Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses

Dermatologic presentations of hyper IgE syndrome in pediatric patients

BACKGROUND

Hyper-IgE Syndrome, also known as Job's syndrome, is a rare primary immunodeficiency disorder characterized by recurrent infections and elevated levels of immunoglobulin E. While respiratory and systemic manifestations have been more emphasized, dermatological manifestations in Hyper-IgE Syndrome also play a significant role in disease presentation.

METHODS

This narrative review explores the dermatologic presentations of Hyper-IgE Syndrome in pediatric populations, including descriptions, associated symptoms/findings, and available treatment options.

RESULTS AND CONCLUSION

Neonatal rash, mucocutaneous candidiasis, noma neonatorum, psoriasis, cold staphylococcal abscesses, and candida onychomycosis are among the dermatological manifestations of Hyper-IgE Syndrome. Each manifestation has unique characteristics and treatment considerations, necessitating accurate recognition and diagnosis for effective management. Optimal treatment strategies involve a combination of supportive care, topical/systemic therapies, antifungal medications, and surgical interventions when necessary. Further research is needed to enhance our understanding of these manifestations and evaluate treatment modalities for individuals affected by Hyper-IgE Syndrome.

Hyper IgE Syndrome: Bridging the Gap Between Immunodeficiency, Atopy, and Allergic Diseases

PURPOSE OF REVIEW

It seeks to answer key questions about the molecular and cellular mechanisms underlying Hyper IgE Syndrome (HIES), the genetic mutations responsible, and their contributions to both immunodeficiency and allergic manifestations. Additionally, it aims to explore diagnostic strategies and therapeutic approaches that address these overlapping domains, thereby improving disease management.

RECENT FINDINGS

Recent research has identified several pivotal genetic mutations, including those in STAT3, DOCK8, and PGM3, which play critical roles in disrupting immune pathways such as Th17 differentiation and IgE regulation. These molecular defects have been linked to the hallmark features of HIES, including recurrent infections and elevated serum IgE levels, as well as its overlap with atopic conditions like eczema, asthma, and food allergies. Advances in diagnostic tools, such as biomarker identification and genetic testing, have improved the differentiation of HIES from more common atopic disorders. Therapeutic advancements, including the use of targeted biologics and interventions addressing both immunodeficiency and allergic symptoms, have shown promise in enhancing patient outcomes. This review highlights the role of specific genetic mutations in shaping the clinical and immunological phenotype of HIES. Key takeaways include the necessity of integrating molecular insights with clinical observations for accurate diagnosis and the potential of emerging targeted therapies to address both immunological and allergic aspects of the syndrome.

Alterations in the Skin Microbiome in Dermatologic Diseases and with External Exposures: CME Part 2

In Part I of our CME we reviewed the skin microbiome in healthy individuals. Part II reviews the evolving understanding of alterations in the skin microbiome in specific human diseases. We also discuss how the skin microbiome can change with environmental exposures and medications such as antibiotics as well as ongoing research on microbiome-based interventions.

The Human Skin Microbiome in Health: CME Part 1

Human skin is home to a myriad of microorganisms, including bacteria, viruses, fungi, and mites, many of which are considered commensal microbes that aid in maintaining the overall homeostasis or steady-state condition of the skin and contribute to skin health. Our understanding of the complexities of the skin's interaction with its microorganisms is evolving. This knowledge is based primarily on in vitro and animal studies, and more work is needed to understand how this knowledge relates to humans. Here, we introduce the concept of the skin microbiome and discuss skin microbial ecology, some intrinsic factors with potential influence on the human skin microbiome, and possible microbiome-host interactions. The second article of this two-part CME series describes how microbiome alterations may be associated with skin disease, how medications can affect the microbiome, and what microbiome-based therapies are under investigation.

Advancing precision rheumatology: applications of machine learning for rheumatoid arthritis management

Rheumatoid arthritis (RA) is an autoimmune disease causing progressive joint damage. Early diagnosis and treatment is critical, but remains challenging due to RA complexity and heterogeneity. Machine learning (ML) techniques may enhance RA management by identifying patterns within multidimensional biomedical data to improve classification, diagnosis, and treatment predictions. In this review, we summarize the applications of ML for RA management. Emerging studies or applications have developed diagnostic and predictive models for RA that utilize a variety of data modalities, including electronic health records, imaging, and multi-omics data. High-performance supervised learning models have demonstrated an Area Under the Curve (AUC) exceeding 0.85, which is used for identifying RA patients and predicting treatment responses. Unsupervised learning has revealed potential RA subtypes. Ongoing research is integrating multimodal data with deep learning to further improve performance. However, key challenges remain regarding model overfitting, generalizability, validation in clinical settings, and interpretability. Small sample sizes and lack of diverse population testing risks overestimating model performance. Prospective studies evaluating real-world clinical utility are lacking. Enhancing model interpretability is critical for clinician acceptance. In summary, while ML shows promise for transforming RA management through earlier diagnosis and optimized treatment, larger scale multisite data, prospective clinical validation of interpretable models, and testing across diverse populations is still needed. As these gaps are addressed, ML may pave the way towards precision medicine in RA.

The yeast-human coevolution: Fungal transition from passengers, colonizers, and invaders

Fungi are the cause of more than a billion infections in humans every year, although their interactions with the host are still neglected compared to bacteria. Major systemic fungal infections are very unusual in the healthy population, due to the long history of coevolution with the human host. Humans are routinely exposed to environmental fungi and can host a commensal mycobiota, which is increasingly considered as a key player in health and disease. Here, we review the current knowledge on host-fungi coevolution and the factors that regulate their interaction. On one hand, fungi have learned to survive and inhabit the host organisms as a natural ecosystem, on the other hand, the host immune system finely tunes the response toward fungi. In turn, recognition of fungi as commensals or pathogens regulates the host immune balance in health and disease. In the human gut ecosystem, yeasts provide a fingerprint of the transient microbiota. Their status as passengers or colonizers is related to the integrity of the gut barrier and the risk of multiple disorders. Thus, the study of this less known component of the microbiota could unravel the rules of the transition from passengers to colonizers and invaders, as well as their dependence on the innate component of the host's immune response. This article is categorized under: Infectious Diseases > Environmental Factors Immune System Diseases > Environmental Factors Infectious Diseases > Molecular and Cellular Physiology.

Genomic characterization of the C. tuberculostearicum species complex, a prominent member of the human skin microbiome

IMPORTANCE

Amplicon sequencing data combined with isolate whole genome sequencing have expanded our understanding of Corynebacterium on the skin. Healthy human skin is colonized by a diverse collection of Corynebacterium species, but Corynebacterium tuberculostearicum predominates on many skin sites. Our work supports the emerging idea that C. tuberculostearicum is a species complex encompassing several distinct species. We produced a collection of genomes that help define this complex, including a potentially new species we term Corynebacterium hallux based on a preference for sites on the feet, whole-genome average nucleotide identity, pangenomic analysis, and growth in skin-like media. This isolate collection and high-quality genome resource set the stage for developing engineered strains for both basic and translational clinical studies.

The Impact of Stress, Microbial Dysbiosis, and Inflammation on Necrotizing Enterocolitis

Necrotizing enterocolitis (NEC) is the leading cause of intestinal morbidity and mortality in neonates. A large body of work exists; however, the pathogenesis of NEC remains poorly understood. Numerous predictors have been implicated in the development of NEC, with relatively less emphasis on maternal factors. Utilizing human tissue plays a crucial role in enhancing our comprehension of the underlying mechanisms accountable for this devastating disease. In this review, we will discuss how maternal stress affects the pathogenesis of NEC and how changes in the intestinal microbiome can influence the development of NEC. We will also discuss the results of transcriptomics-based studies and analyze the gene expression changes in NEC tissues and other molecular targets associated with the pathogenesis of NEC.

Dysbiosis and primary B-cell immunodeficiencies: current knowledge and future perspective

According to Elie Metchnikoff, an originator of modern immunology, several pivotal functions for disease and health are provided by indigenous microbiota. Nonetheless, important mechanistic insights have been elucidated more recently, owing to the growing availability of DNA sequencing technology. There are 10 to 100 trillion symbiotic microbes (such as viruses, bacteria, and yeast) in each human gut microbiota. Both locally and systemically, the gut microbiota has been demonstrated to impact immune homeostasis. Primary B-cell immunodeficiencies (PBIDs) are a group of primary immunodeficiency diseases (PIDs) referring to the dysregulated antibody production due to either intrinsic genetic defects or failures in functions of B cells. Recent studies have found that PBIDs cause disruptions in the gut's typical homeostatic systems, resulting in inadequate immune surveillance in the gastrointestinal (GI) tract, which is linked to increased dysbiosis, which is characterized by a disruption in the microbial homeostasis. This study aimed to review the published articles in this field to provide a comprehensive view of the existing knowledge about the crosstalk between the gut microbiome and PBID, the factors shaping the gut microbiota in PBID, as well as the potential clinical approaches for restoring a normal microbial community.

Quorum sensing gene regulation in Staphylococcus epidermidis reduces the attraction of Aedes aegypti (L.) (Diptera: Culicidae)

Introduction

Identifying mechanisms regulating mosquito attraction to hosts is key to suppressing pathogen transmission. Historically, the ecology of the host microbial community and its influence on mosquito attraction, specifically, whether bacterial communication through quorum sensing (QS) modulates VOC production that affects mosquito behavior have not been extensively considered.

Methods

Behavioral choice assays were applied along with volatile collection, followed by GC-MS and RNA transcriptome analyses of bacteria with and without a quorum-sensing inhibitor, furanone C-30.

Results

Utilizing the quorum-sensing inhibitor on a skin-inhabiting bacterium, Staphylococcus epidermidis, we disrupted its interkingdom communication with adult Aedes aegypti and mitigated their attraction to a blood-meal by 55.1%.

Discussion

One potential mechanism suppressing mosquito attraction could be the reduction (31.6% in our study) of bacterial volatiles and their associated concentrations by shifting S. epidermidis metabolic (12 of 29 up regulated genes) and stress (5 of 36 down regulated genes) responses. Manipulating the quorum-sensing pathways could serve as a mechanism to reduce mosquito attraction to a host. Such manipulations could be developed into novel control methods for pathogen-transmitting mosquitoes and other arthropods.

Genomic characterization of the C. tuberculostearicum species complex, a ubiquitous member of the human skin microbiome

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.

Human skin bacterial microbiota homeostasis: A delicate balance between health and disease

As the largest organ of the body, the skin acts as a barrier to prevent diseases and harbors a variety of beneficial bacteria. Furthermore, the skin bacterial microbiota plays a vital role in health and disease. Disruption of the barrier or an imbalance between symbionts and pathogens can lead to skin disorders or even systemic diseases. In this review, we first provide an overview of research on skin bacterial microbiota and human health, including the composition of skin bacteria in a healthy state, as well as skin bacterial microbiota educating the immune system and preventing the invasion of pathogens. We then discuss the diseases that result from skin microbial dysbiosis, including atopic dermatitis, common acne, chronic wounds, psoriasis, viral transmission, cutaneous lupus, cutaneous lymphoma, and hidradenitis suppurativa. Finally, we highlight the progress that utilizes skin microorganisms for disease therapeutics, such as bacteriotherapy and skin microbiome transplantation. A deeper knowledge of the interaction between human health and disease and the homeostasis of the skin bacterial microbiota will lead to new insights and strategies for exploiting skin bacteria as a novel therapeutic target.

Primary Invasive Cutaneous Fusariosis in Patients with STAT3 Hyper-IgE Syndrome

Dominant negative (DN) mutations in signal transducer and activator of transcription 3 (STAT3) are known to cause hyper-IgE syndrome, a rare primary immunodeficiency. STAT3 DN patients are prone to develop fungal infections, including chronic mucocutaneous candidiasis due to impaired IL-17-mediated immunity, and pulmonary aspergillosis. Despite having preserved phagocyte functions, STAT3 DN patients present connective tissue abnormalities and a defect in the immunological skin barrier. Fusarium species are ubiquitous molds, whose potential to infect humans depends on the host's innate and cellular immune status. Our aim was to describe four STAT3 DN patients with fusariosis confined to the skin. Medical records were reviewed and summarized. Four patients, aged 4, 11, 30, and 33 years, presented with chronic skin lesions which started in the extremities. Two patients had remote lesions, and none had systemic involvement. Skin biopsies showed mycelial threads with deep inflammatory-occasionally granulomatous-infiltrates, reaching the dermis; cultures grew Fusarium solani. Response to treatment was heterogeneous, often requiring multimodal therapies, including topical antifungal preparations. In this work, we describe primary invasive cutaneous fusariosis as a syndromic entity in four STAT3 DN patients.

Sodium hyaluronates applied in the face affects the diversity of skin microbiota in healthy people

OBJECTIVE

A healthy and stable microbiome has many beneficial effects on the host, while an unbalanced or disordered microbiome can lead to various skin diseases. Hyaluronic acid is widely used in the cosmetics and pharmaceutical industries; however, specific reports on its effect on the skin microflora of healthy people have not been published. This study aimed to determine the effect of sodium hyaluronate on the facial microflora of healthy individuals.

METHODS

Face of 20 healthy female volunteers between 18 and 24 years was smeared with sodium hyaluronate solution once per day. Cotton swabs were used to retrieve samples on days 0, 14, and 28, and high-throughput sequencing of 16 S rRNA was used to determine the changes in bacterial community composition.

RESULTS

Facial application of HA can reduce the abundance of pathogenic bacteria, such as Cutibacterium and S. aureus, and increase the colonization of beneficial bacteria.

CONCLUSION

This is the first intuitive report to demonstrate the effect of hyaluronic acid on facial microflora in healthy people. Accordingly, sodium hyaluronate was found to have a positive effect on facial skin health.

Ophidiomyces ophidiicola detection and infection: a global review on a potential threat to the world’s snake populations

Ophidiomyces ophidiicola (Oo) is one of the most relevant fungal pathogens for snakes. It is the etiological agent of ophidiomycosis, an emerging disease causing dysecdysis, skin abnormalities, crusting cutaneous lesions, and ulcerations. Despite this major tegumentary “tropism”, Oo infection can be systemic and it is capable of inducing visceral lesions. Moreover, ophidiomycosis may lead to abnormalities of reproductive physiology, hunting behavior, and thermoregulation, thus increasing the risks of sublethal effects and predation on affected snakes. Oo seems horizontally transmitted and can induce postnatal mortality. This article reviews published data on Oo detection and infection in all snake species in countries around the world and categorizes these data using new classification parameters. The presence of this fungus has been recorded in 11 states (considering the USA as a whole); however, in four states, the mycosis has only been reported in snakes held in captivity. Detection and/or infection of Oo has been ascertained in 62 snake species, divided into nine families. The taxa have been categorized with diagnostic criteria in order to report, for each species, the highest rank of categorization resulting from all cases. Therefore, 20 species have been included within the class “Ophidiomycosis and Oo shedder”, 11 within “Ophidiomycosis”, 16 in “Apparent ophidiomycosis”, and 15 within “Ophidiomyces ophidiicola present”. We also discuss the significance and limits of case classifications and Oo’s impact on wild populations, and we suggest methods for preliminary surveillance. Standardized methods, interdisciplinary studies, and cooperation between various research institutions may facilitate further Oo screening studies, elucidate the unclear aspects of the disease, and protect ophidiofauna from this emerging threat at the global level.

Inborn errors of immunity and related microbiome

Inborn errors of immunity (IEI) are characterized by diverse clinical manifestations that are dominated by atypical, recurrent, chronic, or severe infectious or non-infectious features, including autoimmunity, lymphoproliferative disease, granulomas, and/or malignancy, which contribute substantially to morbidity and mortality. Some data suggest a correlation between clinical manifestations of IEI and altered gut microbiota. Many IEI display microbial dysbiosis resulting from the proliferation of pro-inflammatory bacteria or a decrease in anti-inflammatory bacteria with variations in the composition and function of numerous microbiota. Dysbiosis is considered more established, mainly within common variable immunodeficiency, selective immunoglobulin A deficiency, severe combined immunodeficiency diseases, Wiskott–Aldrich syndrome, Hyper-IgE syndrome, autoimmune polyendocrinopathy–candidiasis–ectodermal-dystrophy (APECED), immune dysregulation, polyendocrinopathy, enteropathy X-linked (IPEX) syndrome, IL-10 receptor deficiency, chronic granulomatous disease, and Kostmann disease. For certain IEIs, the specific predominance of gastrointestinal, respiratory, and cutaneous involvement, which is frequently associated with dysbiosis, justifies the interest for microbiome identification. With the better understanding of the relationship between gut microbiota, host immunity, and infectious diseases, the integration of microbiota modulation as a therapeutic approach or a preventive measure of infection becomes increasingly relevant. Thus, a promising strategy is to develop optimized prebiotics, probiotics, postbiotics, and fecal microbial transplantation to rebalance the intestinal microbiota and thereby attenuate the disease activity of many IEIs.

Characterization of the Skin Bacteriome and Histology Changes in Diabetic Pigs

Chronic wound is one of the most common complications that are associated with diabetes. The cutaneous microbiome is known to play essential roles in the regulation of barrier function and protecting against potential assault. Thus, it is necessary to gain a better understanding of the relationship between microbial community and skin structures in unwounded diabetic skin to explore possible preventive strategies. To achieve the same, a pig diabetic model was built in the present study. Further,16S rDNA sequencing was used to characterize the skin bacteriome. It was observed that the pigs showed skin bacteriome similar to humans in the non-diabetes group, while it varied in the case of diabetes. Further, the β-diversity analysis showed that the bacterial community was significantly different under the diabetes group. More species differences were identified between the two groups at genus level. The predictive function analysis also showed the involvement of significantly different pathways of microbial gene function in diabetes. In agreement with this, skin histology analysis also showed signs of reduced epidermal thickness and rete ridges in diabetic skin. Less proliferation of keratinocytes and impaired TJ barrier was also detected. This evidence suggested that pigs might serve as the best surrogate for cutaneous microbiome studies. Altogether, the present study reported that the skin bacteriome and histology changed significantly in unwounded diabetic skin, which provided a theoretical basis for the regulation of disordered skin bacteriome. The findings of the study would assist in the improvement of the skin environment and prevention of skin infection and chronic wounds.

The Oral Microbiota: Community Composition, Influencing Factors, Pathogenesis, and Interventions

The human oral cavity provides a habitat for oral microbial communities. The complexity of its anatomical structure, its connectivity to the outside, and its moist environment contribute to the complexity and ecological site specificity of the microbiome colonized therein. Complex endogenous and exogenous factors affect the occurrence and development of the oral microbiota, and maintain it in a dynamic balance. The dysbiotic state, in which the microbial composition is altered and the microecological balance between host and microorganisms is disturbed, can lead to oral and even systemic diseases. In this review, we discuss the current research on the composition of the oral microbiota, the factors influencing it, and its relationships with common oral diseases. We focus on the specificity of the microbiota at different niches in the oral cavity, the communities of the oral microbiome, the mycobiome, and the virome within oral biofilms, and interventions targeting oral pathogens associated with disease. With these data, we aim to extend our understanding of oral microorganisms and provide new ideas for the clinical management of infectious oral diseases.

Habitats Show More Impacts Than Host Species in Shaping Gut Microbiota of Sympatric Rodent Species in a Fragmented Forest

Gut microbiota play a significant role for animals to adapt to the changing environment. Host species and habitats are key drivers in shaping the diversity and composition of the microbiota, but the determinants of composition of the sympatric host gut microbiome remain poorly understood within an ecosystem. In this study, we examined the effects of habitats of different succession stages and host species on the diversity and composition of fecal gut microbiota in four sympatric rodent species (Apodemus draco, Leopoldamys edwardsi, Niviventer confucianus, and Niviventer fulvescens) in a subtropical forest. We found, as compared to the differences between species, habitat types showed a much larger effect on the gut microbiota of rodents. Alpha diversity of the microbial community of A. draco, N. fulvescens, and N. confucianus was highest in farmland, followed by primary forest and shrubland, and lowest in secondary forest. Beta diversity of the three rodent species showed significant different among habitats. The alpha diversity of gut microbiota of L. edwardsi was significantly higher than those of A. draco and N. confucianus, and its beta diversity showed significant difference from A. draco. Our results suggested that gut microbiota were important for animals in responding to diet changes in different habitats under human disturbances.

Patients with senile pruritus have a distinct skin microbiota and epidermal barrier in comparison with healthy controls

Senile pruritus (SP) is a common skin disease in the elderly. The role of skin dysbacteriosis in the development of various skin diseases has been studied in recent years. However, the research about the skin microbiota of senile pruritus patients is lacking at present. The purpose of this cross-sectional study was to investigate the differences of skin microbiota in senile pruritus patients and their relationship with the epidermal barrier. Thirty patients with senile pruritus and 30 age- and sex-matched healthy controls were enrolled in this study. The skin barrier indexes were recorded by multi-functional skin tester. The skin bacterial diversity was analyzed by using hyper-variable tag sequencing of the V3-V4 region of the 16S rDNA. Compared with the healthy control group, the patients had significantly lower skin hydration (p = 0.014) and higher pH value (p = 0.021). Skin microbial diversity was significantly increased in patients according to the alpha diversity. At the genus level, Acinetobacter (p = 0.002) and Lactobacillus (p = 0.002) increased and Cutibacterium (p = 0.043) decreased. The pH value was positively associated with observed_species diversity (p = 0.026). The transdermal water loss was negatively related to the genus of Lactobacillus (p = 0.036), while the skin hydration was positively associated with the genus of Lactobacillus (p = 0.038). As a result, the damaged skin barrier function and skin dysbacteriosis complemented each other and may be associated with the occurrence of senile pruritus, but their role still needs further study.

The ocular microbiome and microbiota and their effects on ocular surface pathophysiology and disorders

The ocular surface flora perform an important role in the defense mechanisms of the ocular surface system. Its regulation of the immunological activity and the barrier effect against pathogen invasion are remarkable. Composition of the flora differs according to the methods of investigation, because the microbiome, composed of the genetic material of bacteria, fungi, viruses, protozoa, and eukaryotes on the ocular surface, differs from the microbiota, which are the community of microorganisms that colonize the ocular surface. The observed composition of the ocular surface flora depends on harvesting and examining methods, whether with traditional culture or with more refined genetic analysis based on rRNA and DNA sequencing. Environment, diet, sex, and age influence the microbial flora composition, thus complicating the analysis of the baseline status. Moreover, potentially pathogenic organisms can affect its composition, as do various disorders, including chronic inflammation, and therapies applied to the ocular surface. A better understanding of the composition and function of microbial communities at the ocular surface could bring new insights and clarify the epidemiology and pathology of ocular surface dynamics in health and disease. The purpose of this review is to provide an up-to-date overview of knowledge about this topic.

Investigation of Age-Related Changes in the Skin Microbiota of Korean Women

The microbiota of human skin is influenced by host and environmental factors. To determine if chronological age influences the composition of the skin microbiota on the forehead and hands, 73 Korean women were sorted into one of three age groups: (1) 10-29 years (n = 24), (2) 30-49 years (n = 21), and (3) 50-79 years (n = 28). From the 73 women, 146 skin samples (two skin sites per person) were collected. 16S rRNA gene amplicon sequencing was then conducted to analyze the skin microbiota. The overall microbial distribution varied on the forehead but was similar on the hands across the three age groups. In addition, the composition of the skin microbiota differed between the forehead and hands. Commensal microbiota, such as Streptococcus, Staphylococcus, Cutibacterium, and Corynebacterium, which contribute to maintaining skin health via dominant occupation, were affected by increasing age on forehead and hand skin. Alpha diversity indices increased significantly with age on forehead skin. This study indicates that older people may be more susceptible to pathogenic invasions due to an imbalanced skin microbiota resulting from age-related changes. The results of our study may help develop new strategies to rebalance skin microbiota shifted during aging.

[Microbiology of chronic rhinosinusitis with different clinical phenotypes]

Objective:To observe the microbiological characteristics and clinical correlation of chronic rhinosinusitis with different clinical phenotypes. Method:One hundred and ninety-six patients with chronic rhinosinusitis（CRS） underwent nasal endoscopic surgery, including 126 patients with Chronic rhinosinusitis with nasal polyps（CRSwNP） and 70 patients with chronic rhinosinusitis without nasal polyps（CRSsNP）; 78 patients with nasal septum deviation（control group） were enrolled. The nasal discharge samples were collected before operation, and the bacteria were isolated and identified by the traditional culture method. The bacteria were compared between the two groups by Pearson chi-square test or Fisher exact test, and the bacteria were compared between groups by Kruskal-Wallis rank sum test. Out statistically significant variables（P<0.05）. Result:The total bacterial detection rate was 73.0% in the three groups, 76.2% in the CRSwNP group, 68.6% in the CRSsNP group and 71.8% in the control group, respectively（P=0.579）. The detection rate of the bacteria was mainly Gram-positive bacteria. The higher detection rate included: Staphylococcus epidermidis, Pseudodiphtheria, Staphylococcus aureus, Haemophilus influenzaemola, Haemella influenzaemola. The detection rate of Haemophilus influenzae in the CRSwNP group and the control group（13.5% vs 2.6%, P=0.009）, but there were statistical differences CRSsNP.There was no statistically significant difference in the detection rate of the bacteria（8.6% vs 2.6%, P=0.15） between the CRSsNP group and the control group; The difference of staphylococcus aureus detection rate between NonECRSwNP group and ECRSwNP group was statistically significant （9.6% vs 28.1%,P=0.017）.There was no significant difference in staphylococcus aureus detection rate between NonECRSsNP group and ECRSsNP group （9.4% vs 16.7%, P=0.482）. Conclusion:Haemophilus influenzae may be a potential cause of CRSwNP; S. aureus may promote the eosinophilic granulocyte inflammatory response to CRSwNP.

Factors causing oral and skin pathological features in the hyperimmunoglobulin E syndrome patient including the environmental component: a review of the literature and own experience

The hyperimmunoglobulin E syndrome (HIES) is a rare multi-system disease with non-immunological as well as immunological abnormalities. The syndrome is characterized by a triad of the most distinctive symptoms, such as pneumonia with pneumatocele formation, recurring staphylococcal skin abscesses and a high serum concentration of IgE. Central mediators of immune responses such as STAT1 and STAT3 affect immune responses and contribute to changes of the skin microbiome which subsequently can amplify the defective immune response against microbial and fungal pathogens. Reactions related to an environmental factor, such as sun-induced skin changes, in individuals during long-term medication therapy have also been reported. The dermatological symptoms, oral status and other health problems of a hyperimmunoglobulin E syndrome paediatric patient are presented. HIES is of great importance to different professionals because sufferers require special preventive and therapeutic management from early infancy in order to avoid complications which can even prove to be life-saving for such patients.

Intestinal dysbiosis in pediatric Crohn's disease patients with IL10RA mutations

BACKGROUND

Several studies have employed animal models to explore the association between microbiota and interleukin (IL) 10 signaling; however, limited information is available about the human microbiome.

AIM

To characterize the microbiome in patients with IL10RA mutations and to explore the association between gut dysbiosis and disease severity.

METHODS

Fecal samples were collected from patients who were diagnosed with loss-of-function mutations in the IL10RA gene between January 2017 and July 2018 at the Children's Hospital of Fudan University. Age-matched volunteer children were recruited as healthy controls. Patients with Crohn's disease (CD) were used as disease controls to standardize the antibiotic exposure. Microbial DNA was extracted from the fecal samples. All analyses were based on the 16S rRNA gene sequencing data.

RESULTS

Seventeen patients with IL10RA mutations (IL10RA group), 17 patients with pediatric CD, and 26 healthy children were included. Both patients with IL10RA mutations and those with CD exhibited a reduced diversity of gut microbiome with increased variability. The relative abundance of Firmicutes was substantially increased in the IL10RA group (P = 0.02). On further comparison of the relative abundance of taxa between patients with IL10RA mutations and healthy children, 13 taxa showed significant differences. The IL10RA-specific dysbiosis indices exhibited a significant positive correlation with weighted pediatric CD activity index and simple endoscopic score for CD.

CONCLUSION

In patients with IL10RA mutations and early onset inflammatory bowel disease, gut dysbiosis shows a moderate association with disease severity.

Temporal shifts in the mycobiome structure and network architecture associated with a rat (Rattus norvegicus) deep partial-thickness cutaneous burn

With a diverse physiological interface to colonize, mammalian skin is the first line of defense against pathogen invasion and harbors a consortium of microbes integral in maintenance of epithelial barrier function and disease prevention. While the dynamic roles of skin bacterial residents are expansively studied, contributions of fungal constituents, the mycobiome, are largely overlooked. As a result, their influence during skin injury, such as disruption of skin integrity in burn injury and impairment of host immune defense system, is not clearly delineated. Burn patients experience a high risk of developing hard-to-treat fungal infections in comparison to other hospitalized patients. To discern the changes in the mycobiome profile and network assembly during cutaneous burn-injury, a rat scald burn model was used to survey the mycobiome in healthy (n = 30) (sham-burned) and burned (n = 24) skin over an 11-day period. The healthy skin demonstrated inter-animal heterogeneity over time, while the burned skin mycobiome transitioned toward a temporally stabile community with declining inter-animal variation starting at day 3 post-burn injury. Driven primarily by a significant increase in relative abundance of Candida, fungal species richness and abundance of the burned skin decreased, especially in days 7 and 11 post-burn. The network architecture of rat skin mycobiome displayed community reorganization toward increased network fragility and decreased stability compared to the healthy rat skin fungal network. This study provides the first account of the dynamic diversity observed in the rat skin mycobiome composition, structure, and network assembly associated with postcutaneous burn injury.

Elevation is Associated with Human Skin Microbiomes

Human skin microbiota plays a crucial role in the defense against pathogens, and is associated with various skin diseases. High elevation is positively correlated with various extreme environmental conditions (i.e., high ultraviolet radiation), which may exert selection pressure on skin microbiota, and therefore influence human health. Most studies regarding skin microbial communities have focused on low-elevation hosts. Few studies have explored skin microbiota in high-elevation humans. Here, we investigated the diversity, function, assembly, and co-occurrence patterns of skin microbiotas from 35 health human subjects across three body sites (forehead, opisthenar, and palm) and seven elevation gradients from 501 to 3431 m. Alpha diversity values (i.e., Shannon diversity and observed operational taxonomic units (OTUs)) decreased with increasing elevation regardless of the body site, while beta diversity (Jaccard and Bray–Curtis dissimilarities) showed an increasing trend with elevation. Elevation is a significant factor that influences human skin microbiota, even after controlling host-related factors. Skin microbiotas at high elevation with more than 3000 m on the Qinghai–Tibet Plateau, had a significant structural or functional separation from those at low elevation with less than 3000 m. Notably, the clustering coefficient, average degree, and network density were all lower at high-elevation than those at low-elevation, suggesting that high-elevation skin networks were more fragile and less connected. Phylogenetic analysis showed that human skin microbiotas are mainly dominated by stochastic processes (58.4%–74.6%), but skin microbiotas at high-elevation harbor a greater portion of deterministic processes than those at low-elevation, indicating that high-elevation may be conducive to the promotion of deterministic processes. Our results reveal that the filtering and selection of the changeable high-elevation environment on the Qinghai–Tibet Plateau may lead to less stable skin microbial community structures.

A Stealthy Fungal Attack Requires an Equally Clandestine Approach to Onychomycosis Treatment

Onychomycosis is a chronic fungal infection of the nail that is recalcitrant to treatment. It is unclear why normally effective antifungal therapy results in low cure rates. Evidence suggests that there may be a plethora of reasons that include the limited immune presence in the nail, reduced circulation, presence of commensal microbes, and fungal influence on immune signaling. Therefore, treatment should be designed to address these possibilities and work synergistically with both the innate and adaptive immune responses.

Characterization of Skin Microbiome in Tinea Pedis

Tinea pedis has been associated with Trichophyton rubrum infection. However, it's not clear whether other microbes were implicated in disease pathogenesis. The composition of microbial communities of patients with tinea pedis and healthy controls were analyzed to identify the characteristics of tinea pedis and differences associated with clinical patterns. We found that microbial community structures were different in patients with tinea pedis compared with healthy controls. Moreover, skin microbiome varied in different forms of tinea pedis. Healthy controls exhibited greater fungal diversity than patients with tinea pedis. In patients with tinea pedis, the dominant bacterial and fungal genera were Staphylococcus and Trichophyton. Compared with healthy controls, Corynebacterium tuberculostearicum was decreased and T. rubrum was increased. C. tuberculostearicum was more abundant in vesicular tinea pedis than in hyperkeratotic and interdigital tinea pedis. Interdigital tinea pedis had a higher detection rate of Corynebacterium minutissimum and T. rubrum than the other forms. These results indicated that bacterial microbes may take part in the development of tinea pedis.

Conjunctival dysbiosis in mucosa-associated lymphoid tissue lymphoma

To investigate the conjunctival microbiota and the association between the development of conjunctival mucosa-associated lymphoid tissue (MALT) lymphoma and dysbiosis, DNA samples were collected from 25 conjunctival MALT lymphoma patients and 25 healthy controls. To compare the microbiota, samples were collected from the following four body locations: conjunctiva, meibomian gland, periocular skin and hand. Extracted DNA was analyzed by 16S rRNA sequences, and libraries were sequenced on an Illumina MiSeq sequencer. The differences in bacteria were characterized by using principal coordinate analysis of metagenomics data, and the differences in bacterial compositions were evaluated by linear discriminant analysis effect size. The conjunctival microbiota of MALT lymphoma patients was compositionally different from that of healthy controls. For the conjunctival MALT lymphoma patients, alterations in the microbial composition were detected, and a remarkable change was detected at the conjunctiva. Detailed analysis showed that a specific population of the microbiota, the genus Delftia, was significantly more abundant in conjunctival MALT lymphoma patients, and the genera Bacteroides and Clostridium were less abundant in the MALT lymphoma patients. A specific microbiota on the ocular surface in conjunctival MALT lymphoma patients was detected, and dysbiosis may play an important role in the pathophysiology of conjunctival MALT lymphoma.

The microbiome and immunodeficiencies: Lessons from rare diseases

Primary immunodeficiencies (PIDs) are inherited disorders of the immune system, associated with a considerable increase in susceptibility to infections. PIDs can also predispose to malignancy, inflammation and autoimmunity. There is increasing awareness that some aspects of the immune dysregulation in PIDs may be linked to intestinal microbiota. Indeed, the gut microbiota and its metabolites have been shown to influence immune functions and immune homeostasis both locally and systemically. Recent studies have indicated that genetic defects causing PIDs lead to perturbations in the conventional mechanisms underlying homeostasis in the gut, resulting in poor immune surveillance at the intestinal barrier, which associates with altered intestinal permeability and bacterial translocation. Consistently, a substantial proportion of PID patients presents with clinically challenging IBD-like pathology. Here, we describe the current body of literature reporting on dysbiosis of the gut microbiota in different PIDs and how this can be either the result or cause of immune dysregulation. Further, we report how infections in PIDs enhance pathobionts colonization and speculate how, in turn, pathobionts may be responsible for increased disease susceptibility and secondary infections in these patients. The potential relationship between the microbial composition in the intestine and other sites, such as the oral cavity and skin, is also highlighted. Finally, we provide evidence, in preclinical models of PIDs, for the efficacy of microbiota manipulation to ameliorate disease complications, and suggest that the potential use of dietary intervention to correct dysbiotic flora in PID patients may hold promise.

Melanoma-related changes in skin microbiome

Melanoma is the least common form of skin tumor, but it is potentially the most dangerous and responsible for the majority of skin cancer deaths. We suggest that the skin microbiome might be changed during the progression of melanoma. The aim of this study is to compare the composition of the skin microbiota between different locations (skin and melanoma) of a MeLiM (Melanoma-bearing Libechov Minipig) pig model (exophytic melanoma). Ninety samples were used for PCR-DGGE analysis with primers specifically targeting the V3 region of the 16S rRNA gene. The profiles were used for cluster analysis by UPGMA and principal coordinate analysis PCoA and also to calculate the diversity index (Simpson index of diversity). By comparing the obtained results, we found that both bacterial composition and diversity were significantly different between the skin and melanoma microbiomes. The abundances of Fusobacterium and Trueperella genera were significantly increased in melanoma samples, suggesting a strong relationship between melanoma development and skin microbiome changes.

Human defects in STAT3 promote oral mucosal fungal and bacterial dysbiosis

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.

Human defects in STAT3 promote oral mucosal fungal and bacterial dysbiosis

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.

Skin microbiota and human 3D skin models

Although the role of the microbiota in skin homeostasis is still emerging, there is growing evidence that an intact microbiota supports the skin barrier. The increasing number of research efforts that are trying to shed more light on the human skin-microbiota interaction requires the use of suitable experimental models. Three-dimensional (3D) skin equivalents have been established as a valuable tool in dermatological research because they contain a fully differentiated epidermal barrier that reflects the morphological and molecular characteristics of normal human epidermis. In this review, we provide an overview of current 3D skin models and illustrate the potential of 3D skin models to study the human skin-microbiota interplay.

The microbiology of chronic rhinosinusitis with and without nasal polyps

OBJECTIVE

To compare the microbiological features in middle meatus samples from chronic rhinosinusitis (CRS) patients with nasal polyps (CRSwNP) and those without nasal polyps (CRSsNP), and control subjects.

METHODS

A total of 136 CRSwNP patients, 66 CRSsNP patients, and 49 control subjects who underwent endoscopic surgery in Beijing TongRen Hospital were enrolled between January 2014 and January 2016. Swab samples were obtained from the middle meatus during surgery and processed for the presence of aerobic and non-aerobic bacteria and fungi. Information on the allergic rhinitis, asthma, the percentage of eosinophils in peripheral blood, and the history of smoking and surgery was collected.

RESULTS

The overall isolation rate for bacteria was 81.3% for the three groups, with the lowest in the CRSsNP group (77.3%) and the highest in the CRSwNP group (88.4%). There were no significant differences in isolation rates among the three groups (P = 0.349). The three most common bacterial species were: Coagulase-negative Staphylococcus (24.3%), Corynebacterium (19.9%), and Staphylococcus epidermidis (19.1%) in the CRSwNP group; S. epidermidis (21.2%), Corynebacterium (21.2%), Coagulase-negative staphylococcus (18.2%), and Staphylococcus aureus (13.6%) in the CRSsNP group; S. epidermidis (30.6%), Coagulase-negative Staphylococcus (28.6%), and S. aureus (14.3%) in the control group. For the bacterial species with high isolation rates, no significant difference in the microbial cultures was observed among the three groups; whereas in the CRSwNP group, a relatively high proportion of Citrobacter (5.9%, a bacterium with low isolation rate) was observed compared with the CRSsNP and control groups (all 0.0%). Furthermore, when samples were categorized into subgroups according to the percentage of eosinophils, some bacterial species showed different rates in the CRSwNP group (e.g., S. aureus, 3.3% in the subgroup with normal percentage of eosinophils, 17.2% in the subgroup with increased percentage of eosinophils, P = 0.011).

CONCLUSIONS

There were no significant differences in the microbiological features (except Citrobacter) in middle meatus samples from CRSwNP patients, CRSsNP patients, and control subjects. S. aureus may promote eosinophilic inflammatory response, while S. epidermidis may promote non-eosinophilic inflammatory response.

Common Cutaneous Bacteria Isolated from Snakes Inhibit Growth of Ophidiomyces ophiodiicola

There is increasing concern regarding potential impacts of snake fungal disease (SFD), caused by Ophidiomyces ophiodiicola (Oo), on free-ranging snake populations in the eastern USA. The snake cutaneous microbiome likely serves as the first line of defense against Oo and other pathogens; however, little is known about microbial associations in snakes. The objective of this study was to better define the composition and immune function of the snake cutaneous microbiome. Eight timber rattlesnakes (Crotalus horridus) and four black racers (Coluber constrictor) were captured in Arkansas and Tennessee, with some snakes exhibiting signs of SFD. Oo was detected through real-time qPCR in five snakes. Additional histopathological techniques confirmed a diagnosis of SFD in one racer, the species' first confirmed case of SFD in Tennessee. Fifty-eight bacterial and five fungal strains were isolated from skin swabs and identified with Sanger sequencing. Non-metric multidimensional scaling and PERMANOVA analyses indicated that the culturable microbiome does not differ between snake species. Fifteen bacterial strains isolated from rattlesnakes and a single strain isolated from a racer inhibited growth of Oo in vitro. Results shed light on the culturable cutaneous microbiome of snakes and probiotic members that may play a role in fighting an emergent disease.

The human skin microbiome

Functioning as the exterior interface of the human body with the environment, skin acts as a physical barrier to prevent the invasion of foreign pathogens while providing a home to the commensal microbiota. The harsh physical landscape of skin, particularly the desiccated, nutrient-poor, acidic environment, also contributes to the adversity that pathogens face when colonizing human skin. Despite this, the skin is colonized by a diverse microbiota. In this Review, we describe amplicon and shotgun metagenomic DNA sequencing studies that have been used to assess the taxonomic diversity of microorganisms that are associated with skin from the kingdom to the strain level. We discuss recent insights into skin microbial communities, including their composition in health and disease, the dynamics between species and interactions with the immune system, with a focus on Propionibacterium acnes, Staphylococcus epidermidis and Staphylococcus aureus.

Patient Susceptibility to Candidiasis-A Potential for Adjunctive Immunotherapy

Candida spp. are colonizing fungi of human skin and mucosae of the gastrointestinal and genitourinary tract, present in 30-50% of healthy individuals in a population at any given moment. The host defense mechanisms prevent this commensal fungus from invading and causing disease. Loss of skin or mucosal barrier function, microbiome imbalances, or defects of immune defense mechanisms can lead to an increased susceptibility to severe mucocutaneous or invasive candidiasis. A comprehensive understanding of the immune defense against Candida is essential for developing adjunctive immunotherapy. The important role of underlying genetic susceptibility to Candida infections has become apparent over the years. In most patients, the cause of increased susceptibility to fungal infections is complex, based on a combination of immune regulation gene polymorphisms together with other non-genetic predisposing factors. Identification of patients with an underlying genetic predisposition could help determine which patients could benefit from prophylactic antifungal treatment or adjunctive immunotherapy. This review will provide an overview of patient susceptibility to mucocutaneous and invasive candidiasis and the potential for adjunctive immunotherapy.

Medical mycology and fungal immunology: new research perspectives addressing a major world health challenge

Fungi cause more than a billion skin infections, more than 100 million mucosal infections, 10 million serious allergies and more than a million deaths each year. Global mortality owing to fungal infections is greater than for malaria and breast cancer and is equivalent to that owing to tuberculosis (TB) and HIV. These statistics evidence fungal infections as a major threat to human health and a major burden to healthcare budgets worldwide. Those patients who are at greatest risk of life-threatening fungal infections include those who have weakened immunity or have suffered trauma or other predisposing infections such as HIV. To address these global threats to human health, more research is urgently needed to understand the immunopathology of fungal disease and human disease susceptibility in order to augment the advances being made in fungal diagnostics and drug development. Here, we highlight some recent advances in basic research in medical mycology and fungal immunology that are beginning to inform clinical decisions and options for personalized medicine, vaccine development and adjunct immunotherapies.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

Gut microbiota profile in systemic sclerosis patients with and without clinical evidence of gastrointestinal involvement

Recent evidence suggests that there is a link between the gut microbial community and immune-mediated disorders. Systemic sclerosis (SSc) is an autoimmune disease characterized by immunonological abnormalities, vascular lesions, and extensive fibrosis. Since the gastrointestinal tract is one of the organs most involved, the goal of this study was to explore the composition of the intestinal microbiota in SSc patients with (SSc/GI+) and without gastrointestinal involvement (SSc/GI-) in comparison to healthy controls (HC). The fecal bacterial composition was investigated by Illumina sequencing of 16 S rRNA gene amplicons. The fecal microbiota of SSc/GI+ subjects was characterized by higher levels of Lactobacillus, Eubacterium and Acinetobacter compared with healthy controls, and lower proportions of Roseburia, Clostridium, and Ruminococcus. The gut microbiota of SSc/GI- subjects was more similar to the microbiota of HC than to that of SSc/GI+ subjects albeit Streptococcus salivarius was over-represented in SSc/GI- fecal samples compared with both SSc/GI+ subjects and controls. Our study reveals microbial signatures of dysbiosis in the gut microbiota of SSc patients that are associated with clinical evidence of gastrointestinal disease. Further studies are needed to elucidate the potential role of these perturbations in the onset and progression of systemic sclerosis, and gastrointestinal involvement in particular.

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs

While the skin microbiome has been shown to play important roles in health and disease in several species, the effects of altitude on the skin microbiome and how high-altitude skin microbiomes may be associated with health and disease states remains largely unknown. Using 16S rRNA marker gene sequencing, we characterized the skin microbiomes of people from two racial groups (the Tibetans and the Hans) and of three local pig breeds (Tibetan pig, Rongchang pig, and Qingyu pig) at high and low altitudes. The skin microbial communities of low-altitude pigs and humans were distinct from those of high-altitude pigs and humans, with five bacterial taxa (Arthrobacter, Paenibacillus, Carnobacterium, and two unclassified genera in families Cellulomonadaceae and Xanthomonadaceae) consistently enriched in both pigs and humans at high altitude. Alpha diversity was also significantly lower in skin samples collected from individuals living at high altitude compared to individuals at low altitude. Several of the taxa unique to high-altitude humans and pigs are known extremophiles adapted to harsh environments such as those found at high altitude. Altogether our data reveal that altitude has a significant effect on the skin microbiome of pigs and humans.

Fungal dysbiosis: immunity and interactions at mucosal barriers

Fungi and mammals share a co-evolutionary history and are involved in a complex web of interactions. Studies focused on commensal bacteria suggest that pathological changes in the microbiota, historically known as dysbiosis, are at the root of many inflammatory diseases of non-infectious origin. However, the importance of dysbiosis in the fungal community - the mycobiota - was only recently acknowledged to have a pathological role, as novel findings have suggested that mycobiota disruption can have detrimental effects on host immunity. Fungal dysbiosis and homeostasis are dynamic processes that are probably more common than actual fungal infections, and therefore constantly shape the immune response. In this Review, we summarize specific mycobiota patterns that are associated with fungal dysbiosis, and discuss how mucosal immunity has evolved to distinguish fungal infections from dysbiosis and how it responds to these different conditions. We propose that gut microbiota dysbiosis is a collective feature of complex interactions between prokaryotic and eukaryotic microbial communities that can affect immunity and that can influence health and disease.

The Skin as a Route of Allergen Exposure: Part II. Allergens and Role of the Microbiome and Environmental Exposures

PURPOSE OF REVIEW

This second part of the article aims to highlight recent contributions in the literature that enhance our understanding of the cutaneous immune response to allergen.

RECENT FINDINGS

Several properties of allergens facilitate barrier disruption and cutaneous sensitization. There is a strong epidemiologic relationship between the microbiome, both the gut and skin, and atopic dermatitis (AD). The mechanisms connecting these two entities remain enigmatic; however, recent murine models show that commensal skin bacteria play an active role in supporting skin barrier homeostasis and defense against microbial penetration. Likewise, the association between the lack of colonization with Staph species and AD development suggests a potentially functional role for these organisms in regulating the skin barrier and response to environmental allergens. In undisrupted skin, evidence suggests that the cutaneous route may promote allergen tolerance. Properties of environmental allergens and commensal bacteria add to the complex landscape of skin immunity. Further investigation is needed to elucidate how these properties regulate the cutaneous immune response to allergen.

Molecular Typing of Staphylococcus aureus Isolated from Patients with Autosomal Dominant Hyper IgE Syndrome

Autosomal dominant hyper IgE syndrome (AD-HIES) is a primary immunodeficiency caused by a loss-of-function mutation in the Signal Transducer and Activator of Transcription 3 (STAT3). This immune disorder is clinically characterized by increased susceptibility to cutaneous and sinopulmonary infections, in particular with Candida and Staphylococcus aureus. It has recently been recognized that the skin microbiome of patients with AD-HIES is altered with an overrepresentation of certain Gram-negative bacteria and Gram-positive staphylococci. However, these alterations have not been characterized at the species- and strain-level. Since S. aureus infections are influenced by strain-specific expression of virulence factors, information on colonizing strain characteristics may provide insights into host-pathogen interactions and help guide management strategies for treatment and prophylaxis. The aim of this study was to determine whether the immunodeficiency of AD-HIES selects for unique strains of colonizing S. aureus. Using multi-locus sequence typing (MLST), protein A (spa) typing, and PCR-based detection of toxin genes, we performed a detailed analysis of the S. aureus isolates (n = 13) found on the skin of twenty-one patients with AD-HIES. We found a low diversity of sequence types, and an abundance of strains that expressed methicillin resistance, Panton-Valentine leukocidin (PVL), and staphylococcal enterotoxins K and Q (SEK, SEQ). Our results indicate that patients with AD-HIES may often carry antibiotic-resistant strains that harbor key virulence factors.

Homeostatic Immunity and the Microbiota

The microbiota plays a fundamental role in the induction, education, and function of the host immune system. In return, the host immune system has evolved multiple means by which to maintain its symbiotic relationship with the microbiota. The maintenance of this dialogue allows the induction of protective responses to pathogens and the utilization of regulatory pathways involved in the sustained tolerance to innocuous antigens. The ability of microbes to set the immunological tone of tissues, both locally and systemically, requires tonic sensing of microbes and complex feedback loops between innate and adaptive components of the immune system. Here we review the dominant cellular mediators of these interactions and discuss emerging themes associated with our current understanding of the homeostatic immunological dialogue between the host and its microbiota.

Paucibacterial Microbiome and Resident DNA Virome of the Healthy Conjunctiva

Purpose

To characterize the ocular surface microbiome of healthy volunteers using a combination of microbial culture and high-throughput DNA sequencing techniques.

Methods

Conjunctival swab samples from 107 healthy volunteers were analyzed by bacterial culture, 16S rDNA gene deep sequencing (n = 89), and biome representational in silico karyotyping (BRiSK; n = 80). Swab samples of the facial skin (n = 42), buccal mucosa (n = 50), and environmental controls (n = 27) were processed in parallel. 16S rDNA gene quantitative PCR was used to calculate the bacterial load in each site. Bacteria were characterized by site using principal coordinate analysis of metagenomics data. BRiSK data were analyzed for presence of fungi and viruses.

Results

Corynebacteria, Propionibacteria, and coagulase-negative Staphylococci were the predominant organisms identified by all three techniques. Quantitative 16S PCR demonstrated approximately 0.1 bacterial 16S rDNA/human actin copy on the ocular surface compared with greater than 10 16S rDNA/human actin copy for facial skin or the buccal mucosa. The conjunctival bacterial community structure is distinct compared with the facial skin (R = 0.474, analysis of similarities P = 0.0001), the buccal mucosa (R = 0.893, P = 0.0001), and environmental control samples (R = 0.536, P = 0.0001). 16S metagenomics revealed substantially more bacterial diversity on the ocular surface than other techniques, which appears to be artifactual. BRiSK revealed presence of torque teno virus (TTV) on the healthy ocular surface, which was confirmed by direct PCR to be present in 65% of all conjunctiva samples tested.

Conclusions

Relative to adjacent skin or other mucosa, healthy ocular surface microbiome is paucibacterial. Its flora are distinct from adjacent skin. Torque teno virus is a frequent constituent of the ocular surface microbiome. (ClinicalTrials.gov number, NCT02298881.)

Performing Skin Microbiome Research: A Method to the Madness

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.