Human skin microbiota: high diversity of DNA viruses identified on the human skin by high throughput sequencing

The influence of lifestyle and environmental factors on host resilience through a homeostatic skin microbiota: An EAACI Task Force Report

Human skin is colonized with skin microbiota that includes commensal bacteria, fungi, arthropods, archaea and viruses. The composition of the microbiota varies at different anatomical locations according to changes in body temperature, pH, humidity/hydration or sebum content. A homeostatic skin microbiota is crucial to maintain epithelial barrier functions, to protect from invading pathogens and to interact with the immune system. Therefore, maintaining homeostasis holds promise to be an achievable goal for microbiome-directed treatment strategies as well as a prophylactic strategy to prevent the development of skin diseases, as dysbiosis or disruption of homeostatic skin microbiota is associated with skin inflammation. A healthy skin microbiome is likely modulated by genetic as well as environmental and lifestyle factors. In this review, we aim to provide a complete overview of the lifestyle and environmental factors that can contribute to maintaining the skin microbiome healthy. Awareness of these factors could be the basis for a prophylactic strategy to prevent the development of skin diseases or to be used as a therapeutic approach.

Presence of Merkel cell polyomavirus DNA and large-T antigen in keratinocyte carcinomas and its correlation with immunohistochemical markers p16, p53 and ki67

BACKGROUND

Merkel cell polyomavirus (MCPyV), a human polyomavirus that is unequivocally linked to merkel cell carcinoma (MCC), has been found in association with keratinocytes carcinomas (KC), especially basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC). Nevertheless, there is scarce information about the possible involvement of MCPyV in the development of KC.

OBJECTIVES

To assess the presence of MCPyV DNA and Large-T Antigen (LT-Ag) via Polymerase Chain Reaction (PCR) and Immunohistochemistry (IHC) in cases of KC, and to correlate its presence with immunohistochemical markers p16, p53, and ki67, tumor type and subtype, sun-exposed location, and epidemiological data.

METHODS

The prevalence of MCPyV DNA, LT-Ag, and immunohistochemical markers p16, p53, and ki67 was assessed by PCR and Immunohistochemistry (IHC) in 127 cases of KC, these results were correlated with tumor type and subtype, sun-exposed location, and epidemiological data.

RESULTS

The MCPyV DNA was detected in 42.57% (43 of 101) cases by PCR, the LT-Ag was detected in 16.4% (20 of 122) of cases, p16 in 81.5% (97 of 119), p53 in 66.4% (83 of 125), ki67 in 89% (73 of 82). No correlation between MCPyV LT-Ag and DNA confronted with tumor type, subtype, location site, and immunohistochemical markers was found. A single correlation between the MCPyV LT-Ag and cSCC tumors and peri-tumoral lymphocyte cells was noted.

STUDY LIMITATIONS

Further steps need to be taken to better evaluate the MCPyV influence and its possible role in KC carcinogenesis, as the evaluation of the virus genome state, the gene sequence that encodes LT-Ag in the KC tumor cells, and in situ hybridization for viral DNA or RNA in these cells.

CONCLUSIONS

Despite the frequent detection of MCPyV in KC, the data available so far does not support the hypothesis of a causal relationship between them.

Commensal HPVs Have Evolved to Be More Immunogenic Compared with High-Risk α-HPVs

Commensal human papillomaviruses (HPVs) are responsible for persistent asymptomatic infection in the human population by maintaining low levels of the episomal genome in the stratified epithelia. Herein, we examined the immunogenicity of cutaneotropic HPVs that are commonly found in the skin. Using an in silico platform to determine human leukocyte antigen (HLA)-peptide complex binding affinity, we observed that early genes of cutaneotropic HPV types within the same species can generate multiple conserved, homologous peptides that bind with high affinity to HLA class I alleles. Interestingly, we discovered that commensal β, γ, μ, and ν HPVs contain significantly more immunogenic peptides compared with α-HPVs, which include high-risk, oncogenic HPV types. Our findings indicate that commensal HPV proteins have evolved to generate peptides that better complement their host's HLA repertoire. Promoting higher control by host T cell immunity in this way could be a mechanism by which HPVs achieve widespread asymptomatic colonization in humans. This work supports the role of commensal HPVs as immunogenic targets within epithelial cells, which may contribute to the immune regulation of the skin and mucosa.

Merkel cell polyomavirus protein ALTO modulates TBK1 activity to support persistent infection

While Merkel cell polyomavirus (MCPyV or MCV) is an abundant virus frequently shed from healthy skin, it is one of the most lethal tumor viruses in immunocompromised individuals, highlighting the crucial role of host immunity in controlling MCPyV oncogenic potential. Despite its prevalence, very little is known about how MCPyV interfaces with the host immune response to maintain asymptomatic persistent infection and how inadequate control of MCPyV infection triggers MCC tumorigenesis. In this study, we discovered that the MCPyV protein, known as the Alternative Large Tumor Open Reading Frame (ALTO), also referred to as middle T, effectively primes and activates the STING signaling pathway. It recruits Src kinase into the complex of STING downstream kinase TBK1 to trigger its autophosphorylation, which ultimately activates the subsequent antiviral immune response. Combining single-cell analysis with both loss- and gain-of-function studies of MCPyV infection, we demonstrated that the activity of ALTO leads to a decrease in MCPyV replication. Thus, we have identified ALTO as a crucial viral factor that modulates the STING-TBK1 pathway, creating a negative feedback loop that limits viral infection and maintains a delicate balance with the host immune system. Our study reveals a novel mechanism by which a tumorigenic virus-encoded protein can link Src function in cell proliferation to the activation of innate immune signaling, thereby controlling viral spread, and sustaining persistent infection. Our previous findings suggest that STING also functions as a tumor suppressor in MCPyV-driven oncogenesis. This research provides a foundation for investigating how disruptions in the finely tuned virus-host balance, maintained by STING, could alter the fate of MCPyV infection, potentially encouraging malignancy.

Facial Skin Microbiome Composition and Functional Shift with Aging

The change in the skin microbiome as individuals age is only partially known. To provide a better understanding of the impact of aging, whole-genome sequencing analysis was performed on facial skin swabs of 100 healthy female Caucasian volunteers grouped by age and wrinkle grade. Volunteers' metadata were collected through questionnaires and non-invasive biophysical measurements. A simple model and a biological statistical model were used to show the difference in skin microbiota composition between the two age groups. Taxonomic and non-metric multidimensional scaling analysis showed that the skin microbiome was more diverse in the older group (≥55 yo). There was also a significant decrease in Actinobacteria, namely in Cutibacterium acnes, and an increase in Corynebacterium kroppenstedtii. Some Streptococcus and Staphylococcus species belonging to the Firmicutes phylum and species belonging to the Proteobacteria phylum increased. In the 18-35 yo younger group, the microbiome was characterized by a significantly higher proportion of Cutibacterium acnes and Lactobacillus, most strikingly, Lactobacillus crispatus. The functional analysis using GO terms revealed that the young group has a higher significant expression of genes involved in biological and metabolic processes and in innate skin microbiome protection. The better comprehension of age-related impacts observed will later support the investigation of skin microbiome implications in antiaging protection.

Fabrication and evaluation of ribavirin-loaded electrospun nanofibers as an antimicrobial wound dressing

Background

Skin is regarded as an essential first line of defense against harmful pathogens and it hosts an ecosystem of microorganisms that create a widely diverse skin microbiome. In chronic wounds, alterations in the host-microbe interactions occur forming polymicrobial biofilms that hinder the process of wound healing. Ribavirin, an antiviral drug, possesses antimicrobial activity, especially against Pseudomonas aeruginosa and Candida albicans, which are known as the main opportunistic pathogens in chronic wounds.

Rationale

In this study, electrospun nanofiber systems loaded with ribavirin were developed as a potential wound dressing for topical application in chronic wounds. Ribavirin was chosen in this study owing to the emerging cases of antimicrobial (antibiotics and antifungal) resistance and the low attempts to discover new antimicrobial agents, which encouraged the repurposing use of current medication as an alternative solution in case of resistance to the available agents. Additionally, the unique mechanism of action of ribavirin, i.e., perturbing the bacterial virulence system without killing or stopping their growth and rendering the pathogens disarmed, might be a promising choice to prevent drug resistance. Cyclodextrin (CD) was utilized to formulate ribavirin as an electrospun nanofibers delivery system to enhance the absorption and accelerate the release of ribavirin for topical use.

Results

The results demonstrated a successful ribavirin nanofibers fabrication that lacked beads and pores on the nanofibrous surfaces. Ribavirin underwent a physical transformation from crystalline to amorphous form, as confirmed by X-ray diffraction analysis. This change occurred due to the molecular dispersion after the electrospinning process. Additionally, the CD enhanced the encapsulation efficiency of ribavirin in the nanofibers as observed from the drug-loading results. Polyvinylpyrrolidone (PVP) and CD increased ribavirin released into the solution and the disintegration of fibrous mats which shrank and eventually dissolved into a gel-like substance as the ribavirin-loaded fibers began to break down from their border toward the midpoint. Cytotoxicity of ribavirin and CD was evaluated against human dermal fibroblasts (HFF-1) and the results showed a relatively safe profile of ribavirin upon 24-hour cell exposure, while CD was safe within 24- and 48-hour.

Conclusion

This study provides valuable insights into the potential application of our nanofibrous system for treating chronic wounds; however, further antimicrobial and in-vivo studies are required to confirm its safety and effectiveness.

Interactions between avian viruses and skin in farm birds

This article reviews the avian viruses that infect the skin of domestic farm birds of primary economic importance: chicken, duck, turkey, and goose. Many avian viruses (e.g., poxviruses, herpesviruses, Influenza viruses, retroviruses) leading to pathologies infect the skin and the appendages of these birds. Some of these viruses (e.g., Marek's disease virus, avian influenza viruses) have had and/or still have a devasting impact on the poultry economy. The skin tropism of these viruses is key to the pathology and virus life cycle, in particular for virus entry, shedding, and/or transmission. In addition, for some emergent arboviruses, such as flaviviruses, the skin is often the entry gate of the virus after mosquito bites, whether or not the host develops symptoms (e.g., West Nile virus). Various avian skin models, from primary cells to three-dimensional models, are currently available to better understand virus-skin interactions (such as replication, pathogenesis, cell response, and co-infection). These models may be key to finding solutions to prevent or halt viral infection in poultry.

Detection of α-papillomaviruses in extragenital cutaneous squamous cell carcinomas

Previous studies have demonstrated that human papillomaviruses (HPVs) of the beta genus can contribute to the onset of cutaneous carcinomas in organ transplant recipients. In contrast, there are limited data related to the oncogenicity of alpha (α)-HPVs in the skin. Herein, we explore the characteristics of three cutaneous squamous cell carcinomas presenting α-HPV infection occurring in patients with HIV, in order to determine the role of α-HPV in these skin cancers.

A quantitative assay for the assessment of cutaneous human papillomaviruses and polyomaviruses over time: A proof-of-concept in two patients with atopic dermatitis and psoriasis

The human skin virome, unlike commensal bacteria, is an under investigated component of the human skin microbiome. We developed a sensitive, quantitative assay to detect cutaneous human resident papillomaviruses (HPV) and polyomaviruses (HPyV) and we first used it to describe these viral populations at the skin surface of two patients with atopic dermatitis (AD) and psoriasis (PSO). We performed skin swabs on lesional and non-lesional skin in one AD and one PSO patient at M0, M1 and M3. After extraction, DNA was amplified using an original multiplex PCR technique before high throughput sequencing (HTS) of the amplicons (named AmpliSeq-HTS). Quantitative results were ultimately compared with monoplex quantitative PCRs (qPCRs) for previously detected viruses and were significantly correlated (R2 = 0.95, ρ = 0.75). Fifteen and 13 HPV types (mainly gamma and beta-HPVs) or HPyV species (mainly Merkel Cell Polyomavirus (MCPyV)) were detected on the skin of the AD and PSO patients, respectively. In both patients, the composition of the viral flora was variable across body sites but remained stable over time in non-lesional skin samples, mostly colonized with gamma-papillomaviruses. In lesional skin samples, beta-papillomaviruses and MCPyV were the major components of a viral flora more prone to vary over time especially with treatment and subsequent clinical improvement. We believe this method might be further used in extensive studies to further enhance the concept of an individual cutaneous viral fingerprint and the putative role of its alterations through various skin diseases and their treatments.

A New Inovirus from the Human Blood Encodes Proteins with Nuclear Subcellular Localization

Viruses infecting bacteria (bacteriophages) represent the most abundant viral particles in the human body. They participate in the control of the human-associated bacterial communities and play an important role in the dissemination of virulence genes. Here, we present the identification of a new filamentous single-stranded DNA phage of the family Inoviridae, named Ralstonia Inoviridae Phage 1 (RIP1), in the human blood. Metagenomics and PCR analyses detected the RIP1 genome in blood serum, in the absence of concomitant bacterial infection or contamination, suggesting inovirus persistence in the human blood. Finally, we have experimentally demonstrated that the RIP1-encoded rolling circle replication initiation protein and serine integrase have functional nuclear localization signals and upon expression in eukaryotic cells both proteins were translocated into the nucleus. This observation adds to the growing body of data suggesting that phages could have an overlooked impact on the evolution of eukaryotic cells.

The Medicinal Phage-Regulatory Roadmap for Phage Therapy under EU Pharmaceutical Legislation

Bacteriophage therapy is a promising approach to treating bacterial infections. Research and development of bacteriophage therapy is intensifying due to the increase in antibiotic resistance and the faltering development of new antibiotics. Bacteriophage therapy uses bacteriophages (phages), i.e., prokaryotic viruses, to specifically target and kill pathogenic bacteria. The legal handling of this type of therapy raises several questions. These include whether phage therapeutics belong to a specially regulated class of medicinal products, and which legal framework should be followed with regard to the various technical ways in which phage therapeutics can be manufactured and administered. The article shows to which class of medicinal products phage therapeutics from wild type phages and from genetically modified (designer) phages do or do not belong. Furthermore, the article explains which legal framework is relevant for the manufacture and administration of phage therapeutics, which are manufactured in advance in a uniform, patient-independent manner, and for tailor-made patient-specific phage therapeutics. For the systematically coherent, successful translation of phage therapy, the article considers pharmaceutical law and related legal areas, such as genetic engineering law. Finally, the article shows how the planned legislative revisions of Directive 2001/83/EC and Regulation (EC) No 726/2004 may affect the legal future of phage therapy.

The role of the skin microbiome in wound healing

The efficient management of skin wounds for rapid and scarless healing represents a major clinical unmet need. Nonhealing skin wounds and undesired scar formation impair quality of life and result in high healthcare expenditure worldwide. The skin-colonizing microbiota contributes to maintaining an intact skin barrier in homeostasis, but it also participates in the pathogenesis of many skin disorders, including aberrant wound healing, in many respects. This review focuses on the composition of the skin microbiome in cutaneous wounds of different types (i.e. acute and chronic) and with different outcomes (i.e. nonhealing and hypertrophic scarring), mainly based on next-generation sequencing analyses; furthermore, we discuss the mechanistic insights into host-microbe and microbe-microbe interactions during wound healing. Finally, we highlight potential therapeutic strategies that target the skin microbiome to improve healing outcomes.

Novel equid papillomavirus from domestic donkey

BACKGROUND

Papillomaviruses can be of great medical importance as they infect humans and animals such as Equus species, other livestock and pets. They are responsible for several papillomas and benign tumours in their host.

OBJECTIVES

To describe a novel equid papillomavirus detected in oral swab samples collected from donkeys (Equus asinus) found on the Northwest plateau of China.

STUDY DESIGN

Cross-sectional.

METHODS

Swab samples collected from the oral mucosa of 32 donkeys in the Gansu Province of China, were subjected to viral metagenomic analysis to detect the presence of Papillomavirus. After de novo assembly, a novel papillomavirus genome designated as Equus asinus papillomavirus 3 (EaPV3) was identified in the studied samples. Additional bioinformatic analysis of the assembled genome was done using the Geneious prime software (version 2022.0.2).

RESULTS

The complete circular genome of EaPV3 is 7430 bp in length with a GC content of 50.8%. The genome was predicted to contain five ORFs coding for three early proteins (E7, E1, and E2) and two late proteins (L1 and L2). Phylogenic analysis of the nucleotide sequences of the concatenated amino acid sequences of the E1E2L1L2 genes revealed that EaPV3 is most closely related to Equus asinus papillomavirus 1 (EaPV1). The genome analysis of EaPV3 revealed similar genome organisation with other equine papillomavirus and the presence of E7 papillomavirus oncoprotein.

MAIN LIMITATIONS

Since there were no warts in the oral cavity of the donkeys in this study, and no biopsy samples taken, we are unable to conclusively link the novel virus to any clinical condition in the donkeys.

CONCLUSIONS

The Comparative characterisation of EaPV3 and its closest relatives, as well as phylogenetic analysis demonstrated that it is a novel virus specie that clusters within the Dyochipapilloma PV genus.

Innovative Approaches for Maintaining and Enhancing Skin Health and Managing Skin Diseases through Microbiome-Targeted Strategies

The skin microbiome is crucial in maintaining skin health, and its disruption is associated with various skin diseases. Prebiotics are non-digestible fibers and compounds found in certain foods that promote the activity and growth of beneficial bacteria in the gut or skin. On the other hand, live microorganisms, known as probiotics, benefit in sustaining healthy conditions when consumed in reasonable quantities. They differ from postbiotics, which are by-product compounds from bacteria that release the same effects as their parent bacteria. The human skin microbiome is vital when it comes to maintaining skin health and preventing a variety of dermatological conditions. This review explores novel strategies that use microbiome-targeted treatments to maintain and enhance overall skin health while managing various skin disorders. It is important to understand the dynamic relationship between these beneficial microorganisms and the diverse microbial communities present on the skin to create effective strategies for using probiotics on the skin. This understanding can help optimize formulations and treatment regimens for improved outcomes in skincare, particularly in developing solutions for various skin problems.

Skin Microbiota and the Cosmetic Industry

Skin harbors an important microbial ecosystem - the skin microbiota that is in homeostasis with its host and is beneficial for human health. Cosmetic products have the potential to interfere with this microbial community; therefore their impact should be assessed. The aim of this review is to highlight the importance of skin microbiota in the cosmetic industry. Several studies determined that cosmetic ingredients have the potential to disrupt the skin microbiota equilibrium leading to the development of skin diseases and dysregulation of immune response. These studies led their investigation by using different methodologies and models, concluding that methods must be chosen according to the aim of the study, the skin site to be evaluated, and the target population of the cosmetics. Overall, it is crucial to test the impact of cosmetics in the skin microbiota and to stablish standard procedures, as well as specific criteria that allow to classify a cosmetic product as skin microbiota friendly.

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.

Reprogramming of connexin landscape fosters fast gap junction intercellular communication in human papillomavirus-infected epithelia

Human papillomaviruses (HPVs) are highly prevalent commensal viruses that require epithelial stratification to complete their replicative cycle. While HPV infections are most often asymptomatic, certain HPV types can cause lesions, that are usually benign. In rare cases, these infections may progress to non-replicative viral cycles associated with high HPV oncogene expression promoting cell transformation, and eventually cancer when not cleared by host responses. While the consequences of HPV-induced transformation on keratinocytes have been extensively explored, the impact of viral replication on epithelial homeostasis remains largely unexplored. Gap junction intercellular communication (GJIC) is critical for stratified epithelium integrity and function. This process is ensured by a family of proteins named connexins (Cxs), including 8 isoforms that are expressed in stratified squamous epithelia. GJIC was reported to be impaired in HPV-transformed cells, which was attributed to the decreased expression of the Cx43 isoform. However, it remains unknown whether and how HPV replication might impact on the expression of Cx isoforms and GJIC in stratified squamous epithelia. To address this question, we have used 3D-epithelial cell cultures (3D-EpCs), the only model supporting the productive HPV life cycle. We report a transcriptional downregulation of most epithelial Cx isoforms except Cx45 in HPV-replicating epithelia. At the protein level, HPV replication results in a reduction of Cx43 expression while that of Cx45 increases and displays a topological shift toward the cell membrane. To quantify GJIC, we pioneered quantitative gap-fluorescence loss in photobleaching (FLIP) assay in 3D-EpCs, which allowed us to show that the reprogramming of Cx landscape in response to HPV replication translates into accelerated GJIC in living epithelia. Supporting the pathophysiological relevance of our observations, the HPV-associated Cx43 and Cx45 expression pattern was confirmed in human cervical biopsies harboring HPV. In conclusion, the reprogramming of Cx expression and distribution in HPV-replicating epithelia fosters accelerated GJIC, which may participate in epithelial homeostasis and host immunosurveillance.

Characterization of the Impact of Merkel Cell Polyomavirus-Induced Interferon Signaling on Viral Infection

Merkel cell polyomavirus (MCPyV) has been associated with approximately 80% of Merkel cell carcinoma (MCC), an aggressive and increasingly incident skin cancer. The link between host innate immunity, viral load control, and carcinogenesis has been established but poorly characterized. We previously established the importance of the STING and NF-κB pathways in the host innate immune response to viral infection. In this study, we further discovered that MCPyV infection of human dermal fibroblasts (HDFs) induces the expression of type I and III interferons (IFNs), which in turn stimulate robust expression of IFN-stimulated genes (ISGs). Blocking type I IFN downstream signaling using an IFN-β antibody, JAK inhibitors, and CRISPR knockout of the receptor dramatically repressed MCPyV infection-induced ISG expression but did not significantly restore viral replication activities. These findings suggest that IFN-mediated induction of ISGs in response to MCPyV infection is not crucial to viral control. Instead, we found that type I IFN exerts a more direct effect on MCPyV infection postentry by repressing early viral transcription. We further demonstrated that growth factors normally upregulated in wounded or UV-irradiated human skin can significantly stimulate MCPyV gene expression and replication. Together, these data suggest that in healthy individuals, host antiviral responses, such as IFN production induced by viral activity, may restrict viral propagation to reduce MCPyV burden. Meanwhile, growth factors induced by skin abrasion or UV irradiation may stimulate infected dermal fibroblasts to promote MCPyV propagation. A delicate balance of these mutually antagonizing factors provides a mechanism to support persistent MCPyV infection. IMPORTANCE Merkel cell carcinoma is an aggressive skin cancer that is particularly lethal to immunocompromised individuals. Though rare, MCC incidence has increased significantly in recent years. There are no lasting and effective treatments for metastatic disease, highlighting the need for additional treatment and prevention strategies. By investigating how the host innate immune system interfaces with Merkel cell polyomavirus, the etiological agent of most of these cancers, our studies identified key factors necessary for viral control, as well as conditions that support viral propagation. These studies provide new insights for understanding how the virus balances the effects of the host immune defenses and of growth factor stimulation to achieve persistent infection. Since virus-positive MCC requires the expression of viral oncogenes to survive, our observation that type I IFN can repress viral oncogene transcription indicates that these cytokines could be explored as a viable therapeutic option for treating patients with virus-positive MCC.

Cutavirus on the skin in an Asian cohort: identification of a novel geographically related genotype

BACKGROUND

Cutavirus (CuV) is the newest human parvovirus and is currently receiving increasing attention because of its possible association with cutaneous T-cell lymphoma. Despite the pathogenetic potential of CuV, it has been detected in normal skin; however, little is known about the prevalence, infection levels, and genetic variations of this virus in the skin of the general population.

METHODS

We investigated the CuV DNA prevalence and viral loads concerning age, sampling location, and gender using 678 skin swabs collected from the normal-appearing skins of 339 Japanese participants aged 2-99 years. Phylogenetic analyses were also conducted based on the near-full-length CuV sequences identified in this study.

RESULTS

Both the CuV DNA prevalence and viral loads were significantly higher in the skin of elderly persons aged ≥60 years compared with those of persons aged < 60 years. CuV DNA tended to persist in the skin of elderly individuals. No significant difference in viral loads was observed between the skin of the upper arm and the skin of the forehead in CuV DNA-positive specimens. Significantly higher viral loads were evident in men vs. women, although no gender-associated differences in viral prevalence were noted. Phylogenetic analyses demonstrated the existence of Japanese-specific viruses that were genetically distinct from viruses prevalent in other areas, especially Europe.

CONCLUSIONS

This large study suggests that high levels of CuV DNA are prevalent on the skin of elderly adults. Our findings also indicated the prevalence of geographically related CuV genotypes. A follow-up study of this cohort should provide helpful information on whether CuV may become pathogenic.

Evolving approaches to profiling the microbiome in skin disease

Despite its harsh and dry environment, human skin is home to diverse microbes, including bacteria, fungi, viruses, and microscopic mites. These microbes form communities that may exist at the skin surface, deeper skin layers, and within microhabitats such as the hair follicle and sweat glands, allowing complex interactions with the host immune system. Imbalances in the skin microbiome, known as dysbiosis, have been linked to various inflammatory skin disorders, including atopic dermatitis, acne, and psoriasis. The roles of abundant commensal bacteria belonging to Staphylococcus and Cutibacterium taxa and the fungi Malassezia, where particular species or strains can benefit the host or cause disease, are increasingly appreciated in skin disorders. Furthermore, recent research suggests that the interactions between microorganisms and the host's immune system on the skin can have distant and systemic effects on the body, such as on the gut and brain, known as the "skin-gut" or "skin-brain" axes. Studies on the microbiome in skin disease have typically relied on 16S rRNA gene sequencing methods, which cannot provide accurate information about species or strains of microorganisms on the skin. However, advancing technologies, including metagenomics and other functional 'omic' approaches, have great potential to provide more comprehensive and detailed information about the skin microbiome in health and disease. Additionally, inter-species and multi-kingdom interactions can cause cascading shifts towards dysbiosis and are crucial but yet-to-be-explored aspects of many skin disorders. Better understanding these complex dynamics will require meta-omic studies complemented with experiments and clinical trials to confirm function. Evolving how we profile the skin microbiome alongside technological advances is essential to exploring such relationships. This review presents the current and emerging methods and their findings for profiling skin microbes to advance our understanding of the microbiome in skin disease.

The persistence and stabilization of auxiliary genes in the human skin virome

BACKGROUND

The human skin contains a diverse microbiome that provides protective functions against environmental pathogens. Studies have demonstrated that bacteriophages modulate bacterial community composition and facilitate the transfer of host-specific genes, potentially influencing host cellular functions. However, little is known about the human skin virome and its role in human health. Especially, how viral-host relationships influence skin microbiome structure and function is poorly understood.

RESULTS

Population dynamics and genetic diversity of bacteriophage communities in viral metagenomic data collected from three anatomical skin locations from 60 subjects at five different time points revealed that cutaneous bacteriophage populations are mainly composed of tailed Caudovirales phages that carry auxiliary genes to help improve metabolic remodeling to increase bacterial host fitness through antimicrobial resistance. Sequence variation in the MRSA associated antimicrobial resistance gene, erm(C) was evaluated using targeted sequencing to further confirm the presence of antimicrobial resistance genes in the human virome and to demonstrate how functionality of such genes may influence persistence and in turn stabilization of bacterial host and their functions.

CONCLUSIONS

This large temporal study of human skin associated viruses indicates that the human skin virome is associated with auxiliary metabolic genes and antimicrobial resistance genes to help increase bacterial host fitness.

Seroprevalence of Four Polyomaviruses Linked to Dermatological Diseases: New Findings and a Comprehensive Analysis

Our aim was to study the seroprevalence of human polyomaviruses (HPyV) linked to skin diseases. A total of 552 serum samples were analysed by the enzyme-linked immunosorbent assay to detect IgG antibodies against Merkel cell polyomavirus (MCPyV), HPyV6, HPyV7 and Trichodysplasia spinulosa-associated polyomavirus (TSPyV) using recombinant major capsid proteins of these viruses. The individuals (age 0.8−85 years, median 33) were sorted into seven age groups: <6, 6−10, 10−14, 14−21, 21−40, 40−60 and >60 years. The adulthood seroprevalence was 69.3%, 87.7%, 83.8% and 85% for MCPyV, HPyV6, HPyV7 and TSPyV, respectively. For all four polyomaviruses, there was increasing seropositivity with age until reaching the adulthood level. There was a significant increase in seroreactivity for those age groups in which the rate of already-infected individuals also showed significant differences. The adulthood seropositvity was relatively stable with ageing, except for TSPyV, for which elevated seropositivity was observed for the elderly (>60 years) age group. Since seroepidemiological data have been published with wide ranges for all the viruses studied, we performed a comprehensive analysis comparing the published age-specific seropositivities to our data. Although the cohorts, methods and even the antigens were variable among the studies, there were similar results for all studied polyomaviruses. For MCPyV, geographically distinct genotypes might exist, which might also result in the differences in the seroprevalence data. Additional studies with comparable study groups and methods are required to clarify whether there are geographical differences.

An Improved Protocol for Comprehensive Etiological Characterization of Skin Warts and Determining Causative Human Papillomavirus Types in 128 Histologically Confirmed Common Warts

Human papillomaviruses (HPVs) are etiologically associated with various benign and malignant neoplasms of cutaneous and mucosal epithelia. We describe an improved diagnostic protocol for comprehensive characterization of causative HPV types in common warts, in which broad-spectrum PCRs followed by Sanger sequencing, two previously described and seven newly developed type-specific quantitative real-time PCRs (qPCRs) coupled with the human beta-globin qPCR were used for: (i) diagnosis of HPV infection in warts; (ii) estimation of cellular viral loads of all HPV types detected; and (iii) determination of their etiological role in 128 histologically confirmed fresh-frozen common wart tissue samples. A total of 12 different causative HPV types were determined in 122/126 (96.8%) HPV-positive warts, with HPV27 being most prevalent (27.0%), followed by HPV57 (26.2%), HPV4 (15.1%), HPV2 (13.5%), and HPV65 (7.9%). The cellular viral loads of HPV4 and HPV65 were estimated for the first time in common warts and were significantly higher than the viral loads of HPV2, HPV27, and HPV57. In addition, we showed for the first time that HPV65 is etiologically associated with the development of common warts in significantly older patients than HPV27 and HPV57, whereas HPV4-induced warts were significantly smaller than warts caused by HPV2, HPV27, HPV57, and HPV65.

Comparison of Quantitative Real-Time PCR and Digital PCR to Detect the Polyomavirus in Merkel Cell Carcinoma

Merkel cell polyomavirus (MCPyV) prevalence in Merkel cell carcinoma (MCC) cases is controversial. The detection and quantification of MCPyV DNA is mainly performed by PCR techniques using formalin-fixed, paraffin-embedded (FFPE) tissues. The aim of this study is to compare the performance of two different molecular techniques, specifically the quantitative Real-Time PCR (qPCR) and digital PCR (dPCR). Samples from 31 cases of MCC excisional surgical biopsies were analyzed. DNA extraction and purification from clinical samples were performed using the QIAcube Qiagen automated nucleic acid extractor. After the extraction, MCPyV was detected by qPCR and dPCR using specially designed primers and probes. Of the 31 MCC samples under study, the MCPyV genome was detected in 11 samples (35%) by qPCR compared with 20 samples (65%) detected by dPCR. Notably, 65% of primary tumors were positive for MCPyV (15/23). The viral genome was detected in 75% of tumors located at UV-exposed sites (6/8), 55% of tumors at partially UV-protected sites (5/9), and 67% of tumors at UV-protected sites (4/6). Our results showed a better sensitivity of dPCR in detecting the MCPyV genome in MCC samples compared with traditional qPCR techniques.

Towards standardized and reproducible research in skin microbiomes

Skin is a complex organ serving a critical role as a barrier and mediator of interactions between the human body and its environment. Recent studies have uncovered how resident microbial communities play a significant role in maintaining the normal healthy function of the skin and the immune system. In turn, numerous host-associated and environmental factors influence these communities' composition and diversity across the cutaneous surface. In addition, specific compositional changes in skin microbiota have also been connected to the development of several chronic diseases. The current era of microbiome research is characterized by its reliance on large data sets of nucleotide sequences produced with high-throughput sequencing of sample-extracted DNA. These approaches have yielded new insights into many previously uncharacterized microbial communities. Application of standardized practices in the study of skin microbial communities could help us understand their complex structures, functional capacities, and health associations and increase the reproducibility of the research. Here, we overview the current research in human skin microbiomes and outline challenges specific to their study. Furthermore, we provide perspectives on recent advances in methods, analytical tools and applications of skin microbiomes in medicine and forensics.

Psoriasis: Interplay between dysbiosis and host immune system

With advancement in human microbiome research, an increasing number of scientific evidences have endorsed the key role of both gut and skin microbiota in the pathogenesis of psoriasis. Microbiome dysbiosis, characterized by altered diversity and composition, as well as rise of pathobionts, have been identified as possible triggers for recurrent episodes of psoriasis. Mechanistically, gut dysbiosis leads to "leaky gut syndrome" via disruption of epithelial bilayer, thereby, resulting in translocation of bacteria and other endotoxins to systemic circulation, which in turn, results in inflammatory response. Similarly, skin dysbiosis disrupts the cutaneous homeostasis, leading to invasion of bacteria and other pathogens to deeper layers of skin or even systemic circulation further enhanced by injury caused by pruritus-induced scratching, and elicit innate and adaptive inflammation. The present review explores the correlation of both skin and gut microbiota dysbiosis with psoriasis. Also, the studies highlighting the potential of bacteriotherapeutic approaches including probiotics, prebiotics, metabiotics, and fecal microbiota transplantation for the management of psoriasis have been discussed.

Microbiota succession throughout life from the cradle to the grave

Associations between age and the human microbiota are robust and reproducible. The microbial composition at several body sites can predict human chronological age relatively accurately. Although it is largely unknown why specific microorganisms are more abundant at certain ages, human microbiota research has elucidated a series of microbial community transformations that occur between birth and death. In this Review, we explore microbial succession in the healthy human microbiota from the cradle to the grave. We discuss the stages from primary succession at birth, to disruptions by disease or antibiotic use, to microbial expansion at death. We address how these successions differ by body site and by domain (bacteria, fungi or viruses). We also review experimental tools that microbiota researchers use to conduct this work. Finally, we discuss future directions for studying the microbiota's relationship with age, including designing consistent, well-powered, longitudinal studies, performing robust statistical analyses and improving characterization of non-bacterial microorganisms.

Benchmarking and Assessment of Eight De Novo Genome Assemblers on Viral Next-Generation Sequencing Data, Including the SARS-CoV-2

Viral genomics has become crucial in clinical diagnostics and ecology, not to mention to stem the COVID-19 pandemic. Whole-genome sequencing (WGS) is pivotal in gaining an improved understanding of viral evolution, genomic epidemiology, infectious outbreaks, pathobiology, clinical management, and vaccine development. Genome assembly is one of the crucial steps in WGS data analyses. A series of different assemblers has been developed with the advent of high-throughput next-generation sequencing (NGS). Various studies have reported the evaluation of these assembly tools on distinct datasets; however, these lack data from viral origin. In this study, we performed a comparative evaluation and benchmarking of eight de novo assemblers: SOAPdenovo, Velvet, assembly by short sequences (ABySS), iterative De Bruijn graph assembler (IDBA), SPAdes, Edena, iterative virus assembler, and VICUNA on the viral NGS data from distinct Illumina (GAIIx, Hiseq, Miseq, and Nextseq) platforms. WGS data of diverse viruses, that is, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), dengue virus 3, human immunodeficiency virus 1, hepatitis B virus, human herpesvirus 8, human papillomavirus 16, rhinovirus A, and West Nile virus, were utilized to assess these assemblers. Performance metrics such as genome fraction recovery, assembly lengths, NG50, N50, contig length, contig numbers, mismatches, and misassemblies were analyzed. Overall, three assemblers, that is, SPAdes, IDBA, and ABySS, performed consistently well, including for genome assembly of SARS-CoV-2. These assembly methods should be considered and recommended for future studies of viruses. The study also suggests that implementing two or more assembly approaches should be considered in viral NGS studies, especially in clinical settings. Taken together, the benchmarking of eight de novo genome assemblers reported in this study can inform future public health and ecology research concerning the viruses, the COVID-19 pandemic, and viral outbreaks.

Unbalanced relationships: insights into the interaction between gut microbiota, geohelminths, and schistosomiasis

Hosts and their microbiota and parasites have co-evolved in an adaptative relationship since ancient times. The interaction between parasites and intestinal bacteria in terms of the hosts' health is currently a subject of great research interest. Therapeutic interventions can include manipulations of the structure of the intestinal microbiota, which have immunological interactions important for modulating the host's immune system and for reducing inflammation. Most helminths are intestinal parasites; the intestinal environment provides complex interactions with other microorganisms in which internal and external factors can influence the composition of the intestinal microbiota. Moreover, helminths and intestinal microorganisms can modulate the host's immune system either beneficially or harmfully. The immune response can be reduced due to co-infection, and bacteria from the intestinal microbiota can translocate to other organs. In this way, the treatment can be compromised, which, together with drug resistance by the parasites makes healing even more difficult. Thus, this work aimed to understand interactions between the microbiota and parasitic diseases caused by the most important geohelminths and schistosomiasis and the consequences of these associations.

Quantifying and Cataloguing Unknown Sequences within Human Microbiomes

Advances in genome sequencing technologies and lower costs have enabled the exploration of a multitude of known and novel environments and microbiomes. This has led to an exponential growth in the raw sequence data that are deposited in online repositories. Metagenomic and metatranscriptomic data sets are typically analysed with regard to a specific biological question. However, it is widely acknowledged that these data sets are comprised of a proportion of sequences that bear no similarity to any currently known biological sequence, and this so-called "dark matter" is often excluded from downstream analyses. In this study, a systematic framework was developed to assemble, identify, and measure the proportion of unknown sequences present in distinct human microbiomes. This framework was applied to 40 distinct studies, comprising 963 samples, and covering 10 different human microbiomes including fecal, oral, lung, skin, and circulatory system microbiomes. We found that while the human microbiome is one of the most extensively studied, on average 2% of assembled sequences have not yet been taxonomically defined. However, this proportion varied extensively among different microbiomes and was as high as 25% for skin and oral microbiomes that have more interactions with the environment. A rate of taxonomic characterization of 1.64% of unknown sequences being characterized per month was calculated from these taxonomically unknown sequences discovered in this study. A cross-study comparison led to the identification of similar unknown sequences in different samples and/or microbiomes. Both our computational framework and the novel unknown sequences produced are publicly available for future cross-referencing. Our approach led to the discovery of several novel viral genomes that bear no similarity to sequences in the public databases. Some of these are widespread as they have been found in different microbiomes and studies. Hence, our study illustrates how the systematic characterization of unknown sequences can help the discovery of novel microbes, and we call on the research community to systematically collate and share the unknown sequences from metagenomic studies to increase the rate at which the unknown sequence space can be classified.

The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes

Two leading impediments to chronic wound healing are polymicrobial infection and biofilm formation. Recent studies have characterized the bacterial fraction of these microbiomes and have begun to elucidate compositional correlations to healing outcomes. However, the factors that drive compositional shifts are still being uncovered. The virome may play an important role in shaping bacterial community structure and function. Previous work on the skin virome determined that it was dominated by bacteriophages, viruses that infect bacteria. To characterize the virome, we enrolled 20 chronic wound patients presenting at an outpatient wound care clinic in a microbiome survey, collecting swab samples from healthy skin and chronic wounds (diabetic, venous, arterial, or pressure) before and after a single, sharp debridement procedure. We investigated the virome using a virus-like particle enrichment procedure, shotgun metagenomic sequencing, and a k-mer-based, reference-dependent taxonomic classification method. Taxonomic composition, diversity, and associations with covariates are presented. We find that the wound virome is highly diverse, with many phages targeting known pathogens, and may influence bacterial community composition and functionality in ways that impact healing outcomes.

IMPORTANCE Chronic wounds are an increasing medical burden. These wounds are known to be rich in microbial content, including both bacteria and bacterial viruses (phages). The viruses may play an important role in shaping bacterial community structure and function. We analyzed the virome and bacterial composition of 20 patients with chronic wounds. The viruses found in wounds are highly diverse compared to normal skin, unlike the bacterial composition, where diversity is decreased. These data represent an initial look at this relatively understudied component of the chronic wound microbiome and may help inform future phage-based interventions.

The Interplay between Viruses and Host DNA Sensors

DNA virus infections are often lifelong and can cause serious diseases in their hosts. Their recognition by the sensors of the innate immune system represents the front line of host defence. Understanding the molecular mechanisms of innate immunity responses is an important prerequisite for the design of effective antivirotics. This review focuses on the present state of knowledge surrounding the mechanisms of viral DNA genome sensing and the main induced pathways of innate immunity responses. The studies that have been performed to date indicate that herpesviruses, adenoviruses, and polyomaviruses are sensed by various DNA sensors. In non-immune cells, STING pathways have been shown to be activated by cGAS, IFI16, DDX41, or DNA-PK. The activation of TLR9 has mainly been described in pDCs and in other immune cells. Importantly, studies on herpesviruses have unveiled novel participants (BRCA1, H2B, or DNA-PK) in the IFI16 sensing pathway. Polyomavirus studies have revealed that, in addition to viral DNA, micronuclei are released into the cytosol due to genotoxic stress. Papillomaviruses, HBV, and HIV have been shown to evade DNA sensing by sophisticated intracellular trafficking, unique cell tropism, and viral or cellular protein actions that prevent or block DNA sensing. Further research is required to fully understand the interplay between viruses and DNA sensors.

Skin Microbiota in Atopic Dermatitis

The skin microbiota represents an ecosystem composed of numerous microbial species interacting with each other, as well as with host epithelial and immune cells. The microbiota provides health benefits to the host by supporting essential functions of the skin and inhibiting colonization with pathogens. However, the disturbance of the microbial balance can result in dysbiosis and promote skin diseases, such as atopic dermatitis (AD). This review provides a current overview of the skin microbiota involvement in AD and its complex interplay with host immune response mechanisms, as well as novel therapeutic strategies for treating AD focused on restoring skin microbial homeostasis.

The Chemokine System in Oncogenic Pathways Driven by Viruses: Perspectives for Cancer Immunotherapy

Simple Summary

Oncoviruses are viruses with oncogenic potential, responsible for almost 20% of human cancers worldwide. They are from various families, some of which belong to the microbial communities that inhabit several sites in the body of healthy humans. As a result, they most often establish latent infections controlled by the arsenal of human host responses that include the chemokine system playing key roles at the interface between tissue homeostasis and immune surveillance. Yet, chemokines and their receptors also contribute to oncogenic processes as they are targeted by the virus-induced deregulations of host responses and/or directly encoded by viruses. Thus, the chemokine system offers a strong rationale for therapeutic options, some few already approved or in trials, and future ones that we are discussing in view of the pharmacological approaches targeting the different functions of chemokines operating in both cancer cells and the tumor microenvironment.

Abstract

Chemokines interact with glycosaminoglycans of the extracellular matrix and activate heptahelical cellular receptors that mainly consist of G Protein-Coupled Receptors and a few atypical receptors also with decoy activity. They are well-described targets of oncogenic pathways and key players in cancer development, invasiveness, and metastasis acting both at the level of cancer cells and cells of the tumor microenvironment. Hence, they can regulate cancer cell proliferation and survival and promote immune or endothelial cell migration into the tumor microenvironment. Additionally, oncogenic viruses display the potential of jeopardizing the chemokine system by encoding mimics of chemokines and receptors as well as several products such as oncogenic proteins or microRNAs that deregulate their human host transcriptome. Conversely, the chemokine system participates in the host responses that control the virus life cycle, knowing that most oncoviruses establish asymptomatic latent infections. Therefore, the deregulated expression and function of chemokines and receptors as a consequence of acquired or inherited mutations could bias oncovirus infection toward pro-oncogenic pathways. We here review these different processes and discuss the anticancer therapeutic potential of targeting chemokine availability or receptor activation, from signaling to decoy-associated functions, in combination with immunotherapies.

Microbial pathogenesis in inflammatory bowel diseases

Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal system. Previously, it is considered the disease of the western world but now the incidence and prevalence of IBD are increasing globally with urbanization and modernization. Additionally, the major problem is the highest incidence of IBD among children and adolescents. The precise etiology of IBD is unknown and there is no cure for IBD, which is also the reason for increasing the number of cases worldwide. The IBD is a complex interplay of environment, immune system, and microbiota in a genetically susceptible host. Among these factors, the alteration in intestinal microbiota has been detected in IBD patients. The bacterial species associated with IBD include Mycobacterium paratuberculosis, adherent-invasive E. coli (AIEC), Helicobacter pylori, and Campylobacter concisus. Moreover, the efficacy of antibiotics and probiotics further suggests the role of microbes in IBD. However, no study confirmed the bacterial species as a cause of IBD as per Koch's postulates. Thus, still controversies exist regarding the role of microbes in IBD. Therefore, this paper aims to review the current literature to evaluate the role of microbes in IBD that would be a useful inventory of researchers working in this area.

Periodontal Disease: The Good, The Bad, and The Unknown

Periodontal disease is classically characterized by progressive destruction of the soft and hard tissues of the periodontal complex, mediated by an interplay between dysbiotic microbial communities and aberrant immune responses within gingival and periodontal tissues. Putative periodontal pathogens are enriched as the resident oral microbiota becomes dysbiotic and inflammatory responses evoke tissue destruction, thus inducing an unremitting positive feedback loop of proteolysis, inflammation, and enrichment for periodontal pathogens. Keystone microbial pathogens and sustained gingival inflammation are critical to periodontal disease progression. However, recent studies have revealed the importance of previously unidentified microbes involved in disease progression, including various viruses, phages and bacterial species. Moreover, newly identified immunological and genetic mechanisms, as well as environmental host factors, including diet and lifestyle, have been discerned in recent years as further contributory factors in periodontitis. These factors have collectively expanded the established narrative of periodontal disease progression. In line with this, new ideologies related to maintaining periodontal health and treating existing disease have been explored, such as the application of oral probiotics, to limit and attenuate disease progression. The role of systemic host pathologies, such as autoimmune disorders and diabetes, in periodontal disease pathogenesis has been well noted. Recent studies have additionally identified the reciprocated importance of periodontal disease in potentiating systemic disease states at distal sites, such as in Alzheimer's disease, inflammatory bowel diseases, and oral cancer, further highlighting the importance of the oral cavity in systemic health. Here we review long-standing knowledge of periodontal disease progression while integrating novel research concepts that have broadened our understanding of periodontal health and disease. Further, we delve into innovative hypotheses that may evolve to address significant gaps in the foundational knowledge of periodontal disease.

Detection of viral gene expression in risk-stratified biopsies reveals no active HPV in cutaneous squamous cell carcinoma

BACKGROUND

Human papillomavirus (HPV) infection is known to promote the development of mucosal squamous cell carcinoma (mSCC), including pathologically high-grade lesions, but its role in cutaneous squamous cell carcinoma (cuSCC) remains unclear, particularly in lesions that are considered high risk.

OBJECTIVE

We aimed to determine whether enhanced HPV transcriptional activity can be detected in high-risk cuSCC samples compared with low-grade SCC samples or normal skin.

METHODS

We performed RNA sequencing of cuSCC across 23 risk-stratified skin lesions. A subset of samples was tested for the presence of HPV DNA. High-quality, non-human reads from each sample group were used for viral analysis using Microbiome Coverage Profiler.

RESULTS

None of the samples analysed had detectable expression of HPV RNA, while 64% of samples tested positive for HPV DNA. All samples were found to have expression of human endogenous retrovirus, and multiple samples showed expression of other viruses.

CONCLUSIONS

Viral and prophage gene expression can be monitored in cuSCC or normal skin biopsies, yet no sample in our study showed evidence of active HPV gene expression despite evidence of HPV genome presence. This suggests HPV transcription does not play a role in differentiating high-risk cuSCCs from low-risk cuSCCs or normal skin.

Human Papillomavirus Oral Infection: Review of Methodological Aspects and Epidemiology

Oral infection by Human Papillomavirus (HPV) has recently gained great attention because of its involvement in the development of a subset of head and neck squamous cell carcinoma. The role of specific Alpha-HPVs in this regard has been well established, whereas the contribution of other genera is under investigation. Despite their traditional classification as “cutaneous” types, Beta and Gamma HPVs are frequently detected in oral samples. Due to the lack of a standardized protocol, a large variety of methodologies have been used for oral sample collection, DNA extraction, HPV detection and genotyping. Laboratory procedures influence the evaluation of oral HPV prevalence, which largely varies also according to the population characteristics, e.g., age, gender, sexual behavior, Human Immunodeficiency Virus (HIV) status. Nevertheless, oral infection by Beta and Gamma HPVs seems to be even more common than Alpha-HPVs. The latter is 5–7% in the general population, and increases up to 30% approximately in HIV-infected men who have sex with men. Despite major advances in the evaluation of oral HPV prevalence, its natural history is still little understood, especially for Beta and Gamma HPVs. The latest technologies, such as Next Generation Sequencing (NGS), can be exploited to gain new insights into oral HPV, and to improve the identification of novel HPV types.

Natural History of Cutaneous Human Polyomavirus Infection in Healthy Individuals

Several human polyomaviruses (HPyVs) were recently discovered. Merkel cell polyomavirus (MCPyV) induces Merkel cell carcinoma. HPyV6, HPyV7, and TSPyV have been associated with rare skin lesions in immunosuppressed patients. HPyV9, HPyV10, and Saint Louis Polyomavirus (STLPyV) have not been convincingly associated with any disease. The aim of this prospective study was to evaluate the cutaneous prevalence, persistence and viral load of HPyVs in healthy individuals. Eight hundred seventy forehead and hand swabs were collected from 109 volunteers 4-6 weeks apart (collection period-1). Fifty-nine participants were available for follow-up a decade later (collection period-2). HPyV-DNA prevalence and viral loads of MCPyV, HPyV6, HPyV7, TSPyV, HPyV9, HPyV10, and STLPyV were determined by virus-specific real-time PCRs. Risk factors for HPyV prevalence, short- and long-term persistence were explored by logistic regression analyses. Baseline prevalence rates were similar for forehead and hand: MCPyV 67.9/67.0%, HPyV6 31.2/25.7%, HPyV7 13.8/11.0%, HPyV10 11.9/15.6%, STLPyV 7.3/8.3%, TSPyV 0.9/0.9%, and HPyV9 0.9/0.9%. Short-term persistence in period-1 was found in 59.6% (MCPyV), 23.9% (HPyV6), 10.1% (HPyV7), 6.4% (HPyV10), 5.5% (STLPyV), and 0% (TSPyV and HPyV9) on the forehead, with similar values for the hand. Long-term persistence for 9-12 years occurred only for MCPyV (forehead/hand 39.0%/44.1% of volunteers), HPyV6 (16.9%/11.9%), and HPyV7 (3.4%/5.1%). Individuals with short-term persistence had significantly higher viral loads at baseline compared to those with transient DNA-positivity (p < 0.001 for MCPyV, HPyV6, HPyV7, and HPyV10, respectively). This was also true for median viral loads in period-1 of MCPyV, HPyV6, and HPyV7 of volunteers with long-term persistence. Multiplicity (two or more different HPyVs) was a risk factor for prevalence and persistence for most HPyVs. Further risk factors were older age for HPyV6 and male sex for MCPyV on the forehead. Smoking was not a risk factor. In contrast to MCPyV, HPyV6, HPyV7, and rarely STLPyV, polyomaviruses TSPyV, HPyV9, and HPyV10 do not seem to be long-term constituents of the human skin virome of healthy individuals. Furthermore, this study showed that higher viral loads are associated with both short- and long-term persistence of HPyVs on the skin. HPyV multiplicity is a risk factor for prevalence, short-term and/or long-term persistence of MCPyV, HPyV6, HPyV7, and HPyV10.

The Keratinocyte as a Crucial Cell in the Predisposition, Onset, Progression, Therapy and Study of the Atopic Dermatitis

The keratinocyte (KC) is the main functional and structural component of the epidermis, the most external layer of the skin that is highly specialized in defense against external agents, prevention of leakage of body fluids and retention of internal water within the cells. Altered epidermal barrier and aberrant KC differentiation are involved in the pathophysiology of several skin diseases, such as atopic dermatitis (AD). AD is a chronic inflammatory disease characterized by cutaneous and systemic immune dysregulation and skin microbiota dysbiosis. Nevertheless, the pathological mechanisms of this complex disease remain largely unknown. In this review, we summarize current knowledge about the participation of the KC in different aspects of the AD. We provide an overview of the genetic predisposing and environmental factors, inflammatory molecules and signaling pathways of the KC that participate in the physiopathology of the AD. We also analyze the link among the KC, the microbiota and the inflammatory response underlying acute and chronic skin AD lesions.

A Journey on the Skin Microbiome: Pitfalls and Opportunities

The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the "core" and "transient" types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.

From Merkel Cell Polyomavirus Infection to Merkel Cell Carcinoma Oncogenesis

Merkel cell polyomavirus (MCPyV) infection causes near-ubiquitous, asymptomatic infection in the skin, but occasionally leads to an aggressive skin cancer called Merkel cell carcinoma (MCC). Epidemiological evidence suggests that poorly controlled MCPyV infection may be a precursor to MCPyV-associated MCC. Clearer understanding of host responses that normally control MCPyV infection could inform prophylactic measures in at-risk groups. Similarly, the presence of MCPyV in most MCCs could imbue them with vulnerabilities that-if better characterized-could yield targeted intervention solutions for metastatic MCC cases. In this review, we discuss recent developments in elucidating the interplay between host cells and MCPyV within the context of viral infection and MCC oncogenesis. We also propose a model in which insufficient restriction of MCPyV infection in aging and chronically UV-damaged skin causes unbridled viral replication that licenses MCC tumorigenesis.

Effects of Ulva sp. Extracts on the Growth, Biofilm Production, and Virulence of Skin Bacteria Microbiota: Staphylococcus aureus, Staphylococcus epidermidis, and Cutibacterium acnes Strains

Ulva sp. is known to be a source of bioactive compounds such as ulvans, but to date, their biological activity on skin commensal and/or opportunistic pathogen bacteria has not been reported. In this study, the effects of poly- and oligosaccharide fractions produced by enzyme-assisted extraction and depolymerization were investigated, for the first time in vitro, on cutaneous bacteria: Staphylococcus aureus, Staphylococcus epidermidis, and Cutibacterium acnes. At 1000 μg/mL, poly- and oligosaccharide fractions did not affect the growth of the bacteria regarding their generation time. Polysaccharide Ulva sp. fractions at 1000 μg/mL did not alter the bacterial biofilm formation, while oligosaccharide fractions modified S. epidermidis and C. acnes biofilm structures. None of the fractions at 1000 μg/mL significantly modified the cytotoxic potential of S. epidermidis and S. aureus towards keratinocytes. However, poly- and oligosaccharide fractions at 1000 μg/mL induced a decrease in the inflammatory potential of both acneic and non-acneic C. acnes strains on keratinocytes of up to 39.8%; the strongest and most significant effect occurred when the bacteria were grown in the presence of polysaccharide fractions. Our research shows that poly- and oligosaccharide Ulva sp. fractions present notable biological activities on cutaneous bacteria, especially towards C. acnes acneic and non-acneic strains, which supports their potential use for dermo-cosmetic applications.

Antimicrobial peptides and proteins: Interaction with the skin microbiota

The cutaneous microbiota comprises all living skin microorganisms. There is increasing evidence that the microbiota plays a crucial role in skin homeostasis. Accordingly, a dysbiosis of the microbiota may trigger cutaneous inflammation. The need for a balanced microbiota requires specific regulatory mechanisms that control and shape the microbiota. In this review, we highlight the present knowledge suggesting that antimicrobial peptides (AMPs) may exert a substantial influence on the microbiota by controlling their growth. This is supported by own data showing the differential influence of principal skin-derived AMPs on commensal staphylococci. Vice versa, we also illuminate how the cutaneous microbiota interacts with skin-derived AMPs by modulating AMP expression and how microbiota members protect themselves from the antimicrobial activity of AMPs. Taken together, the current picture suggests that a fine-tuned and well-balanced AMP-microbiota interplay on the skin surface may be crucial for skin health.

Explainable deep neural networks for novel viral genome prediction

Viral infection causes a wide variety of human diseases including cancer and COVID-19. Viruses invade host cells and associate with host molecules, potentially disrupting the normal function of hosts that leads to fatal diseases. Novel viral genome prediction is crucial for understanding the complex viral diseases like AIDS and Ebola. While most existing computational techniques classify viral genomes, the efficiency of the classification depends solely on the structural features extracted. The state-of-the-art DNN models achieved excellent performance by automatic extraction of classification features, but the degree of model explainability is relatively poor. During model training for viral prediction, proposed CNN, CNN-LSTM based methods (EdeepVPP, EdeepVPP-hybrid) automatically extracts features. EdeepVPP also performs model interpretability in order to extract the most important patterns that cause viral genomes through learned filters. It is an interpretable CNN model that extracts vital biologically relevant patterns (features) from feature maps of viral sequences. The EdeepVPP-hybrid predictor outperforms all the existing methods by achieving 0.992 mean AUC-ROC and 0.990 AUC-PR on 19 human metagenomic contig experiment datasets using 10-fold cross-validation. We evaluate the ability of CNN filters to detect patterns across high average activation values. To further asses the robustness of EdeepVPP model, we perform leave-one-experiment-out cross-validation. It can work as a recommendation system to further analyze the raw sequences labeled as ‘unknown’ by alignment-based methods. We show that our interpretable model can extract patterns that are considered to be the most important features for predicting virus sequences through learned filters.

Merkel Cell Polyomavirus Infection Induces an Antiviral Innate Immune Response in Human Dermal Fibroblasts

Merkel cell polyomavirus (MCPyV) infects most of the human population asymptomatically, but in rare cases it leads to a highly aggressive skin cancer called Merkel cell carcinoma (MCC). MCC incidence is much higher in aging and immunocompromised populations. The epidemiology of MCC suggests that dysbiosis between the host immune response and the MCPyV infectious cycle could contribute to the development of MCPyV-associated MCC. Insufficient restriction of MCPyV by normal cellular processes, for example, could promote the incidental oncogenic MCPyV integration events and/or entry into the original cell of MCC. Progress toward understanding MCPyV biology has been hindered by its narrow cellular tropism. Our discovery that primary human dermal fibroblasts (HDFs) support MCPyV infection has made it possible to closely model cellular responses to different stages of the infectious cycle. The present study reveals that the onset of MCPyV replication and early gene expression induces an inflammatory cytokine and interferon-stimulated gene (ISG) response. The cGAS-STING pathway, in coordination with NF-κB, mediates induction of this innate immune gene expression program. Further, silencing of cGAS or NF-κB pathway factors led to elevated MCPyV replication. We also discovered that the PYHIN protein IFI16 localizes to MCPyV replication centers but does not contribute to the induction of ISGs. Instead, IFI16 upregulates inflammatory cytokines in response to MCPyV infection by an alternative mechanism. The work described herein establishes a foundation for exploring how changes to the skin microenvironment induced by aging or immunodeficiency might alter the fate of MCPyV and its host cell to encourage carcinogenesis. IMPORTANCE MCC has a high rate of mortality and an increasing incidence. Immune-checkpoint therapies have improved the prognosis of patients with metastatic MCC. Still, a significant proportion of the patients fail to respond to immune-checkpoint therapies or have a medical need for iatrogenic immune-suppression. A greater understanding of MCPyV biology could inform targeted therapies for MCPyV-associated MCC. Moreover, cellular events preceding MCC oncogenesis remain largely unknown. The present study aims to explore how MCPyV interfaces with innate immunity during its infectious cycle. We describe how MCPyV replication and/or transcription elicit an innate immune response via cGAS-STING, NF-κB, and IFI16. We also explore the effects of this response on MCPyV replication. Our findings illustrate how healthy cellular conditions may allow low-level infection that evades immune destruction until highly active replication is restricted by host responses. Conversely, pathological conditions could result in unbridled MCPyV replication that licenses MCC tumorigenesis.

Human Three-Dimensional Models for Studying Skin Pathogens

Skin is the most exposed surface of the human body, separating the microbe-rich external environment, from the sterile inner part. When skin is breached or its homeostasis is perturbed, bacterial, fungal and viral pathogens can cause local infections or use the skin as an entry site to spread to other organs. In the last decades, it has become clear that skin provides niches for permanent microbial colonization, and it actively interacts with microorganisms. This crosstalk promotes skin homeostasis and immune maturation, preventing expansion of harmful organisms. Skin commensals, however, are often found to be skin most prevalent and dangerous pathogens. Despite the medical interest, mechanisms of colonization and invasion for most skin pathogens are poorly understood. This limitation is due to the lack of reliable skin models. Indeed, animal models do not adequately mimic neither the anatomy nor the immune response of human skin. Human 3D skin models overcome these limitations and can provide new insights into the molecular mechanisms of microbial pathogenesis. Herein, we address the strengths and weaknesses of different types of human skin models and we review the main findings obtained using these models to study skin pathogens.

Transcription of human papillomaviruses in nonmelanoma skin cancers of the immunosuppressed

Nonmelanoma skin cancer (NMSC) has a greatly increased incidence among the immunosuppressed and the DNA of human papillomavirus (HPV) is commonly found in these tumors. To investigate if there are any actively transcribed HPV infections in these tumors, we identified all skin cancers diagnosed after solid organ transplantation in Sweden during 1964-2011 (n = 7614 NMSCs) and requested the diagnostic tumor blocks from the corresponding pathology archives. For the present study, we selected diagnostic specimens from 345 NMSC and performed whole genome transcriptome analysis using NovaSeq (Illumina), in comparison with three cervical cancers. Although we obtained an abundance of high-quality paired reads per sample (median of 35 million reads), only 15 NMSC specimens contained HPV transcription. Three specimens had transcription of oncogenic anogenital HPVs (HPV16 and 56), six tumors had transcription of HPVs from the beta-2 species (three HPV38, two with HPV23 and one with HPV107) and then there was one observation each of transcription of HPVs 3, 26, 57, 147, 158, 168 and of two nonestablished HPV types belonging to the gamma genus. In conclusion, transcription of specific HPV types can be found in NMSC among the immunosuppressed, but this is not common.

CXCR4 signaling controls dendritic cell location and activation at steady state and in inflammation

Dendritic cells (DCs) encompass several cell subsets that collaborate to initiate and regulate immune responses. Proper DC localization determines their function and requires the tightly controlled action of chemokine receptors. All DC subsets express CXCR4, but the genuine contribution of this receptor to their biology has been overlooked. We addressed this question using natural CXCR4 mutants resistant to CXCL12-induced desensitization and harboring a gain of function that cause the warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome (WS), a rare immunodeficiency associated with high susceptibility to the pathogenesis of human papillomavirus (HPV). We report a reduction in the number of circulating plasmacytoid DCs (pDCs) in WHIM patients, whereas that of conventional DCs is preserved. This pattern was reproduced in an original mouse model of WS, enabling us to show that the circulating pDC defect can be corrected upon CXCR4 blockade and that pDC differentiation and function are preserved, despite CXCR4 dysfunction. We further identified proper CXCR4 signaling as a critical checkpoint for Langerhans cell and DC migration from the skin to lymph nodes, with corollary alterations of their activation state and tissue inflammation in a model of HPV-induced dysplasia. Beyond providing new hypotheses to explain the susceptibility of WHIM patients to HPV pathogenesis, this study shows that proper CXCR4 signaling establishes a migration threshold that controls DC egress from CXCL12-containing environments and highlights the critical and subset-specific contribution of CXCR4 signal termination to DC biology.