound vacuum devices and antibiotics for secondary infection. Myeloma was treated with bortezomib and steroids. All aspects of the patient's manifestations improved. We conclude that calciphylaxis can be a prominent feature of POEMS and can appear prior to recognition of the full-blown syndrome.

Abstract The skin microbiome is an extensive community of bacteria, fungi, mites, viruses and archaea colonizing the skin. Fluctuations in the composition of the skin microbiome have been observed in atopic dermatitis (AD) and food allergy (FA), particularly in early life, established disease, and associated with therapeutics. However, AD is a multifactorial disease characterized by skin barrier aberrations modulated by genetics, immunology, and environmental influences, thus the skin microbiome is not the sole feature of this disease. Future research should focus on mechanistic understanding of how early‐life skin microbial shifts may influence AD and FA onset, to guide potential early intervention strategies or as microbial biomarkers to identify high‐risk infants who may benefit from possible microbiome‐based biotherapeutic strategies. Harnessing skin microbes as AD biotherapeutics is an emerging field, but more work is needed to investigate whether this approach can lead to sustained clinical responses.

Aim: The 4th Davos Declaration, convened during the Global Allergy Forum (GAF) in Davos, aimed to elevate patient care for patients with atopic dermatitis (AD) by uniting experts and stakeholders. The forum addressed the high prevalence of AD, with a strategic focus on advancing research, treatment, and management to meet the evolving challenges in the field. Methods: This multidisciplinary forum brought together top leaders from research, clinical practice, policy, and patient advocacy to discuss the critical aspects of AD, including neuroimmunology, environmental factors, comorbidities, and breakthroughs in prevention, diagnosis, and treatment. The discussions were geared towards fostering a collaborative approach to integrate these advancements into practical, patient-centric care. Results The forum underlined the mounting burden of AD, attributing it to significant environmental and lifestyle changes. It acknowledged the progress in understanding AD and in developing targeted therapies but recognized a gap in translating these innovations into clinical practice. Emphasis was placed on the need for enhanced awareness, education, and stakeholder engagement to address this gap effectively and to consider environmental and lifestyle factors in a comprehensive disease management strategy. Conclusion: The 4th Davos Declaration marks a significant milestone in the journey to improve care for people with AD. By promoting a holistic approach that combines research, education, and clinical application, the Forum sets a roadmap for stakeholders to work together to improve patient outcomes in AD, reflecting a commitment to adapt and respond to the dynamic challenges of AD in a changing world.

Purpose: Pulmonary antibody mediated rejection (AMR) is associated with chronic lung allograft dysfunction (CLAD) and death. The current International Society for Heart and Lung Transplantation (ISHLT) criteria for AMR is predicated on a constellation of clinical, laboratory and histopathological parameters, including the presence of donor-specific antibodies (DSA). The degree of allograft injury on the molecular level, as measured by donor-derived cell-free DNA (dd-cfDNA), is not considered in the ISHLT criteria but may identify patients experiencing a form of antibody mediated rejection.

IMPORTANCE Cutaneous leiomyomas can be associated with severe paroxysmal pain in which nerve conduction may have a key role.Medical management of painful cutaneous leiomyomas is generally unsatisfactory.OBJECTIVE To assess the efficacy of intralesional botulinum toxin A in the management of pain associated with cutaneous leiomyomas.DESIGN, SETTING, AND PARTICIPANTS Randomized, double-blind, placebo-controlled pilot study conducted from January 5, 2009, to March 27, 2014.The setting was a single-center study at the National Institutes of Health among participants 18 years or older with cutaneous leiomyomas characterized by pain at least once weekly and pain of at least 4 on a pain scale ranging from 0 to 10.INTERVENTIONS Eighteen participants were randomized to receive intralesional botulinum toxin A (5 U per 1 cm 2 ) or equivalent volumes of intralesional saline placebo. MAIN OUTCOMES AND MEASURESThe primary outcomes were the differences in average lesional pain assessed by the Brief Pain Inventory and visual analog scale before and after ice provocation over a 4-week period. RESULTSNo significant difference in average lesional pain was observed between the study arms.Decreased pain was reported in the botulinum toxin vs placebo arms by visual analog scale scores before ice provocation (median, 0.00; range, -3.30 to 0.70 for botulinum toxin and median, 0.40; range, -1.30 to 1.50 for placebo; P = .06);however, this finding was nonsignificant.No significant difference was observed in change in pain after ice provocation.A significant difference was seen between the arms in skin-related quality of life by total Dermatology Life Quality Index (median, -4.00; range, -8.00 to 2.00 for botulinum toxin and median, 0.00; range, -1.00 to 4.00 for placebo; P = .007)and with the specific skin pain-related question on the Dermatology Life Quality Index (median, -1.00; range, -2.00 to 1.00 for botulinum toxin and median, 0.00; range, -1.00 to 0.00 for placebo; P = .048).No significant difference was found in pain as ascertained by Patient Global Impression of Change at week 4.No serious adverse events related to botulinum toxin use were observed. CONCLUSIONS AND RELEVANCEThe use of botulinum toxin to treat painful cutaneous leiomyomas was associated with improved quality of life and with a trend toward improved pain at rest.

A 6-year-old white boy of Amish ancestry with chronic lower extremity ulcers was seen in the dermatology clinic at the National Institutes of Health (NIH) Clinical Center in Bethesda, MD. Since the age of 2 years, the patient had experienced numerous deep ulcers on the thighs, legs, and feet that developed without preceding trauma. His wounds typically healed slowly leaving depressed atrophic scars. At the time of presentation, the patient had ulcers limited to the soles of both feet and difficulty ambulating because of associated pain.

Objectives We aimed to assess changes in myositis core set measures and ancillary clinical and laboratory data from the National Institutes of Health's subset of patients enrolled in the Rituximab in Myositis trial. Methods Eighteen patients (5 dermatomyositis, 8 polymyositis, 5 juvenile dermatomyositis) completed more in-depth testing of muscle strength and cutaneous assessments, patient-reported outcomes, and laboratory tests before and after administration of rituximab. Percentage change in individual measures and in the definitions of improvement (DOIs) and standardized response means were examined over 44 weeks. Results Core set activity measures improved by 18-70% from weeks 0-44 and were sensitive to change. Fifteen patients met the DOI at week 44, 9 patients met a DOI 50% response, and 4 met a DOI 70% response. Muscle strength and function measures were more sensitive to change than cutaneous assessments. Constitutional, gastrointestinal, and pulmonary systems improved 44-70%. Patient-reported outcomes improved up to 28%. CD20+ B cells were depleted in the periphery, but B cell depletion was not associated with clinical improvement at week 16. Conclusions This subset of patients had high rates of clinical response to rituximab, similar to patients in the overall trial. Most measures were responsive, and muscle strength had a greater degree of change than cutaneous assessments. Several novel assessment tools, including measures of strength and function, extra-muscular organ activity, fatigue, and health-related quality of life, are promising for use in future myositis trials. Further study of B cell-depleting therapies in myositis, particularly in treatment-naive patients, is warranted.

“Translational research” bridges clinical and basic research to formulate research studies based on clinical observations and to implement the clinical applications of basic research. Although basic and clinical scientists have long collaborated, translational research challenges investigators to move beyond the traditional training of both laboratory scientists and clinicians. In 2007, we—a clinical researcher (Kong) and a basic scientist (Segre)—initiated an interdisciplinary project to characterize the human skin microbiota associated with both common and rare skin disorders (Grice et al., 2008Grice E.A. Kong H.H. Renaud G. et al.A diversity profile of the human skin microbiota.Genome Res. 2008; 18: 1043-1050Crossref PubMed Scopus (587) Google Scholar, Grice et al., 2009Grice E.A. Kong H.H. Conlan S. et al.Topographical and temporal diversity of the human skin microbiome.Science. 2009; 324: 1190-1192Crossref PubMed Scopus (1530) Google Scholar). We set out to better understand the cutaneous microbial landscape in healthy individuals and patients with atopic dermatitis through the use of genomic techniques. The project demanded an understanding of a combination of high-throughput sequencing technology and logistics of clinical research, with knowledge of the subtleties of dermatologic disorders. The requirements of rigorous translational research moved us both beyond the boundaries of our individual disciplines. The paradigm for a translational investigator has been the MD–PhD scientist with training in both patient care and laboratory research. This model results in over 300 MD–PhD graduates per year in the United States, 5.9% of whom enter residencies in dermatology. Of the recent MD–PhD scientists who completed dermatology residencies, 56% (39 of 70) remain in academia and provide a rich source of researchers in the field of dermatology (Brass et al., 2010Brass L.F. Akabas M.H. Burnley L.D. et al.Are MD–PHD programs meeting their goals? An analysis of career choices made by graduates of 24 MD–PHD programs.Acad Med. 2010; 85: 692-701PubMed Google Scholar). In the current state of research, there is an increasing need to build bridges between clinical and basic researchers to translate findings from bench to bedside and back again. Are we adequately preparing clinical researchers and basic scientists to bridge the translational research gap? If not, what skills do we need to learn and teach? Seven years ago, former National Institutes of Health (NIH) director Elias Zerhouni highlighted the complexities and roadblocks inherent to modern translational research. He implemented the NIH Roadmap with the goal of bringing individuals from critical disparate disciplines into translational research teams (Zerhouni, 2003Zerhouni E. Medicine. The NIH Roadmap.Science. 2003; 302: 63-72Crossref PubMed Scopus (749) Google Scholar). His model foreshadowed our path toward collaboration. We participated in the NIH Roadmap's Human Microbiome Project with our study of patients with atopic dermatitis. MDs interested in laboratory-based research face competing demands imposed by patient-care responsibilities. PhDs interested in clinical research face competing demands for projects with shorter turnaround times to publish manuscripts and to compete for grants. MD–PhDs face both sets of competing demands. In addition, it is difficult for PhD scientists to identify ways to work with clinicians and for physicians without a laboratory to find a basic researcher to coinvestigate a clinical question. When we met, one of us (Segre) had training in genetics and basic cell biology, using only animal models and cell culture. The other (Kong) had training in dermatology and patient-oriented research. Although neither of us had prior experience with a translational research team jointly led by a clinical researcher and a basic scientist, our common enthusiasm propelled us into a high-risk research project that proved to be rewarding and fruitful. A critical issue was learning how to foster a collaboration that promoted translational research. We discuss here what enabled our collaboration and highlight features specific to our interactions as MD and PhD. Although we believe that much of our experience is relevant to all collaborations, certain features were specific to the changing landscape of translational research and the inherent differences in our training. Open, transparent communication is vital, including frank discussions about manuscript authorship, abstract and journal submissions, potential disagreements, meeting presentations, and a mechanism by which to make decisions on bringing in additional collaborators. Clearly outline the goals for each collaborator in the project, particularly for junior colleagues. Define timelines and how the combined efforts of the group will allow these goals to be achieved. We intermittently had disagreements and encountered misunderstandings, but issues were resolved with frank discussion. Each of the points delineated below is predicated on effective communication. A priori, we assumed that one large group meeting with all personnel would provide the best opportunity for communication. However, we quickly realized that many team members were engaged primarily in either patient care or molecular sequence analysis. Although it seems antithetical to building one team, we began to hold two separate weekly meetings with only the two of us attending both meetings. Vital information was lost if only one of us attended either meeting, because each of us had a different perspective on the many exchanges of information and data. Our clinical meetings focused on clinical protocol development, effective patient recruitment, accurate clinical phenotyping, and careful, timely specimen collection and storage. Our laboratory meetings reviewed molecular protocol development, technical challenges, sequence data analysis, and statistical methodologies. On an as-needed basis, individuals from one meeting attended the other to present data or to participate in troubleshooting. Quarterly, we held larger meetings involving all team members to assess progress and set the agenda for the next quarter. How then does each individual on the team comprehend the responsibilities of other team members and how each person's role affects the entire project? This requires each individual to develop a greater understanding of the role of team members with whom they directly interact and then use this knowledge to strengthen overall communication and operations. For example, after observing the DNA preparation method, the clinical team saved the laboratory staff frustrating hours at the bench by making simple, but important, changes to the sample-collection process. Similarly, tailoring the data entry and specimen tracking forms to mirror the medical-record forms minimized data errors. In addition to these separate weekly meetings, the two of us devoted at least one hour per week to discussing milestones and roadblocks. We developed this particular arrangement over time, after realizing that we needed a deeper understanding of each discipline's strengths and major questions. Willingness to learn more about each other's area of expertise fosters an efficient transition from bench to bedside and back. Rather than the clinical medicine or the laboratory components remaining terra incognita to the basic scientist or the clinical researcher, respectively, we both work hard to comprehend all parts of the project. This approach enables each of us to understand more clearly the strengths, challenges, and realities of each discipline and of the project as a whole. Before embarking on a complicated project with a new collaborator, begin with a more manageable project. This lays the groundwork for future endeavors by establishing a collaborative relationship. We began with a pilot study examining the feasibility of skin sampling for microbiome investigation (Grice et al., 2008Grice E.A. Kong H.H. Renaud G. et al.A diversity profile of the human skin microbiota.Genome Res. 2008; 18: 1043-1050Crossref PubMed Scopus (587) Google Scholar). The pilot study provided vital knowledge, not only about how to expand our skin microbiome investigation but also about how each individual functioned as part of the research team. Most importantly, the pilot project tested the question “who owns this project?” We crossed a major hurdle when the first microbial diversity sequencing data were brought to the clinic meeting for analysis. Prior to this, there had been unspoken concern that the basic researchers would retain isolated control over the intellectually rewarding component of the data analysis. This element seems obvious, but trust only develops over time and is constantly being challenged. Former colleagues and mentors played an important role leading up to the initial meetings. For example, Maria Turner became more familiar with the work of the Segre lab through two longtime colleagues, and she also supervised and mentored Kong's fellowship. Turner brought us together to pursue what she visualized as a new way to investigate skin microbiota. We shared several other colleagues, and hearing from reliable colleagues that a potential coinvestigator is trustworthy carries significant weight. This emphasizes the importance of having a wide range of colleagues and keeping them informed about long-term goals. The field of dermatologic research is broad and highly interconnected, and it includes many whose expertise spans numerous arenas, such as immunology, pathology, and intriguing clinical observations. On one occasion, Segre submitted a meeting abstract for the team, thinking that she was saving the others time. However, Kong potentially missed an opportunity to write and present the abstract at a shared meeting. Don't be afraid to admit that, however good your intentions, your actions were wrong—and correct your mistake. Obviously, it is important to avoid repeating mistakes. When the team was asked to present at NIH Clinical Center Grand Rounds, the task was better suited for Kong, as the clinician, to communicate the goals and findings of the study. This also brought Kong appropriate recognition for her role as the lead clinical investigator in the project. In turn, Segre presented at the Cold Spring Harbor meeting “The Biology of Genomes,” which recognized her role as the head of a large-scale sequencing project. Understanding and respecting that each person brings a unique strength to the project form the foundation of an effective team approach to science. As our working relationship matured, we learned to build on each other's strengths and compensate for each other's weaknesses. To collaborate effectively requires one to be both a bit selfish and a bit selfless. Small individual sacrifices can achieve a higher satisfaction quotient for everyone. Conversely, stating what you need for professional recognition is an important part of participating in a collaborative effort, and it does not conflict with the goals of the rest of the group. There is often a mechanism in place for producing a win–win outcome if the team takes the time to evaluate the most important criteria for each individual's personal and professional success. Examples may include providing reasonable technical expertise and assistance to further a team member's research, which may be outside the scope of the main project, or alternating first authorship on submitted manuscripts.

Human skin is stably colonized by a distinct microbiota that functions together with epidermal cells to maintain a protective physical barrier. Staphylococcus, a prominent genus of the skin microbiota, participates in colonization resistance, tissue repair, and host immune regulation in strain specific manners. To unlock the potential of engineering skin microbial communities, we aim to fully characterize the functional diversity of this genus within the context of the skin environment. We conducted metagenome and pan-genome analyses of isolates obtained from distinct body sites of healthy volunteers, providing a detailed biogeographic depiction of staphylococcal species that colonize our skin. S. epidermidis, S. capitis, and S. hominis were the most abundant species present in all volunteers and were detected at all body sites. Pan-genome analysis of these three species revealed that the genus-core was dominated by central metabolism genes. Species-specific core genes were enriched in host colonization functions. The majority (~68%) of genes were detected only in a fraction of isolate genomes, underscoring the immense strain-specific gene diversity. Conspecific genomes grouped into phylogenetic clades, exhibiting body site preference. Each clade was enriched for distinct gene-sets that are potentially involved in site tropism. Finally, we conducted gene expression studies of select isolates showing variable growth phenotypes in skin-like medium. In vitro expression revealed extensive intra- and inter-species gene expression variation, substantially expanding the functional diversification within each species. Our study provides an important resource for future ecological and translational studies to examine the role of shared and strain-specific staphylococcal genes within the skin environment.

Human skin is stably colonized by a distinct microbiota that functions together with epidermal cells to maintain a protective physical barrier. Staphylococcus , a prominent genus of the skin microbiota, participates in colonization resistance, tissue repair, and host immune regulation in strain-specific manners. To unlock the potential of engineering skin microbial communities, we aim to characterize the diversity of this genus within the context of the skin environment. We reanalyzed an extant 16S rRNA amplicon dataset obtained from distinct body sites of healthy volunteers, providing a detailed biogeographic depiction of staphylococcal species that colonize our skin. S. epidermidis , S. capitis, and S. hominis were the most abundant staphylococcal species present in all volunteers and were detected at all body sites. Pan-genome analysis of isolates from these three species revealed that the genus-core was dominated by central metabolism genes. Species-restricted-core genes encoded known host colonization functions. The majority (~68%) of genes were detected only in a fraction of isolate genomes, underscoring the immense strain-specific gene diversity. Conspecific genomes grouped into phylogenetic clades, exhibiting body site preference. Each clade was enriched for distinct gene sets that are potentially involved in site tropism. Finally, we conducted gene expression studies of select isolates showing variable growth phenotypes in skin-like medium. In vitro expression revealed extensive intra- and inter-species gene expression variation, substantially expanding the functional diversification within each species. Our study provides an important resource for future ecological and translational studies to examine the role of shared and strain-specific staphylococcal genes within the skin environment.

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KEY TEACHING POINTS • We describe a 45-year-old woman with GATA2 deficiency associated with verrucae, lymphedema, immunodeficiency, and a history of infections and skin cancer. • GATA2 deficiency has variable clinical expressivity with differing presentations, including infection, hematopoietic abnormalities, immunodeficiency, lymphedema, and cancer. • Cutaneous manifestations include verruca vulgaris, soft tissue infections, lymphedema, and panniculitis. • Patients may have verrucae that can progress to squamous cell carcinomas; dermatologists therefore play an important role in managing these patients as members of a multidisciplinary team.

Introduction Atopic eczema affects 20% of UK children, and environmental factors are important in its aetiology. Several observational studies suggest an increased risk of atopic eczema in children living in hard water areas. The Softened Water for Eczema Prevention pilot trial tests the feasibility of installing domestic ion-exchange water softeners around the time of birth to reduce the risk of atopic eczema in children with a family history of atopy. A further aim is to explore the pathophysiological mechanisms for this in an embedded mechanistic study. Methods and analysis Multicentre parallel group assessor-blinded randomised controlled pilot trial. Participants are newborn babies (n=80) living in a hard water (&gt;250 mg/L calcium carbonate) area at risk of developing atopic eczema because of a family history of atopy. Participants will be randomised prior to birth in a 1:1 ratio. The intervention group will have an ion-exchange water softener installed prior to birth. The control group will receive their usual domestic hard water supply. Follow-up will be until 6 months of age. Data will be collected at birth (baseline), 1, 3 and 6 months of age. The main outcome is the proportion of eligible families screened who are willing and able to be randomised. Several secondary feasibility and clinical endpoints will also be evaluated, alongside mechanistic outcomes. Data will be analysed on an intention-to-treat basis. There will be no hypothesis testing for the clinical outcomes. Study acceptability will be evaluated through semistructured interviews. Ethics and dissemination This study has been reviewed and given a favourable opinion by the North West–Liverpool East Research Ethics Committee (Ref: 17/NW/0661). The results of the study will be reported at international conferences and in peer-reviewed scientific journals. We will send participating families a summary of the pilot trial results. Trial registration number NCT03270566 .

Certain polyomaviruses (PyVs), such as JC and BK, are known to cause severe disease in immunocompromised hosts (Moens et al., 2017Moens U. Krumbholz A. Ehlers B. Zell R. Johne R. Calvignac-Spencer S. et al.Biology, evolution, and medical importance of polyomaviruses: an update.Infect Genet Evol. 2017; 54: 18-38Crossref PubMed Scopus (76) Google Scholar). Human PyV (HPyV)6 and HPyV7 can be shed from skin surfaces without apparent disease (Hashida et al., 2018Hashida Y. Higuchi T. Matsuzaki S. Nakajima K. Sano S. Daibata M. Prevalence and genetic variability of human polyomaviruses 6 and 7 in healthy skin among asymptomatic individuals.J Infect Dis. 2018; 217: 483-493Crossref PubMed Scopus (14) Google Scholar; Schowalter et al., 2010Schowalter R.M. Pastrana D.V. Pumphrey K.A. Moyer A.L. Buck C.B. Merkel cell polyomavirus and two previously unknown polyomaviruses are chronically shed from human skin.Cell Host Microbe. 2010; 7: 509-515Abstract Full Text Full Text PDF PubMed Scopus (403) Google Scholar), whereas in immunocompromised patients, the viruses may be associated with a pruritic eruption (Canavan et al., 2018Canavan T.N. Baddley J.W. Pavlidakey P. Tallaj J.A. Elewski B.E. Human polyomavirus-7-associated eruption successfully treated with acitretin.Am J Transplant. 2018; 18: 1278-1284Crossref PubMed Scopus (16) Google Scholar; Ho et al., 2015Ho J. Jedrych J.J. Feng H. Natalie A.A. Grandinetti L. Mirvish E. et al.Human polyomavirus 7-associated pruritic rash and viremia in transplant recipients.J Infect Dis. 2015; 211: 1560-1565Crossref PubMed Scopus (79) Google Scholar; Nguyen et al., 2017Nguyen K.D. Lee E.E. Yue Y. Stork J. Pock L. North J.P. et al.Human polyomavirus 6 and 7 are associated with pruritic and dyskeratotic dermatoses.J Am Acad Dermatol. 2017; 76: 932-940.e3Abstract Full Text Full Text PDF PubMed Scopus (53) Google Scholar; Smith et al., 2018Smith S.D.B. Erdag G. Cuda J.D. Rangwala S. Girardi N. Bibee K. et al.Treatment of human polyomavirus-7-associated rash and pruritus with topical cidofovir in a lung transplant patient: case report and literature review.Transpl Infect Dis. 2018; 20: e12793Crossref Scopus (11) Google Scholar). We report the case of a 38-year-old woman who developed intractable pruritus and burning associated with a skin eruption 1 year after her second renal transplantation (Supplementary Figure S1a–c). Her immunosuppressive regimen consisted of tacrolimus and mycophenolate mofetil. Histopathology was characteristic of HPyV6- and HPyV7-associated eruptions (Ho et al., 2015Ho J. Jedrych J.J. Feng H. Natalie A.A. Grandinetti L. Mirvish E. et al.Human polyomavirus 7-associated pruritic rash and viremia in transplant recipients.J Infect Dis. 2015; 211: 1560-1565Crossref PubMed Scopus (79) Google Scholar; Nguyen et al., 2017Nguyen K.D. Lee E.E. Yue Y. Stork J. Pock L. North J.P. et al.Human polyomavirus 6 and 7 are associated with pruritic and dyskeratotic dermatoses.J Am Acad Dermatol. 2017; 76: 932-940.e3Abstract Full Text Full Text PDF PubMed Scopus (53) Google Scholar). Immunohistochemistry confirmed the expression of PyV large tumor antigen, and immunofluorescence identified HPyV7 tumor antigen and HPyV6 and/or HPyV7 VP1 expression (Supplementary Figure S1d). Shotgun metagenomic sequencing revealed HPyV7 DNA and the absence of HPyV6 (Supplementary Figure S2). The addition of acitretin and reduction of mycophenolate mofetil dose eventually led to the resolution of symptoms (Supplementary Figure S1b and c). Detectable viral protein expression was absent in apparently normal skin after 15 weeks on acitretin and mycophenolate mofetil dose reduction (late-treatment time point) (Supplementary Figure S1d). Shotgun metagenomic sequencing of skin swabs from before treatment and early treatment (3 weeks on acitretin) revealed that 99.99% of mappable nonhuman reads were HPyV7, which is a high frequency, even in patients with viral skin disease (Tirosh et al., 2018Tirosh O. Conlan S. Deming C. Lee-Lin S.Q. Huang X. NISC Comparative Sequencing Program, et al.Expanded skin virome in DOCK8-deficient patients.Nat Med. 2018; 24: 1815-1821Crossref PubMed Scopus (42) Google Scholar). Surprisingly, HPyV7 continued to constitute 99.96% of nonhuman reads at the late-treatment time point (Figure 1a). However, the percentage of nonhuman reads among total reads was 59% before treatment compared with 4.5% at late treatment (Supplementary Figure S3), suggesting that the overall HPyV7 DNA burden had decreased. Bulk RNA sequencing revealed a 940-fold decrease in totally normalized HPyV7 transcripts in a late-treatment clinically normal-appearing skin specimen compared with the more affected pretreatment specimen (Figure 1b), demonstrating that clinical resolution was associated with a large reduction in viral transcription. During pathogenic infection with some PyVs, the regulatory region undergoes sequence rearrangements and can accumulate insertion or deletion nucleotide variants (indels) that affect transcription factor binding (Ajuh et al., 2018Ajuh E.T. Wu Z. Kraus E. Weissbach F.H. Bethge T. Gosert R. et al.Novel human polyomavirus noncoding control regions differ in bidirectional gene expression according to host cell, large T-antigen expression, and clinically occurring rearrangements.J Virol. 2018; 92 (e02231-17)Crossref PubMed Scopus (24) Google Scholar). The comparison of HPyV7 DNA and RNA sequences from our patient with a reference viral genome revealed subclonal polymorphisms scattered throughout the viral genome. Of note, a section of the regulatory region contained a high diversity of indels. Interestingly, an 8 bp deletion variant in this region (variant 2) was predominantly expressed in the more affected skin compared with that in the less affected skin, despite representing a minor variant at the DNA level in both samples when compared with the nonindel-containing species (variant 1) (Figure 1c and Supplementary Figure S4a and b). Functional prediction of this variant suggested disruption of a TATA-box, but no other definitive effects on likely transcription factor‒binding sites could be identified. Further investigation revealed that the novel transcript likely encodes a previously unrecognized agnoprotein. In addition to the expression of various agnoprotein sequence variants at this site, there were also multiple splice isoforms (Supplementary Figure S4c). Human BK and JC PyVs express agnoproteins, with little amino acid identity to the proposed HPyV7 agnoprotein, which have been suggested to regulate multiple viral and host functions (De Gascun and Carr, 2013De Gascun C.F. Carr M.J. Human polyomavirus reactivation: disease pathogenesis and treatment approaches.Clin Dev Immunol. 2013; 2013: 373579Crossref PubMed Scopus (53) Google Scholar). We next compared the DNA sequences from this highly variable region with those of the skin of 20 healthy volunteers with asymptomatic HPyV7 colonization (healthy Sequence Read Archive datasets). We identified a small number of common indels in the healthy volunteers, in contrast to the numerous distinct indels in our patient (uncommon indels). Similar distinct regulatory region indels were detected in the skin of a second, previously reported patient with HPyV7-associated eruption (Canavan et al., 2018Canavan T.N. Baddley J.W. Pavlidakey P. Tallaj J.A. Elewski B.E. Human polyomavirus-7-associated eruption successfully treated with acitretin.Am J Transplant. 2018; 18: 1278-1284Crossref PubMed Scopus (16) Google Scholar), upstream of the agnogene. The variants from this patient were also rare or absent in healthy volunteers, suggesting that these highly mutated viral regions were relatively restricted to diseased skin and may be associated with pathogenicity (Figure 1d and Supplementary Figure S4b). Pathway analysis of host gene expression in the RNA sequencing samples revealed induction of inflammatory genes associated with Type I IFNs, the antiviral response, and NKG2D ligands (Figure 2a). Consistent with this, there was a strong expression of the IFN-induced antiviral protein, MX1, in pretreatment epidermis, which was absent during late treatment (Figure 2b). Two of the most upregulated genes included innate antiviral defense proteins, APOBEC3A and APOBEC3B (Figure 2a). These single-stranded DNA deaminases potentially promote the generation of indels upon DNA repair (Burns et al., 2013Burns M.B. Temiz N.A. Harris R.S. Evidence for APOBEC3B mutagenesis in multiple human cancers.Nat Genet. 2013; 45: 977-983Crossref PubMed Scopus (487) Google Scholar; Green et al., 2016Green A.M. Landry S. Budagyan K. Avgousti D.C. Shalhout S. Bhagwat A.S. et al.APOBEC3A damages the cellular genome during DNA replication.Cell Cycle. 2016; 15: 998-1008Crossref PubMed Scopus (46) Google Scholar). APOBEC3A and/or APOBEC3B exhibited cytoplasmic and nuclear expression, most often within or near virally infected cells (Figure 2c). BK PyV has been shown to upregulate APOBEC3B (Verhalen et al., 2016Verhalen B. Starrett G.J. Harris R.S. Jiang M. Functional upregulation of the DNA cytosine deaminase APOBEC3B by polyomaviruses.J Virol. 2016; 90: 6379-6386Crossref PubMed Scopus (52) Google Scholar), which can produce viral mutations that alter glycan usage for viral entry and conversely facilitate escape from neutralizing antibodies (Peretti et al., 2018Peretti A. Geoghegan E.M. Pastrana D.V. Smola S. Feld P. Sauter M. et al.Characterization of BK polyomaviruses from kidney transplant recipients suggests a role for APOBEC3 in driving in-host virus evolution.Cell Host Microbe. 2018; 23 (628–35.e7)Abstract Full Text Full Text PDF PubMed Scopus (33) Google Scholar). Although the RNA sequencing data suggested that affected skin exhibited innate immune activation, the host response was inadequate to achieve viral clearance. Considering the clinical resolution after tapering immunosuppression, we characterized the changes in the host immune response. Immunohistochemistry revealed a moderate CD4+ infiltrate before treatment and during late treatment, but CD8+ T cells infiltrated the epidermis only during late treatment (Figure 2d and Supplementary Figure S5). An HPyV7-like particle ELISA detected a high titer of circulating antiviral antibodies at late treatment but not at earlier time points. In contrast, antibodies to BK virus were present at each time point (Figure 2e). By using multiple orthogonal approaches, these data support a causative role for HPyV7 in this eruption. These results suggest that HPyV7 stimulates an innate immune response, but a protective antiviral response is impaired by treatment with mycophenolate mofetil. We further identified a previously undescribed agnogene within the HPyV7 genome prone to mutation during infection. Many of the observed mutations in the HPyV7 genome are consistent with host activation of APOBEC3 enzymes, as has been seen for other PyVs. Taken together, our findings are consistent with the hypothesis that iatrogenic impairment of immunosurveillance enabled abnormal viral proliferation and innate immune activation that induced APOBEC3A and/or APOBEC3B expression, which in turn led to viral mutagenesis that correlated with increased HPyV7 pathogenicity and clinical disease. Datasets related to this article can be found at https://www.ncbi.nlm.nih.gov/nuccore/MG674199.1 (human polyomavirus 7 complete genome), hosted at Genbank; https://submit.ncbi.nlm.nih.gov/subs/bioproject/SUB6080707/overview (metagenomic data), hosted at National Center for Biotechnology Information BioProject; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148169 (RNA sequencing data), hosted at Gene Expression Omnibus. There will be no restrictions on data availability. Rachel K. Rosenstein: http://orcid.org/0000-0001-6375-6129 Diana V. Pastrana: http://orcid.org/0000-0002-8084-5665 Gabriel J. Starrett: http://orcid.org/0000-0001-5871-5306 Matthew R. Sapio: http://orcid.org/0000-0002-8855-5419 Natasha T. Hill: http://orcid.org/0000-0001-9043-4643 Jay-Hyun Jo: http://orcid.org/0000-0002-2039-3425 Chyi-Chia R. Lee: http://orcid.org/0000-0002-5306-7781 Michael J. Iadarola: http://orcid.org/0000-0001-7188-9810 Christopher B. Buck: http://orcid.org/0000-0003-3165-8094 Heidi H. Kong: http://orcid.org/0000-0003-4424-064X Isaac Brownell: http://orcid.org/0000-0002-0090-9914 Edward W. Cowen: http://orcid.org/0000-0003-1918-4324 The authors state no conflict of interest. We sincerely thank the patient for participating in these investigations. We appreciate the technical support of the National Cancer Institute Center for Cancer Research genomics core facility and the National Institutes of Health Intramural Sequencing Center. We thank R. Wang and B. Elewski for their assistance with the sequencing of human polyomavirus 7 from the patient reported previously (Canavan et al., 2018Canavan T.N. Baddley J.W. Pavlidakey P. Tallaj J.A. Elewski B.E. Human polyomavirus-7-associated eruption successfully treated with acitretin.Am J Transplant. 2018; 18: 1278-1284Crossref PubMed Scopus (16) Google Scholar). We thank M. Taylor, T. Pillai, and the Segre lab for their underlying contributions. This work utilized the computational resources of the National Institutes of Health High Performing Computation Biowulf cluster (http://hpc.nih.gov). Conceptualization: RKR, CBB, HHK, IB, EWC; Data Curation: RKR, CCRL, HHK, EWC; Formal Analysis: RKR, DVP, GJS, MRS, NTH, JHJ; Funding Acquisition: MJI, CBB, HHK, IB, EWC; Investigation: RKR, DVP, GJS, MRS, NTH, JHJ, CCRL; Methodology: DVP, MRS, MJI, HHK, CBB, IB; Project Administration: RKR; Resources: MJI, CBB, HHK, IB, EWC; Software: GJS, MRS, JHJ; Supervision: MJI, HHK, CBB, IB, EWC; Validation: RKR, MRS; Visualization: RKR, DVP, GJS, MRS, NTH, JHJ, CCRL, IB; Writing - Original Draft Preparation: RKR, IB, EWC; Writing - Review and Editing: RKR, DVP, GJS, MRS, NTH, JHJ, CCRL, MJI, CBB, HHK, IB, EWC Experiments were performed in accordance with approved protocols by the institutional review board at the National Cancer Institute (NCT02471352 and NCT00001506). The patient provided written informed consent for clinical photography, sample acquisition, and subsequent analyses including sequencing studies. Download .xlsx (1.3 MB) Help with xlsx files Supplementary Table S1Host RNA-seq expression values as sFPKM and raw counts. RNA-seq, RNA sequencing; sFPKM, significant fragments per kilobase per million aligned reads.Supplementary Table S2. SRA datasets containing HPyV7 reads. HPyV, human polyomavirus; SRA, Sequence Read Archive. Patient care and sample collection were performed in accordance with approved protocols by the institutional review board at the National Cancer Institute (NCT02471352 and NCT00001506). The individual provided written informed consent for clinical photography, sample acquisition, and subsequent analyses including sequencing studies. QOL measurements such as the Dermatology Life Quality Index and Visual Analog Scales were administered. We have complied with all relevant ethical regulations. Relevant pretreatment medications: 1,000 mg mycophenolate mofetil (MMF) twice daily, 5 mg tacrolimus twice daily. Early-treatment medications included 500 mg MMF twice daily, 5 mg tacrolimus twice daily, and 25 mg acitretin twice daily. Late-treatment medications included 500 mg MMF daily, 5 mg tacrolimus twice daily, and 25 mg acitretin twice daily. After skin swabs were collected as described in each section below, 4–6 mm skin punch biopsy specimens were obtained from the patient and were frozen for RNA sequencing or placed in formalin for H&E and immunohistochemical analyses. The more affected specimen was a site of severe itch with hyperpigmentation and scale over the lower back. The less affected specimen was a site of mild itch, with normal pigmentation and scale over the flank. The late-treatment specimen was from a clinically normal-appearing site over the lower back that was previously affected. Skin swabs (from the abdomen, lower back, posterior thigh) were collected and frozen at pretreatment, early treatment (3 weeks on acitretin and 1 week on a tapered dose of 500 mg MMF twice daily), and late-treatment (15 weeks on acitretin and 9 weeks on a tapered dose of 500 mg MMF daily) time points. Peripheral blood was processed by the clinical laboratory for research purposes. After antigen retrieval (CC1 buffer, Ventana Medical Systems), tissue sections were incubated with the following primary antibodies: anti-CD4 antibody (Clone SP35, Prediluted, Catalog #790-4423, Roche, Basel Switzerland, RRID:AB_2335982), anti-CD8 antibody (Clone SP57, Prediluted, Catalog #790-4460, Roche, RRID:AB_2335985), and anti-simian virus 40 tumor antigen antibody (Clone PAb416, 1:300 dilution, Catalog #DP02, Calbiochem, San Diego, CA, RRID: AB_212848). PAb416 cross reacts with several human polyomavirus (HPyV) types. For the CD4 and/or CD8 double stain, unstained tissue sections were incubated with anti-CD4 antibody and labeled with a brown chromogen; the sections were subsequently incubated with anti-CD8 antibody and labeled with a red chromogen. The staining was performed on the Roche Ventana Medical Systems BenchMark ULTRA automated immunohistochemistry platform using the ultraview Universal DAB Detection Kit (Ventana Medical Systems, Oro Valley, AZ), following standard laboratory protocols established by the histology section of the Laboratory of Pathology at the National Institutes of Health. Microscopy and image acquisition were performed with Olympus BX41 microscope, Olympus UPlanSApo lenses, and Nikon NIS Elements Imaging software (Nikon 5.10.01 [Build, 1307] 64 bit) with Nikon 6 MP camera (Nikon, Tokyo, Japan) (calibrated per manufacturer’s specifications). Saline premoistened swabs were collected and stored at −80 oC; swabs were processed as described (Pastrana et al., 2018Pastrana D.V. Peretti A. Welch N.L. Borgogna C. Olivero C. Badolato R. et al.Metagenomic discovery of 83 new human papillomavirus types in patients with immunodeficiency.mSphere. 2018; 3 (e00645-18)Crossref PubMed Scopus (39) Google Scholar). Briefly, the swabs were soaked in 150 μl of nuclease buffer (Dulbecco’s PBS, 10 mM magnesium chloride, 0.5% Brij-58 [#P5884, Sigma-Aldrich, St. Louis, MO], and 0.1% Benzonase [#E1014, Sigma-Aldrich]) and incubated at room temperature for 15 minutes inside 2 ml of low protein-binding polypropylene centrifuge columns (#89896, Pierce Manufacturing, Appleton, WI). Columns were spun at 1,000g for 5 minutes and the flow through transferred to 2-ml siliconized microcentrifuge tubes. The columns were washed three times with wash buffer (Dulbecco’s PBS, 0.8 M of sodium chloride, and 0.5% Brij-58) by centrifugation as mentioned earlier. Swab extracts were loaded on top of iodixanol (#D1556, Optiprep, Sigma-Aldrich) step gradients consisting of 1.3 ml of each 27%, 33%, and 39% solutions of iodixanol mixed with Dulbecco’s PBS/0.8 M sodium chloride. The gradients were formed on Beckman ½ × 2 inch ml polyallomer centrifuge tubes (#326819) and spun at 234,000g for 3.5 hours at 16 oC. Six fractions of 730 μl were collected, and DNA was extracted from the individual fractions. For the extraction, 200 μl of each fraction was mixed with 50 μl of 5× digest buffer (250 mM Tris pH 8.0, 125 mM EDTA, 2.5% SDS, 2.5% Proteinase K (#191331, Qiagen, Hilden, Germany) and 50 mM dithiothreitol (#20291, Pierce Manufacturing). The samples were allowed to digest at 50 oC for 15 minutes and then heat inactivated at 72 oC for 10 minutes. DNA was precipitated from each sample with 125 μl of 7.5 M ammonium acetate and 2.6 volumes of 95% ethanol for 1 hour at room temperature and then overnight at 4 oC. The next day, samples were spun at 16,000g for 1 hour at room temperature and washed once with 70% ethanol. After air drying, samples were prepared for rolling circle amplification by resuspending with 10 μl of sample buffer from a TempliPhi kit (#GE25-6400-10, Sigma-Aldrich), placed at 95 oC for 3 minutes, allowed to cool down, and mixed with 10 μl of reaction buffer and 0.4 μl of enzyme mix from the TempliPhi kit. Rolling circle amplification reactions were carried out at 30 oC for 16–24 hours and then heat inactivated at 65 oC for 10 minutes. Reactions were ethanol precipitated as before and resuspended in 75 μl of diluted 2 mM Tris-hydrochloric acid pH and 0.2 mM EDTA solution. Samples were processed with the Nextera XT DNA sample kit (Illumina, San Diego, CA) and sent to the National Cancer Institute Center for Cancer Research genomics core facility for deep sequencing with the Illumina MiSeq platform. Reads were assembled into contigs using CLC Genomics Workbench 10.1.1 (RRID: SCR_011853, Qiagen). The contigs were compared with the National Center for Biotechnology Information nr database using BLASTX, and a contig with 99% identity to HPyV7 (GenBank NC_014407) was identified. Of a total of 1,567,812 sample reads, 17% (271,381) successfully mapped to the HPyV7 reference genome (Schowalter et al., 2010Schowalter R.M. Pastrana D.V. Pumphrey K.A. Moyer A.L. Buck C.B. Merkel cell polyomavirus and two previously unknown polyomaviruses are chronically shed from human skin.Cell Host Microbe. 2010; 7: 509-515Abstract Full Text Full Text PDF PubMed Scopus (429) Google Scholar). The complete consensus sequence of the HPyV7 of this patient was generated from this alignment and deposited to GenBank, receiving the accession number MG674199. Formalin-fixed, paraffin-embedded tissue sections were stained for tumor antigen, VP1, APOBEC3A and/or APOBEC3B, and MX1 as previously described (Kommagani et al., 2009Kommagani R. Leonard M.K. Lewis S. Romano R.A. Sinha S. Kadakia M.P. Regulation of VDR by deltaNp63alpha is associated with inhibition of cell invasion.J Cell Sci. 2009; 122: 2828-2835Crossref PubMed Scopus (31) Google Scholar; Leonard et al., 2011Leonard M.K. Kommagani R. Payal V. Mayo L.D. Shamma H.N. Kadakia M.P. ΔNp63α regulates keratinocyte proliferation by controlling PTEN expression and localization.Cell Death Differ. 2011; 18: 1924-1933Crossref PubMed Scopus (46) Google Scholar). mAbs 2t10, 6V32, and 10-87-13 were produced as reported previously (Pastrana et al., 2010Pastrana D.V. Pumphrey K.A. Cuburu N. Schowalter R.M. Buck C.B. Characterization of monoclonal antibodies specific for the Merkel cell polyomavirus capsid.Virology. 2010; 405: 20-25Crossref PubMed Scopus (16) Google Scholar; Leonard et al., 2015Leonard B. McCann J.L. Starrett G.J. Kosyakovsky L. Luengas E.M. Molan A.M. et al.The PKC/NF-κB signaling pathway induces APOBEC3B expression in multiple human cancers.Cancer Res. 2015; 75: 4538-4547Crossref PubMed Scopus (79) Google Scholar). The 2t10 antibody recognizes an epitope present in HPyV7 large tumor and small tumor antigens. The 6V32 antibody recognizes both HPyV6 and HPyV7 VP1. The 10-87-13 antibody was generated against APOBEC3B and cross reacts with APOBEC3A and APOBEC3G and was a generous gift from Dr Reuben Harris (also available from the National Institutes of Health acquired immunodeficiency syndrome reagent program [https://antibodyregistry.org/search.php?q=AB_2721202]). Anti-MX1 (ab95926) was purchased from Abcam (Catalog #, RRID:AB_10677452, Abcam Biotechnology company, Cambridge, United Kingdom). Antibodies were used at a 1:100 dilution (2t10 and 6V32), 1:200 dilution (ab95926), or 1:1,000 dilution (10-87-13) and incubated overnight at 4 oC. The secondary antibodies were anti-mouse Alexa Fluor-488 (Catalog #1858182, RRID: AB_2536161) and anti-rabbit Alexa Fluor-568 (Catalog #A11011, RRID: AB_143157) (ThermoFisher Scientific, Carlsbad, CA). Slides were imaged using a Zeiss A1 Fluorescent Microscope at ×20 magnification (Carl Zeiss AG, Oberkochem, Germany) and an AxioCam MRm with AxioVision Rel 4.8 software. The acquisition time for Supplementary Figure S1d tumor antigen images was FITC 300 ms. The acquisition time for Supplementary Figure S1d VP1 images was FITC 300 ms. The acquisition time for Figure 2b was Texas Red (TR) 150 ms. Acquisition times for Figure 2c VP1 images were DAPI 100 ms for before treatment and 75 ms for late treatment, FITC 750 ms, TR 150 ms. Acquisition times for Figure 2c tumor antigen images were DAPI 40 ms, FITC 300 ms, TR 600 ms. Skin swabs were collected after premoistening with yeast cell lysis buffer (MasterPure Yeast DNA Purification Kit, Epicentre, Madison, WI) and stored at −80 oC. Procedures for DNA extraction, library generation, and sequencing were performed as previously described (Oh et al., 2014Oh J. Byrd A.L. Deming C. Conlan S. NISC Comparative Sequencing Program Kong H.H. et al.Biogeography and individuality shape function in the human skin metagenome.Nature. 2014; 514: 59-64Crossref PubMed Scopus (538) Google Scholar). Samples were incubated in yeast cell lysis buffer and Ready lyse (Epicentre) for 30 minutes at 37 oC and then mechanically disrupted using 5 mm stainless steel beads (Qiagen) in a Tissuelyser (Qiagen) for 2 minutes, 30 Hz. Samples were incubated for 30 minutes at 65 oC and placed on ice for 5 minutes, and debris was spun down after treatment with MPC protein precipitation reagent. Samples were combined with 350 μl of 100% ethanol and column purified using the Invitrogen PureLink Genomic DNA. Finally, samples were eluted in 30 μl of water (Qiagen). Control swabs were collected at the time of sample collection after premoistening with yeast cell lysis buffer and were waved in the ambient environment without contacting the patient’s skin for a similar duration of time as experimental swabs. Control swabs also underwent the same DNA extraction processes and sequencing along with experimental samples, and no apparent contamination from either reagents or experimental procedures were observed. Nextera XT library kits were used to generate Illumina libraries per the manufacturer’s instructions. Libraries were sequenced on an Illumina HiSeq at the National Institutes of Health Intramural Sequencing Center to a target of 30–100 million clusters of 2 × 125 bp reads. In total, for three time points, we obtained 554 million total reads and 172 million of nonhuman, quality-filtered paired-end total reads (median 26 million reads per sample) compared with those of an effective negative control. To assess the abundance of each taxon within the metagenome, MetaPhlAn (RRID: SCR_004915), version 2.0, was used (Truong et al., 2015Truong D.T. Franzosa E.A. Tickle T.L. Scholz M. Weingart G. Pasolli E. et al.MetaPhlAn2 for enhanced metagenomic taxonomic profiling.Nat Methods. 2015; 12: 902-903Crossref PubMed Scopus (931) Google Scholar). The sequence data from this study have been submitted to the National Center for Biotechnology Information BioProject under accession number PRJNA556827. Skin biopsies were flash frozen on dry ice and stored at −80 °C. Qiazol (Qiagen N.V., Venlo, Netherlands) solution was added to frozen samples, and RNA extraction was performed using a Fastprep 24 bead-beating homogenizer (MPBio, Santa Ana, CA; Lysing Matrix D) and the RNeasy Minikit (Qiagen). Stranded paired-end libraries were generated from 1 μg total RNA using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) and sequenced on an Illumina HiSeq4000 (2 × 76 bp read length). Adapters were Integrated DNA Technologies (IDT, Coralville, IA) for Illumina - TruSeq RNA UD Indexes to eliminate index misassignment. Amplification was performed using 10 cycles, which was optimized for the input amount and to minimize overamplification. Libraries were pooled in equimolar amounts for sequencing. Sequencing was performed in two batches according to when the skin biopsy specimens were collected. In the first batch, more affected and less affected sites were biopsied, and two technical replicates of each were sequenced at an average of 45 million reads per technical replicate. For the second batch, a late-treatment biopsy specimen was collected and sequenced together with a third replicate of the original two biopsy specimens at an average read depth of 235 million reads. Alignment and quantification of count data were performed using MAGIC, version 2017.05.10, as previously described (LaPaglia et al., 2018LaPaglia D.M. Sapio M.R. Burbelo P.D. Thierry-Mieg J. Thierry-Mieg D. Raithel S.J. et al.RNA-seq investigations of human post-mortem trigeminal ganglia.Cephalalgia. 2018; 38: 912-932Crossref PubMed Scopus (44) Google Scholar). Expression levels were estimated by calculating significant fragments per kilobase per million aligned reads (Supplementary Table S1), a metric of expression calculated to correct for library and/or protocol biases (Zhang et al., 2015Zhang W. Yu Y. Hertwig F. Thierry-Mieg J. Zhang W. Thierry-Mieg D. et al.Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.Genome Biol. 2015; 16: 133Crossref PubMed Scopus (198) Google Scholar). Host RNA sequencing was displayed with heatmaps. The flame scale illustrates the range of expression ratios from 1.0 (yellow) to 0.0 (blue). To study viral gene expression, all RNA sequencing reads were aligned against a fusion reference containing the hg38 and HPyV7 (GenBank Accession #: NC_014407) reference genomes using STAR 2.5.3ab (RRID: SCR_015899) with the --chimSegmentMin 36 argument (Dobin et al., 2013Dobin A. Davis C.A. Schlesinger F. Drenkow J. Zaleski C. Jha S. et al.STAR: ultrafast universal RNA-seq aligner.Bioinformatics. 2013; 29: 15-21Crossref PubMed Scopus (15203) Google Scholar). Alignments and junctions were visualized using IGV (RRID: SCR_011793) (Robinson et al., 2011Robinson J.T. Thorvaldsdóttir H. Winckler W. Guttman M. Lander E.S. Getz G. et al.Integrative genomics viewer.Nat Biotechnol. 2011; 29: 24-26Crossre

Abstract The composition of the skin microbiome varies widely among individuals sampled at the same body site. A key question is which molecular factors determine strain-level variability within sub-ecosystems of the skin. We used a genomics-guided approach to identify an antibacterial biosynthetic gene cluster in Cutibacterium acnes (formerly Propionibacterium acnes ) that is widely distributed across individuals and skin sites. Experimental characterization of this cluster enabled the identification of a new thiopeptide antibiotic, cutimycin. Analysis of individual human skin hair follicles showed that cutimycin is an important factor regulating colonization resistance against Staphylococcus species. One Sentence Summary Cutimycin, a thiopeptide antibiotic produced by a widespread skin commensal, reduces Staphylococcus colonization of human follicles.

A conference entitled ‘Human microbiome science: Vision for the future’ was organized in Bethesda, MD from July 24 to 26, 2013. The event brought together experts in the field of human microbiome research and aimed at providing a comprehensive overview of the state of microbiome research, but more importantly to identify and discuss gaps, challenges and opportunities in this nascent field. This report summarizes the presentations but also describes what is needed for human microbiome research to move forward and deliver medical translational applications.

Atopic dermatitis (AD) is a common inflammatory skin disease characterized by pruritus and a chronic relapsing course with disease flares. Patients with AD commonly experience sleep disruption related to pruritus and may also experience depression and anxiety. In general, the burden of disease in AD is high and corresponds to disease severity. With AD’s prevalence and disease burden, extensive research has focused on understanding etiology and improving therapeutic management. The pathophysiology of AD is multifactorial and includes genetic susceptibility, skin barrier dysfunction, immunologic dysregulation, and environmental exposures. For example, mutations in the filaggrin gene (FLG), which encodes a protein produced by keratinocytes and contributes to the skin barrier, is associated with skin barrier disturbance and severe AD. In addition, deeper understanding of the immunologic abnormalities in AD have led to recent advances in treatment and management. Understanding AD pathophysiology is further complicated by disease heterogeneity, with subtypes continuing to be defined, and by the inherent complexities of microbiome studies.1Beck L.A. Boguniewicz M. Hata T. Schneider L.C. Hanifin J. Gallo R. et al.Phenotype of atopic dermatitis subjects with a history of eczema herpeticum.J Allergy Clin Immunol. 2009; 124 (269.e1-7): 260-269Abstract Full Text Full Text PDF PubMed Scopus (197) Google Scholar, 2Byrd A.L. Deming C. Cassidy S.K.B. Harrison O.J. Ng W.I. Conlan S. et al.Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis.Sci Transl Med. 2017; 9eaaI4651Crossref PubMed Scopus (276) Google Scholar, 3Chng K.R. Tay A.S.L. Li C. Ng A.H.Q. Wang J. Suri B.K. et al.Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare.Nat Microbiol. 2016; 116106Crossref PubMed Scopus (204) Google Scholar, 4Kong H.H. Oh J. State of residency: microbial strain diversity in the skin.J Invest Dermatol. 2021; 142: 1260-1264Abstract Full Text Full Text PDF PubMed Scopus (5) Google Scholar, 5Kong H.H. Oh J. Deming C. Conlan S. Grice E.A. Beatson M.A. et al.Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis.Genome Res. 2012; 22: 850-859Crossref PubMed Scopus (1075) Google Scholar, 6Tay A.S.L. Li C. Nandi T. Chng K.R. Andiappan A.K. Mettu V.S. et al.Atopic dermatitis microbiomes stratify into ecologic dermotypes enabling microbial virulence and disease severity.J Allergy Clin Immunol. 2021; 147: 1329-1340Abstract Full Text Full Text PDF PubMed Scopus (19) Google Scholar Another key characteristic of AD is microbial imbalance. For instance, patients with AD are susceptible to viral infections, including molluscum contagiosum and herpes simplex virus, and herpes simplex virus infections in AD can lead to severe sequelae, including vision-threatening ocular disease and, in 3% of patients, eczema herpeticum.1Beck L.A. Boguniewicz M. Hata T. Schneider L.C. Hanifin J. Gallo R. et al.Phenotype of atopic dermatitis subjects with a history of eczema herpeticum.J Allergy Clin Immunol. 2009; 124 (269.e1-7): 260-269Abstract Full Text Full Text PDF PubMed Scopus (197) Google Scholar More commonly, Staphylococcus aureus can be cultured in 80% to 100% of patients with AD. With the high frequency of S aureus colonization and infections in AD, treatments often include antimicrobial approaches (eg, topical and systemic antibiotics and dilute sodium hypochlorite baths). The link with S aureus and clinical improvement with antimicrobial approaches in some patients have led to interest in studying the potential contributions of S aureus to disease. Culturing methods can be challenging for some microbes and potentially bias against slow-growing species. Microbiome amplicon sequencing enables identification of the microbial composition within a clinical sample (eg, targeting bacterial 16S ribosomal RNA genes). Earlier amplicon sequencing studies in AD showed higher relative abundances of staphylococci during flared disease than after use of topical steroids or at baseline disease state.5Kong H.H. Oh J. Deming C. Conlan S. Grice E.A. Beatson M.A. et al.Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis.Genome Res. 2012; 22: 850-859Crossref PubMed Scopus (1075) Google Scholar Consistent with culture-based studies, most patients with AD had higher relative abundances of S aureus during disease flares and a smaller subset of patients with AD had higher relative abundances of Staphylococcus epidermidis.5Kong H.H. Oh J. Deming C. Conlan S. Grice E.A. Beatson M.A. et al.Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis.Genome Res. 2012; 22: 850-859Crossref PubMed Scopus (1075) Google Scholar Although sequencing specific regions of the 16S ribosomal RNA gene can help differentiate among staphylococcal species, taxonomic classification beyond the species level is important because of potential biologic differences.4Kong H.H. Oh J. State of residency: microbial strain diversity in the skin.J Invest Dermatol. 2021; 142: 1260-1264Abstract Full Text Full Text PDF PubMed Scopus (5) Google Scholar For example, limited S aureus strains carry the toxin genes responsible for clinical phenotypes of toxic shock syndrome or staphylococcal scalded skin syndrome. Shotgun metagenomics sequencing can permit identification of bacteria, fungi, and DNA viruses within a clinical sample as well as determination of strain-level differences and microbiome functional potential. Prior shotgun metagenomics studies investigating staphylococcal strains in patients with AD showed that the predominant S aureus strains were often clonal whereas S epidermidis strains were much more diverse.2Byrd A.L. Deming C. Cassidy S.K.B. Harrison O.J. Ng W.I. Conlan S. et al.Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis.Sci Transl Med. 2017; 9eaaI4651Crossref PubMed Scopus (276) Google Scholar,3Chng K.R. Tay A.S.L. Li C. Ng A.H.Q. Wang J. Suri B.K. et al.Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare.Nat Microbiol. 2016; 116106Crossref PubMed Scopus (204) Google Scholar In this issue of the Journal of Allergy and Clinical Immunology, Chia et al7Chia M. Naim A.N.M. Tay A.S.L. Lim K. Lee C.K. Yow S.J. et al.Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers.J Allergy Clin Immunol. 2022; 150: 894-908Abstract Full Text Full Text PDF Scopus (2) Google Scholar have built on their prior AD microbiome work to investigate skin microbiomes in children with AD and their healthy primary caregivers. Chia et al7Chia M. Naim A.N.M. Tay A.S.L. Lim K. Lee C.K. Yow S.J. et al.Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers.J Allergy Clin Immunol. 2022; 150: 894-908Abstract Full Text Full Text PDF Scopus (2) Google Scholar have used shotgun metagenomics and whole genome sequencing of cultivated S aureus isolates from pairs of Singaporean patients with AD and their caregivers (n = 30) and control-caregiver pairs (n = 30) to demonstrate that individuals from households containing 1 or more members with AD had skin microbiomes different from those in control households (Fig 1). Chia et al7Chia M. Naim A.N.M. Tay A.S.L. Lim K. Lee C.K. Yow S.J. et al.Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers.J Allergy Clin Immunol. 2022; 150: 894-908Abstract Full Text Full Text PDF Scopus (2) Google Scholar have examined the ratio of S aureus to Staphylococcus hominis, which distinguished households containing 1 or more members with AD from control households (area under the curve > 0.80; fair to good). Interestingly, the stronger correlation between severity based on Scoring Atopic Dermatitis (SCORAD) score and an S aureus–to S–hominis ratio in contrast to normalized relative abundances of S aureus raises the concept that looking beyond S aureus may be important in AD. Consistent with other human microbiome studies, in the study by Chia et al,7Chia M. Naim A.N.M. Tay A.S.L. Lim K. Lee C.K. Yow S.J. et al.Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers.J Allergy Clin Immunol. 2022; 150: 894-908Abstract Full Text Full Text PDF Scopus (2) Google Scholar members of the same household had similar skin microbiota. In comparison with other studies on S aureus culture–positive rates in patients with AD and in general population cohorts, S aureus culture positivity was relatively low in this cohort of patients with AD (55% [n = 10 of 18] of those with lesional skin and 57% [n = 17 of 30] of those with nonlesional skin) and relatively high for control households (40%). The low S aureus positivity in AD may be due to a focus on nonlesional skin; higher positivity in controls may suggest that the findings of the study by Chia et al7Chia M. Naim A.N.M. Tay A.S.L. Lim K. Lee C.K. Yow S.J. et al.Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers.J Allergy Clin Immunol. 2022; 150: 894-908Abstract Full Text Full Text PDF Scopus (2) Google Scholar are population-specific. A total of 55 high-quality genomes were obtained after sequencing, and paired isolates were limited to 6 pairs of patients with AD and their caregivers pairs and 5 control child-caregiver pairs. S aureus strains matched in 5 of 6 pairs of patients with AD and their caregivers and in 1 of 5 control child-caregiver pairs. In contrast to control household strains, the S aureus isolates from households containing 1 or more members with AD were enriched in genes encoding virulence factors, including enterotoxins Q (seq), K2, and K (sek). The study by Chia et al7Chia M. Naim A.N.M. Tay A.S.L. Lim K. Lee C.K. Yow S.J. et al.Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers.J Allergy Clin Immunol. 2022; 150: 894-908Abstract Full Text Full Text PDF Scopus (2) Google Scholar demonstrated that children with AD and their healthy primary caregivers shared more skin species and strains than in the controls. The case-control design with child-caregiver pairs was suited to address shared microbiota, but the low AD culture positivity rate limited the numbers of matched pairs for strain analyses, and combining swabs of different skin sites limited the ability to assess S aureus distribution. The skin sampling was well controlled, requiring at least 12 hours after bathing and additionally restricting use of topical steroids and medications, which would otherwise have resulted in lower S aureus culture rates. A limitation addressed by Chia et al7Chia M. Naim A.N.M. Tay A.S.L. Lim K. Lee C.K. Yow S.J. et al.Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers.J Allergy Clin Immunol. 2022; 150: 894-908Abstract Full Text Full Text PDF Scopus (2) Google Scholar is the cross-sectional study design. Longitudinal studies following the natural history of AD may have potentially increased the yield of cultured S aureus isolates and provided potential insights into the directionality of shared strains among household members. To address whether members of the same household have shared strains, shotgun metagenomics alone would have been insufficient owing to the combined challenges of small amounts of microbial DNA on skin and sequencing resolution limits. The integration of shotgun metagenomics and whole genome sequencing of bacterial isolates from the same individuals was critical for deeper strain-level analyses. Because S aureus is most frequently associated with AD, this study focused on this particular species. Given the prior culture-dependent and culture-independent studies that demonstrated a relative increase in S epidermidis in some AD disease exacerbations,2Byrd A.L. Deming C. Cassidy S.K.B. Harrison O.J. Ng W.I. Conlan S. et al.Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis.Sci Transl Med. 2017; 9eaaI4651Crossref PubMed Scopus (276) Google Scholar,5Kong H.H. Oh J. Deming C. Conlan S. Grice E.A. Beatson M.A. et al.Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis.Genome Res. 2012; 22: 850-859Crossref PubMed Scopus (1075) Google Scholar the role of S epidermidis in AD may also be of interest.8Cau L. Williams M.R. Butcher A.M. Nakatsuji T. Kavanaugh J.S. Cheng J.Y. et al.Staphylococcus epidermidis protease EcpA can be a deleterious component of the skin microbiome in atopic dermatitis.J Allergy Clin Immunol. 2021; 147: 955-966.e16Abstract Full Text Full Text PDF PubMed Scopus (43) Google Scholar An unresolved debate is whether S aureus contributes to the pathophysiology of AD or is a bystander that adheres particularly well to a disrupted skin barrier. Chia et al7Chia M. Naim A.N.M. Tay A.S.L. Lim K. Lee C.K. Yow S.J. et al.Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers.J Allergy Clin Immunol. 2022; 150: 894-908Abstract Full Text Full Text PDF Scopus (2) Google Scholar noted that S aureus on nonlesional skin suggests that microbial communities can precede clinical disease, yet healthy AD caregivers had similar microbiota highlighting the fact that nonmicrobial factors contribute to disease. Analyses of skin biopsy samples of nonlesional skin from patients with AD have described immunologic activation more similar to that in lesional skin than in control samples,9Esaki H. Brunner P.M. Renert-Yuval Y. Czarnowicki T. Huynh T. Tran G. et al.Early-onset pediatric atopic dermatitis is TH2 but also TH17 polarized in skin.J Allergy Clin Immunol. 2016; 138: 1639-1651Abstract Full Text Full Text PDF PubMed Scopus (229) Google Scholar indicating that normal-appearing skin may have subclinical abnormalities that in turn may result in S aureus colonization. This query is clinically relevant in that understanding the role of S aureus in AD directly affects therapeutic approaches as well as the use of antimicrobial treatments and decolonization strategies. Although systematic reviews have not found strong evidence for antistaphylococcal methods in managing AD,10George S.M. Karanovic S. Harrison D.A. Rani A. Birnie A.J. Bath-Hextall F.J. et al.Interventions to reduce Staphylococcus aureus in the management of eczema. 2019. Cochrane Database Syst Rev, 2019Google Scholar the research into subtypes of AD may indicate that in certain patients, antimicrobial approaches may be effective. The study by Chia et al7Chia M. Naim A.N.M. Tay A.S.L. Lim K. Lee C.K. Yow S.J. et al.Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers.J Allergy Clin Immunol. 2022; 150: 894-908Abstract Full Text Full Text PDF Scopus (2) Google Scholar highlights the fact that primary caregivers can share S aureus strains with patients with AD, raising the possibility that caregiver sharing could confound effective antimicrobial therapies in AD. Additional investigations are needed to more deeply assess clinical outcomes of carriage and decolonization. As researchers continue to disentangle the role of staphylococci in AD and potential disease subtypes and determine how findings can inform clinical medicine, it is likely that clinicians will continue to incorporate common antimicrobial and/or decolonization approaches when faced with the driving need to alleviate the burden of disease in patients with AD. Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregiversJournal of Allergy and Clinical ImmunologyVol. 150Issue 4PreviewAtopic dermatitis (AD) is a common chronic skin condition in children (15-20%) that can significantly impair their quality of life. As a result of its relapsing nature and enrichment of Staphylococcus aureus during flares, clinical management can include eradicating S aureus from the skin of children; however, this does not extend to their healthy caregivers, who are potential reservoirs. Full-Text PDF

Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents. Here we used ultra-deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who were part of the VITALITY trial in Australia as well as 67 maternally-matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9,194 bacterial genomes from 1,029 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 25%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also found evidence for vertical transmission at the microbial community, individual skin bacterial species and strain levels between mothers and infants. Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and transmission in early life.

Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. Based on the prevalence of these species, at least two likely coexist in the nasal microbiota of 82% of adults. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the functional protein repertoire and metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the U.S. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution across Africa and North America. All four species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent (core) compared to the accessory genome of each species indicating limited strain-level variability in metabolic capacity. Moreover, core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in the Botswanan clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.

Corynebacterium is a predominant genus in the skin microbiome, yet its genetic diversity on skin is incompletely characterized and lacks a comprehensive set of reference genomes. Our work aims to investigate the distribution of Corynebacterium species on the skin, as well as to expand the existing genome reference catalog to enable more complete characterization of skin metagenomes. We used V1-V3 16S rRNA gene sequencing data from 14 body sites of 23 healthy volunteers to characterize Corynebacterium diversity and distribution across healthy human skin. Corynebacterium tuberculostearicum is the predominant species found on human skin and we identified two distinct C. tuberculostearicum ribotypes (A & B) that can be distinguished by variation in the 16S rRNA V1-V3 sequence. One is distributed across all body sites and the other found primarily on the feet. We performed whole genome sequencing of 40 C. tuberculostearicum isolates cultured from the skin of five healthy individuals across seven skin sites. We generated five closed genomes of diverse C. tuberculostearicum which revealed that C. tuberculostearicum isolates are largely syntenic and carry a diversity of methylation patterns, plasmids and CRISPR/Cas systems. The pangenome of C. tuberculostearicum is open with a core genome size of 1806 genes and a pangenome size of 5451 total genes. This expanded pangenome enabled the mapping of 24% more C. tuberculostearicum reads from shotgun metagenomic datasets derived from skin body sites. Finally, while the genomes from this study all fall within a C. tuberculostearicum species complex, the ribotype B isolates may constitute a new species.

The major histocompatibility complex class II-associated invariant chain is a molecule involved in antigen presentation, specifically in the context of T cells, which are effector cells of adaptive immunity. CD74 is a protein that reacts with MHC class II molecules and functions to transmit signals into cells by interacting with macrophage migration inhibitory factor. Red sea bream is one of the major marine aquaculture fish in Korea. Many studies on breeding but molecular studies are markedly lacking. In this study, CD74b was isolated from red sea bream (Pagrus major) and phylogenetic analysis, tissue expression and expression analysis through pathogen artificial infection were performed. As a result, it showed high expression in gills, brain and intestine. In addition, when analyzing Edwardsiella piscicida, Streptococcus iniae, and red sea bream iridovirus, it was confirmed that CD74b has an immune response function. This study characterizes CD74b may play an important role in the immune response of red sea bream following pathogenic infections.