A Comparison of Techniques for Collecting Skin Microbiome Samples: Swabbing Versus Tape-Stripping

Exploring the skin microbiome in atopic dermatitis pathogenesis and disease modification

Inflammatory skin diseases such as atopic eczema (atopic dermatitis [AD]) affect children and adults globally. In AD, the skin barrier is impaired on multiple levels. Underlying factors include genetic, chemical, immunologic, and microbial components. Increased skin pH in AD is part of the altered microbial microenvironment that promotes overgrowth of the skin microbiome with Staphylococcus aureus. The secretion of virulence factors, such as toxins and proteases, by S aureus further aggravates the skin barrier deficiency and additionally disrupts the balance of an already skewed immune response. Skin commensal bacteria, however, can inhibit the growth and pathogenicity of S aureus through quorum sensing. Therefore, restoring a healthy skin microbiome could contribute to remission induction in AD. This review discusses direct and indirect approaches to targeting the skin microbiome through modulation of the skin pH; UV treatment; and use of prebiotics, probiotics, and postbiotics. Furthermore, exploratory techniques such as skin microbiome transplantation, ozone therapy, and phage therapy are discussed. Finally, we summarize the latest findings on disease and microbiome modification through targeted immunomodulatory systemic treatments and biologics. We believe that targeting the skin microbiome should be considered a crucial component of successful AD treatment in the future.

Investigating Distinct Skin Microbial Communities and Skin Metabolome Profiles in Atopic Dermatitis

Atopic dermatitis (AD) is a chronic inflammatory skin disorder influenced by genetic predisposition, environmental factors, immune dysregulation, and skin barrier dysfunction. The skin microbiome and metabolome play crucial roles in modulating the skin's immune environment and integrity. However, their specific contributions to AD remain unclear. We aimed to investigate the distinct skin microbial communities and skin metabolic compounds in AD patients compared to healthy controls (HCs). Seven patients with AD patients and seven HCs were enrolled, from whom skin samples were obtained for examination. The study involved 16S rRNA metagenomic sequencing and bioinformatics analysis as well as the use of gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) to detect metabolites associated with AD in the skin. We observed significant differences in microbial diversity between lesional and non-lesional skin of AD patients and HCs. Staphylococcus overgrowth was prominent in AD lesions, while Cutibacterium levels were decreased. Metabolomic analysis revealed elevated levels of several metabolites, including hypoxanthine and glycerol-3-phosphate in AD lesions, indicating perturbations in purine metabolism and energy production pathways. Moreover, we found a positive correlation between hypoxanthine and glycerol-3-phosphate and clinical severity of AD and Staphylococcus overgrowth. These findings suggest potential biomarkers for monitoring AD severity. Further research is needed to elucidate the causal relationships between microbial dysbiosis, metabolic alterations, and AD progression, paving the way for targeted therapeutic interventions.

Considerations for performing companion animal skin microbiome studies

The microbiome field has grown significantly in the past decade, and published studies have provided an overview of the microorganisms inhabiting the skin of companion animals. With the continued growth and interest in this field, concerns have been raised regarding sample collection methods, reagent contamination, data processing and environmental factors that may impair data interpretation (especially as related to low-biomass skin samples). In order to assure transparency, it is important to report all steps from sample collection to data analysis, including use of proper controls, and to make sequence data and sample metadata publicly available. Whilst interstudy variation will continue to exist, efforts to standardise methods will reduce confounding variables, and allow for reproducibility and comparability of results between studies. Companion animal microbiome studies often include clinical cases, and small sample sizes may result in lack of statistical significance within small datasets. The ability to combine results from standardised studies through meta-analyses would mitigate the limitations of these smaller studies, providing for more robust interpretation of results which could then inform clinical decisions. In this narrative review, we aim to present considerations for designing a study to evaluate the skin microbiome of companion animals, from conception to data analysis.

Women Skin Microbiota Modifications during Pregnancy

Several studies have shown fluctuations in the maternal microbiota at various body sites (gut, oral cavity, and vagina). The skin microbiota plays an important role in our health, but studies on the changes during pregnancy are limited. Quantitative and qualitative variations in the skin microbiota in pregnant woman could indeed play important roles in modifying the immune and inflammatory responses of the host. These alterations could induce inflammatory disorders affecting the individual's dermal properties, and could potentially predict infant skin disorder in the unborn. The present study aimed to characterize skin microbiota modifications during pregnancy. For this purpose, skin samples were collected from 52 pregnant women in the first, second, and third trimester of non-complicated pregnancies and from 17 age- and sex-matched healthy controls. The skin microbiota composition was assessed by next generation sequencing (NGS) of the V3-V4 region of the bacterial rRNA 16S. Our results indicate that from the first to the third trimester of pregnancy, changes occur in the composition of the skin microbiota, microbial interactions, and various metabolic pathways. These changes could play a role in creating more advantageous conditions for fetal growth.

Skin emitted volatiles analysis for noninvasive diagnosis: the current advances in sample preparation techniques for biomedical application

Human skin emits a series of volatile compounds from the skin due to various metabolic processes, microbial activity, and several external factors. Changes in the concentration of skin volatile metabolites indicate many diseases, including diabetes, cancer, and infectious diseases. Researchers focused on skin-emitted compounds to gain insight into the pathophysiology of various diseases. In the case of skin volatolomics research, it is noteworthy that sample preparation, sampling protocol, analytical techniques, and comprehensive validation are important for the successful integration of skin metabolic profiles into regular clinical settings. Solid-phase microextraction techniques and polymer-based active sorbent traps were developed to capture the skin-emitted volatile compounds. The primary advantage of these sample preparation techniques is the ability to efficiently and targetedly capture skin metabolites, thus improving the detection of the biomarkers associated with various diseases. In further research, polydimethyl-based patches were utilized for skin research due to their biocompatibility and thermal stability properties. The microextraction sampling tools coupled with high sensitive Gas Chromatography-Mass Spectrometer provided a potential platform for skin volatolomes, thus emerging as a state-of-the-art analytical technique. Later, technological advancements, including the design of wearable sensors, have enriched skin-based research as it can integrate the information from skin-emitted volatile profiles into a portable platform. However, individual-specific hydration, temperature, and skin conditions can influence variations in skin volatile concentration. Considering the subject-specific skin depth, sampling time standardization, and suitable techniques may improve the skin sampling techniques for the potential discovery of various skin-based marker compounds associated with diseases. Here, we have summarised the current research progress, limitations, and technological advances in skin-based sample preparation techniques for disease diagnosis, monitoring, and personalized healthcare applications.

Multi-omics analyses reveal interactions between the skin microbiota and skin metabolites in atopic dermatitis

Introduction

Atopic dermatitis (AD) is one of the most common inflammatory skin diseases. Skin microecological imbalance is an important factor in the pathogenesis of AD, but the underlying mechanism of its interaction with humans remains unclear.

Methods

16S rRNA gene sequencing was conducted to reveal the skin microbiota dynamics. Changes in skin metabolites were tracked by LC-MS metabolomics. We then explored the potential mechanism of interaction by analyzing the correlation between skin bacterial communities and metabolites in corresponding skin-associated samples.

Results

Samples from 18 AD patients and 18 healthy volunteers (HVs) were subjected to 16S rRNA gene sequencing and LC-MS metabolomics. AD patients had dysbiosis of the skin bacterial community with decreased species richness and evenness. The relative abundance of the genus Staphylococcus increased significantly in AD, while the abundances of the genera Propionibacterium and Brevundimonas decreased significantly. The relative abundance of the genera Staphylococcus in healthy females was significantly higher than those in healthy males, while it showed no difference in AD patients with or without lesions. The effects of AD status, sex and the presence or absence of rashes on the number of differentially abundant metabolites per capita were successively reduced. Multiple metabolites involved in purine metabolism and phenylalanine metabolism pathways (such as xanthosine/xanthine and L-phenylalanine/trans-cinnamate) were increased in AD patients. These trends were much more obvious between female AD patients and female HVs. Spearman correlation analysis revealed that the genus Staphylococcus was positively correlated with various compounds involved in phenylalanine metabolism and purine metabolic pathways. The genera Brevundimonas and Lactobacillus were negatively correlated with various compounds involved in purine metabolism, phenylalanine metabolism and sphingolipid signaling pathways.

Discussion

We suggest that purine metabolism and phenylalanine metabolism pathway disorders may play a certain role in the pathogenic mechanism of Staphylococcus aureus in AD. We also found that females are more likely to be colonized by the genus Staphylococcus than males. Differentially abundant metabolites involved in purine metabolism and phenylalanine metabolism pathways were more obvious in female. However, we should notice that the metabolites we detected do not necessarily derived from microbes, they may also origin from the host.

Advancements in Skin-Mediated Drug Delivery: Mechanisms, Techniques, and Applications

Skin-mediated drug delivery methods currently are receiving significant attention as a promising approach for the enhanced delivery of drugs through the skin. Skin-mediated drug delivery offers the potential to overcome the limitations of traditional drug delivery methods, including oral administration and intravenous injection. The challenges associated with drug permeation through layers of skin, which act as a major barrier, are explored, and strategies to overcome these limitations are discussed in detail. This review categorizes skin-mediated drug delivery methods based on the means of increasing drug permeation, and it provides a comprehensive overview of the mechanisms and techniques associated with these methods. In addition, recent advancements in the application of skin-mediated drug delivery are presented. The review also outlines the limitations of ongoing research and suggests future perspectives of studies regarding the skin-mediated delivery of drugs.

Skin Barrier-Enhancing Effects of Dermabiotics HDB with Regulation of Skin Microbiota

In the regulation of inflammatory responses and skin homeostasis, the skin and its microbiota are closely related. Studies have reported that lactic acid bacteria extracts can improve the skin condition and microbiota. In our previous study, we developed probiotic lysates, which are efficacious in improvement of human skin cells and the skin barrier. The skin-moisturizing effect of Dermabiotics HDB (HDB) prepared with Lactiplantibacillus plantarum, and the correlation between changes in the skin microbiota and moisture contents, were evaluated and analyzed in clinical trials. The clinical parameters on the cheeks of 21 female participants were measured using biophysical tools before and after (2 weeks) using HDB or control. The skin microbes were collected and identified using 16s rRNA gene sequencing. HDB significantly improved moisture intensity, transepidermal water loss (TEWL), and hot flush level on the cheek. The beta-diversity of the skin microbiota was different from that of the control in the unweighted UniFrac principal coordinate analysis after using HDB. The genus Lawsonella demonstrated a positive correlation with TEWL and a negative correlation with the moisture contents of the keratin layer, regardless of the use of HDB and control. Conversely, after HDB use, the genus Staphylococcus was increased and associated with a lower hot flush level, while the genera of the phylum Proteobacteria tended to decrease, which is associated with an improved skin condition. Overall, HDB showed clinically proven effects, including skin moisturization with regulation of the skin microbiota.

Benchmarking MicrobIEM - a user-friendly tool for decontamination of microbiome sequencing data

BACKGROUND

Microbiome analysis is becoming a standard component in many scientific studies, but also requires extensive quality control of the 16S rRNA gene sequencing data prior to analysis. In particular, when investigating low-biomass microbial environments such as human skin, contaminants distort the true microbiome sample composition and need to be removed bioinformatically. We introduce MicrobIEM, a novel tool to bioinformatically remove contaminants using negative controls.

RESULTS

We benchmarked MicrobIEM against five established decontamination approaches in four 16S rRNA amplicon sequencing datasets: three serially diluted mock communities (108-103 cells, 0.4-80% contamination) with even or staggered taxon compositions and a skin microbiome dataset. Results depended strongly on user-selected algorithm parameters. Overall, sample-based algorithms separated mock and contaminant sequences best in the even mock, whereas control-based algorithms performed better in the two staggered mocks, particularly in low-biomass samples (≤ 106 cells). We show that a correct decontamination benchmarking requires realistic staggered mock communities and unbiased evaluation measures such as Youden's index. In the skin dataset, the Decontam prevalence filter and MicrobIEM's ratio filter effectively reduced common contaminants while keeping skin-associated genera.

CONCLUSIONS

MicrobIEM's ratio filter for decontamination performs better or as good as established bioinformatic decontamination tools. In contrast to established tools, MicrobIEM additionally provides interactive plots and supports selecting appropriate filtering parameters via a user-friendly graphical user interface. Therefore, MicrobIEM is the first quality control tool for microbiome experts without coding experience.

Skin microbiome profile in people living with HIV/AIDS in Cameroon

The presence of pathogens and the state of diseases, particularly skin diseases, may alter the composition of human skin microbiome. HIV infection has been reported to impair gut microbiome that leads to severe consequences. However, with cutaneous manifestations, that can be life-threatening, due to the opportunistic pathogens, little is known whether HIV infection might influence the skin microbiome and affect the skin homeostasis. This study catalogued the profile of skin microbiome of healthy Cameroonians, at three different skin sites, and compared them to the HIV-infected individuals. Taking advantage on the use of molecular assay coupled with next-generation sequencing, this study revealed that alpha-diversity of the skin microbiome was higher and beta-diversity was altered significantly in the HIV-infected Cameroonians than in the healthy ones. The relative abundance of skin microbes such as Micrococcus and Kocuria species was higher and Cutibacterium species was significantly lower in HIV-infected people, indicating an early change in the human skin microbiome in response to the HIV infection. This phenotypical shift was not related to the number of CD4 T cell count thus the cause remains to be identified. Overall, these data may offer an important lead on the role of skin microbiome in the determination of cutaneous disease state and the discovery of safe pharmacological preparations to treat microbial-related skin disorders.

Streptococcus pyogenes carriage acquisition, persistence and transmission dynamics within households in The Gambia (SpyCATS): protocol for a longitudinal household cohort study

Background

Streptococcus pyogenes (StrepA) causes a significant burden of disease globally from superficial infections to invasive disease. It is responsible for over 500,000 deaths each year, predominantly in low- and middle-income countries (LMIC). Superficial StrepA infections of the skin and pharynx can lead to rheumatic heart disease, the largest cause of StrepA-related deaths in LMIC. StrepA can also asymptomatically colonise normal skin and the pharynx (carriage), potentially increasing infection risk. Streptococcus dysgalactiae subsp. equisimilis (SDSE) carriage is also common in LMIC and may interact with StrepA. This study aims to investigate StrepA and SDSE carriage and infection epidemiology, transmission dynamics and naturally acquired immunity within households in The Gambia.

Methods

A longitudinal household observational cohort study will be conducted over one year. 45 households will be recruited from the urban area of Sukuta, The Gambia, resulting in approximately 450 participants. Households will be visited monthly, and available participants will undergo oropharyngeal and normal skin swabbing. Incident cases of pharyngitis and pyoderma will be captured via active case reporting, with swabs taken from disease sites. Swabs will be cultured for the presence of group A, C and G beta-haemolytic streptococci. Isolates will undergo whole genome sequencing. At each visit, clinical, socio-demographic and social mixing data will be collected. Blood serum will be collected at baseline and final visit. Oral fluid and dried blood spot samples will be collected at each visit. Mucosal and serum anti-StrepA antibody responses will be measured.

Outcome

This study will report StrepA and SDSE clinical epidemiology, risk factors, transmission dynamics, and serological responses to carriage and infection. Detailed social mixing behaviour will be combined with phylogenetic relatedness to model the extent of transmission occurring withing and between households. The study will provide data to help meet global strategic StrepA research goals.

Analysis of Microbiomes from Ultra-Low Biomass Surfaces Using Novel Surface Sampling and Nanopore Sequencing

The rapid assessment of microbiomes from ultra-low biomass environments such as cleanrooms or hospital operating rooms has a number of applications for human health and spacecraft manufacturing. Current techniques often employ lengthy protocols using short-read DNA sequencing technology to analyze amplified DNA and have the disadvantage of a longer analysis time and lack of portability. Here, we demonstrate a rapid (~24 hours) on-site nanopore-based sequencing approach to characterize the microbiome of a NASA Class 100K cleanroom where spacecraft components are assembled. This approach employs a modified protocol of Oxford Nanopore's Rapid PCR Barcoding Kit in combination with the recently developed Squeegee-Aspirator for Large Sampling Area (SALSA) surface sampling device. Results for these ultra-low biomass samples revealed DNA amplification ~1 to 2 orders of magnitude above process control samples and were dominated primarily by Paracoccus and Acinetobacter species. Negative control samples were collected to provide critical data on background contamination, including Cutibacerium acnes, which most likely originated from the sampling reagents-associated microbiome (kitome). Overall, these results provide data on a novel approach for rapid low-biomass DNA profiling using the SALSA sampler combined with modified nanopore sequencing. These data highlight the critical need for employing multiple negative controls, along with using DNA-free reagents and techniques, to enable a proper assessment of ultra-low biomass samples.

Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data

Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.

Treatment of fungal infection on left ventricle assist device driveline exit site: a case report and systematic review

OBJECTIVE

The use of ventricular assist devices (VAD) is increasing; however, diagnosis and management of device complications, such as the driveline exit site (DES) being the portal of entry for fungal infection, is not well known.

METHOD

A systematic review involving searching PubMed (2005 to July 2020) was conducted. The case of a 43-year-old female patient who had a left VAD (LVAD) (HeartMate 3, Abbott, US) is also reported.

RESULTS

The patient was successfully treated with ketoconazole cream and oral fluconazole for likely superficial DES fungal infections. We included 36 studies that met our inclusion criteria; however, only one was included in our review. In the literature, five cases of DES fungal infection were reported, with Candida being the only fungal pathogen.

CONCLUSION

LVAD fungal infections are uncommon but can be responsible for high mortality rates, require a prolonged period of treatment, and can present a huge problem when surgical alternatives are not available. However, Candida species are most common. Fungal infections can only produce clear discharge, and so the classic definition of driveline infection based on purulent secretion can vary. Negative skin culture does not exclude the diagnosis of infection of the DES, and so empirical diagnosis may only be clinically based.

Macroscopic Skin Examination Can Determine the Number of Strips Necessary to Study the stratum corneum in Dogs

To evaluate the skin barrier, the stratum corneum (SC) must be isolated and extracted. Currently, skin biopsy is the gold standard method to investigate skin immunology and the presence of biomarkers in dogs. However, a standardized, non-invasive tool to exclusively remove the SC would be of great interest to study healthy and atopic dogs. In this study, we performed D-squames® tape stripping with standardized pressure on seven healthy beagle dogs. A control site was defined and then 25 strips, 50 strips and as many strips as needed to achieve a shiny appearance of the skin were performed on three different experimental sites. After stripping, blinded histopathological examination of a skin biopsy from each site was performed. The number of tape strips required for the skin to become shiny varied between individuals, with a mean of 40 (29-50) strips. There was no significant difference in SC depth between the control site and the site that underwent 25 tape strips. In contrast, the use of 50 strips removed almost all of the SC, with a mean remaining SC depth of 7.82 µm. These data suggest that this non-invasive method can effectively remove the SC, with individual variability, and that a shiny appearance of the skin after stripping can be used as an accurate marker of SC removal.

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.

The Skin Microbiome: Current Techniques, Challenges, and Future Directions

Skin acts as a barrier that promotes the colonization of bacteria, fungi, archaea, and viruses whose membership and function may differ depending on the various specialized niches or micro-environments of the skin. The group of microorganisms inhabiting the skin, also known as the skin microbiome, offers protection against pathogens while actively interacting with the host's immune system. Some members of the skin microbiome can also act as opportunistic pathogens. The skin microbiome is influenced by factors such as skin site, birth mode, genetics, environment, skin products, and skin conditions. The association(s) of the skin microbiome with health and disease has (have) been identified and characterized via culture-dependent and culture-independent methods. Culture-independent methods (such as high-throughput sequencing), in particular, have expanded our understanding of the skin microbiome's role in maintaining health or promoting disease. However, the intrinsic challenges associated with the low microbial biomass and high host content of skin microbiome samples have hindered advancements in the field. In addition, the limitations of current collection and extraction methods and biases derived from sample preparation and analysis have significantly influenced the results and conclusions of many skin microbiome studies. Therefore, the present review discusses the technical challenges associated with the collection and processing of skin microbiome samples, the advantages and disadvantages of current sequencing approaches, and potential future areas of focus for the field.

The Science of Skin: Measuring Damage and Assessing Risk

Significance: Healthy skin provides a barrier to contaminants. Breaches in skin integrity are often encountered in the patient health care journey, owing to intrinsic health issues or to various procedures and medical devices used. The time has come to move clinical practice beyond mere awareness of medical adhesive-related skin injury and toward improved care and outcomes. Recent Advances: Methods developed in research settings allow quantitative assessments of skin damage based on the measurement of baseline skin properties. These properties become altered by stress and over time. Assessment methods typically used by the cosmetic industry to compare product performance could offer new possibilities to improve clinical practice by providing better information on the status of patient skin. This review summarizes available skin assessment methods as well as specific patient risks for skin damage. Critical Issues: Patients in health care settings may be at risk for skin damage owing to predisposing medical conditions, health status, medications taken, and procedures or devices used in their treatment. Skin injuries come as an additional burden to these medical circumstances and could be prevented. Technology should be leveraged to improve care, help maintain patient skin health, and better characterize functional wound closure. Future Directions: Skin testing methods developed to evaluate cosmetic products or assess damage caused by occupational exposure can provide detailed, quantitative information on the integrity of skin. Such methods have the potential to guide prevention and treatment efforts to improve the care of patients suffering from skin integrity issues while in the health care system.

Skin Microbiota: Setting up a Protocol to Evaluate a Correlation between the Microbial Flora and Skin Parameters

The concept of skin microbiota is not really clear and more accurate approaches are necessary to explain how microbial flora can influence skin biophysical parameters in healthy individuals and in pathology patients with non-infectious skin disease. The aim of this work is to provide a suitable, fast and reproducible protocol to correlate skin parameters with the composition of skin microbiota. For this purpose, the work was split into two main phases. The first phase was focused on the selection of volunteers by the administration of a specific questionnaire. The skin microbiota was then collected from the forehead of selected volunteers as a test area and from the shoulder as control area. On the same skin area, the biophysical parameters, such as trans-epidermal water loss (TEWL), sebum level (SL), porphyrin intensity, keratin content and stratum corneum water content were taken. All parameters were taken at t0 and after 15 days without changes in the volunteers' lifestyle. A strong correlation was found between forehead and shoulder area for porphyrin intensity, pH and TEWL parameters, and between Cutibacterium acnes and some biophysical parameters both in the forehead and the shoulder area. The procedural setup in this work represents the starting point for evaluating problematic skins and the efficacy of cosmetic products or treatment against skin dysbiosis.

Laser capture microdissection as a method for investigating the human hair follicle microbiome reveals region-specific differences in the bacteriome profile

OBJECTIVE

Human hair follicles (HFs) are populated by a rich and diverse microbiome, traditionally evaluated by methods that inadvertently sample the skin microbiome and/or miss microbiota located in deeper HF regions. Thereby, these methods capture the human HF microbiome in a skewed and incomplete manner. This pilot study aimed to use laser-capture microdissection of human scalp HFs, coupled with 16S rRNA gene sequencing to sample the HF microbiome and overcome these methodological limitations.

RESULTS

HFs were laser-capture microdissected (LCM) into three anatomically distinct regions. All main known core HF bacterial colonisers, including Cutibacterium, Corynebacterium and Staphylococcus, were identified, in all three HF regions. Interestingly, region-specific variations in α-diversity and microbial abundance of the core microbiome genera and Reyranella were identified, suggestive of variations in microbiologically relevant microenvironment characteristics. This pilot study therefore shows that LCM-coupled with metagenomics is a powerful tool for analysing the microbiome of defined biological niches. Refining and complementing this method with broader metagenomic techniques will facilitate the mapping of dysbiotic events associated with HF diseases and targeted therapeutic interventions.

Progress of metabolomics in atopic dermatitis: a systematic review

Atopic dermatitis (AD), a chronic inflammatory skin disorder characterized by recurrent eczema and intense pruritus, is a major skin-related burden worldwide. The diagnosis and treatment of AD is often challenging due to the high heterogeneity of AD, and its exact etiology is unknown. Metabolomics offers the opportunity to follow continuous physiological and pathological changes in individuals, which allows accurate diagnosis and management as well as providing deep insights into the etiopathogenesis of AD. Several metabolomic studies of AD have been published over the past few years. The aim of this review is to summarize these findings and help researchers to understand the rapid development of metabolomics for AD. A comprehensive and systematic search was performed using the PubMed, Embase, Cochrane Library and Web of Science databases. Twenty-six papers were finally included in the review after quality assessment. Significant differences in metabolite profiles were found between patients with AD and healthy individuals. This study provides a comprehensive overview of metabolomic research in AD. A better understanding of the metabolomics of AD may offer novel diagnostic, prognostic, and therapeutic approaches.

Relationship between healing status and microbial dissimilarity in wound and peri-wound skin in pressure injuries

AIM

Wound infection is the most serious cause of delayed healing for patients with pressure injuries. The wound microbiota, which plays a crucial role in delayed healing, forms by bacterial dissemination from the peri-wound skin. To manage the bioburden, wound and peri-wound skin care has been implemented; however, how the microbiota at these sites contribute to delayed healing is unclear. Therefore, we investigated the relationship between healing status and microbial dissimilarity in wound and peri-wound skin.

METHODS

A prospective cohort study was conducted at a long-term care hospital. The outcome was healing status assessed using the DESIGN-R® tool, a wound assessment tool to monitor the wound healing process. Bacterial DNA was extracted from the wound and peri-wound swabs, and microbiota composition was analyzed using 16S rRNA gene analysis. To evaluate microbial similarity, the weighted UniFrac dissimilarity index between wound and peri-wound microbiota was calculated.

RESULTS

Twenty-two pressure injuries (7 deep and 15 superficial wounds) were included in the study. For deep wounds, the predominant bacteria in wound and peri-wound skin were the same in the healing wounds, whereas they were different in all cases of hard-to-heal wounds. Analysis based on the weighted UniFrac dissimilarity index, there was no significant difference for healing wounds (p = 0.639), while a significant difference was found for hard-to-heal wounds (p = 0.047).

CONCLUSIONS

Delayed healing is possibly associated with formation of wound microbiota that is different in composition from that of the skin commensal microbiota. This study provides a new perspective for assessing wound bioburden.

Streptococcus pyogenes carriage acquisition, persistence and transmission dynamics within households in The Gambia (SpyCATS): protocol for a longitudinal household cohort study

Background Streptococcus pyogenes (StrepA) causes a significant burden of disease globally from superficial infections to invasive disease. It is responsible for over 500,000 deaths each year, predominantly in low- and middle-income countries (LMIC). Superficial StrepA infections of the skin and pharynx can lead to rheumatic heart disease, the largest cause of StrepA-related deaths in LMIC. StrepA can also asymptomatically colonise normal skin and the pharynx (carriage), potentially increasing infection risk. Streptococcus dysgalactiae subsp. equisimilis (SDSE) carriage is also common in LMIC and may interact with StrepA. This study aims to investigate StrepA and SDSE carriage and infection epidemiology, transmission dynamics and naturally acquired immunity within households in The Gambia. Methods A longitudinal household observational cohort study will be conducted over one year. 45 households will be recruited from the urban area of Sukuta, The Gambia, resulting in approximately 450 participants. Households will be visited monthly, and available participants will undergo oropharyngeal and normal skin swabbing. Incident cases of pharyngitis and pyoderma will be captured via active case reporting, with swabs taken from disease sites. Swabs will be cultured for the presence of group A, C and G beta-haemolytic streptococci. Isolates will undergo whole genome sequencing. At each visit, clinical, socio-demographic and social mixing data will be collected. Blood serum will be collected at baseline and final visit. Oral fluid and dried blood spot samples will be collected at each visit. Mucosal and serum anti-StrepA antibody responses will be measured. Outcome This study will report StrepA and SDSE clinical epidemiology, risk factors, transmission dynamics, and serological responses to carriage and infection. Detailed social mixing behaviour will be combined with phylogenetic relatedness to model the extent of transmission occurring withing and between households. The study will provide data to help meet global strategic StrepA research goals.

Skin dysbiosis and Cutibacterium acnes biofilm in inflammatory acne lesions of adolescents

Acne vulgaris is a common inflammatory disorder affecting more than 80% of young adolescents. Cutibacterium acnes plays a role in the pathogenesis of acne lesions, although the mechanisms are poorly understood. The study aimed to explore the microbiome at different skin sites in adolescent acne and the role of biofilm production in promoting the growth and persistence of C. acnes isolates. Microbiota analysis showed a significantly lower alpha diversity in inflammatory lesions (LA) than in non-inflammatory (NI) lesions of acne patients and healthy subjects (HS). Differences at the species level were driven by the overabundance of C. acnes on LA than NI and HS. The phylotype IA1 was more represented in the skin of acne patients than in HS. Genes involved in lipids transport and metabolism, as well as potential virulence factors associated with host-tissue colonization, were detected in all IA1 strains independently from the site of isolation. Additionally, the IA1 isolates were more efficient in early adhesion and biomass production than other phylotypes showing a significant increase in antibiotic tolerance. Overall, our data indicate that the site-specific dysbiosis in LA and colonization by virulent and highly tolerant C. acnes phylotypes may contribute to acne development in a part of the population, despite the universal carriage of the microorganism. Moreover, new antimicrobial agents, specifically targeting biofilm-forming C. acnes, may represent potential treatments to modulate the skin microbiota in acne.

An Advanced Tape-Stripping Approach for High-Efficiency Sampling on Non-Absorbent Surfaces

Surface sampling is a frequent task in laboratory work and field studies. Simple methods usually have low efficiency in collecting target substances from surfaces. This study developed an advanced tape-stripping approach for efficient sampling on non-absorbent surfaces. A film-forming solution, prepared using polyvinyl alcohol, is applied to the target surface, where it covers and engulfs the surface deposits and then solidifies into an elastic membrane as it is exposed to air. The deposits are collected by stripping off the membrane and re-dissolving it in water. This new approach exhibited an efficiency of 100% in collecting uniform-size microspheres from glass surfaces and extremely high efficiencies (>96.6%) in detecting selected target DNA materials from glass and stainless steel surfaces. In comparison, the common swab-rinse method exhibited an efficiency of 72.6% under similar measuring conditions. The viability of S. aureus during sampling using the new approach decreased as the ethanol concentration in the applied solution increased. Using a solution with a mass ratio of ethanol of 17.6% balanced the effects of multiplication and degradation of the S. aureus on glass surfaces during sampling. Overall, the proposed approach exhibits high efficiency in collecting living and abiotic matter from non-absorbent surfaces, complementing existing sampling methods.

A new dexpanthenol-containing liquid cleanser for atopic-prone skin: Results from two prospective clinical studies evaluating cutaneous tolerability, moisturization potential, and effects on barrier function

BACKGROUND

Gentle cleansing of the skin without further compromising its barrier function and moisture content and being simultaneously devoid of adverse effects on the skin microbiome are important features of body cleansers for atopic-prone skin sufferers. For this population, a new dexpanthenol-containing liquid cleanser (DCLC) was developed.

METHODS

Two prospective 4-week studies have been conducted. Study 1 investigated the effect of once-daily DCLC on stratum corneum (SC) hydration, transepidermal water loss (TEWL), skin pH, and skin microbiome (all on the volar forearm) in adult subjects with dry skin (N = 44). Study 2 explored the cutaneous tolerability of DCLC and its effect on the microbiome biodiversity of the volar forearm skin in infants/children with atopic-prone skin (N = 33, aged 6 months to 6 years). In the latter study, DCLC was applied 2-3 days/week in combination with an emollient applied at least twice daily.

RESULTS

In Study 1, on Day 29, the mean change in skin surface capacitance from baseline was significantly greater in the forearm test area treated with DCLC than in the contralateral test area (control) treated with water only (5.16 vs. 3.65 a.u.; p = 0.011), suggesting long-term SC hydration. DCLC use was not associated with changes in TEWL, skin pH, or microbiome biodiversity if compared to control. In Study 2, the 4-week use of DCLC in combination with an emollient was well tolerated according to pediatrician skin assessment, and no flare-ups were recorded. The microbiome biodiversity did not shift during the study.

CONCLUSION

These findings support the use of DCLC in subjects with atopic-prone skin.

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.

Controlling skin microbiome as a new bacteriotherapy for inflammatory skin diseases

The skin serves as the interface between the human body and the environment and interacts with the microbial community. The skin microbiota consists of microorganisms, such as bacteria, fungi, mites, and viruses, and they fluctuate depending on the microenvironment defined by anatomical location and physiological function. The balance of interactions between the host and microbiota plays a pivotal role in the orchestration of skin homeostasis; however, the disturbance of the balance due to an alteration in the microbial communities, namely, dysbiosis, leads to various skin disorders. Recent developments in sequencing technology have provided new insights into the structure and function of skin microbial communities. Based on high-throughput sequencing analysis, a growing body of evidence indicates that a new treatment using live bacteria, termed bacteriotherapy, is a feasible therapeutic option for cutaneous diseases caused by dysbiosis. In particular, the administration of specific bacterial strains has been investigated as an exclusionary treatment strategy against pathogens associated with chronic skin disorders, whereas the safety, efficacy, and sustainability of this therapeutic approach using isolated live bacteria need to be further explored. In this review, we summarize our current understanding of the skin microbiota, as well as therapeutic strategies using characterized strains of live bacteria for skin inflammatory diseases. The ecosystem formed by interactions between the host and skin microbial consortium is still largely unexplored; however, advances in our understanding of the function of the skin microbiota at the strain level will lead to the development of new therapeutic methods.

A 3D-printed transepidermal microprojection array for human skin microbiome sampling

Skin microbiome sampling is currently performed with tools such as swabs and tape strips to collect microbes from the skin surface. However, these conventional approaches may be unable to detect microbes deeper in the epidermis or in epidermal invaginations. We describe a sampling tool with a depth component, a transepidermal microprojection array (MPA), which captures microbial biomass from both the epidermal surface and deeper skin layers. We leveraged the rapid customizability of 3D printing to enable systematic optimization of MPA for human skin sampling. Evaluation of sampling efficacy on human scalp revealed the optimized MPA was comparable in sensitivity to swab and superior to tape strip, especially for nonstandard skin surfaces. We observed differences in species diversity, with the MPA detecting clinically relevant fungi more often than other approaches. This work delivers a tool in the complex field of skin microbiome sampling to potentially address gaps in our understanding of its role in health and disease.

Cutaneous Microbiome Profiles Following Chlorhexidine Treatment in a 72-Hour Daily Follow-Up Paired Design: a Pilot Study

Venous catheter-related bloodstream infections represent a significant problem in the United States. Our objective was to determine daily changes in skin microbiome profiles up to 72h postchlorhexidine treatment. Left and right forearm skin swab samples were obtained from 10 healthy volunteers over 72h at 24h intervals. Dorsal surface of left arm was treated with chlorohexidine gluconate (CHG) at initial time point (T = 0), while the right arm remained untreated (control). Swab samples were obtained shortly before (T = 0) and after CHG treatment (T = 24-48-72h). Bacterial DNA extraction, 16S rRNA gene V1-V3 sequencing and taxonomic annotation were performed using ZymoBIOMICS pipeline. PERMANOVA, linear discriminant and bacterial interaction network analyses were performed. A total of 13 total phyla, 273 genera, and 950 total species were detected across all time points, CHG-treated or CHG-untreated. Most abundant species included Cutibacterium acnes, Staphylococcus epidermidis, and Rothia Mucilaginosa. Low biomass-related inconsistent taxa detection was observed. PERMANOVA suggested a marginal difference between CHG-treated and CHG-untreated microbiome profiles (Genera: P(perm) = 0.0531; Species: P(perm) = 0.0450). Bacterial interaction network guided PERMANOVA analyses detected a microbiome change over time, suggesting a consistent CHG treatment-specific change. LEfSe identified Finegoldia magna, Bacillus pumilus, Bacillus thermoamylovorans as the only distinctive species. These species were more abundant and/or present post-CHG treatment in the CHG-treated group. These findings suggest that the skin microbiome was not significantly different 24, 48, or 72h after CHG treatment. Previous culture-based studies have found similar results after 24h. Future studies will be needed to determine the mechanisms of bacterial regrowth after CHG treatment. IMPORTANCE Annually, over 80,000 central line infections occur in the United States. Understanding the pathogenesis of these infections is crucial. Chlorhexidine is the most commonly used skin preparation before line placement. We hypothesized that the use of chlorhexidine and dressings will alter the normal arm skin microbiome over a period of 72h. We used 16S-rRNA gene next generation sequencing (NGS) to determine the forearm skin microbiome of volunteers. The left arm was swabbed with chlorhexidine and the right arm served as control. The skin microbiome returned to normal after 24h. Our NGS results confirm findings of two previous culture-based studies. Relative abundance of Bacillus spp. in the chlorhexidine-treated samples was increased, consistent with one previous study. Based on the results of this pilot study, we will need to measure viable bacteria during a 24h time course following chlorhexidine treatment to understand the source of skin microbiome replenishment.

Assessing the Oxidative State of the Skin by Combining Classical Tape Stripping with ORAC Assay

The antioxidant barrier system of the skin acts as the main defence against environmental pro-oxidants. Impaired skin oxidative state is linked to unhealthy conditions such as skin autoimmune diseases and cancer. Thus, the evaluation of the overall oxidative state of the skin plays a key role in further understanding and prevention of these disorders. This study aims to present a novel ex vivo model to evaluate the skin oxidative state by the measurement of its antioxidant capacity (AOC). For this the ORAC assay was combined with classical tape stripping and infrared densitometry to evaluate the oxidative state of the stratum corneum (SC). Outcomes implied the suitability of the used model to determine the intrinsic antioxidant capacity (iAOC) of the skin. The average iAOC of untreated skin was determined as 140 ± 7.4 µM TE. Skin exposure to UV light for 1 h reduced the iAOC by about 17%, and exposure for 2 h decreased the iAOC by about 30%. Treatment with ascorbic acid (AA) increased the iAOC in a dose-dependent manner and reached an almost two-fold iAOC when 20% AA solution was applied on the skin. The application of coenzyme Q10 resulted in an increase in the iAOC at low doses but decreased the iAOC when doses > 1% were applied on the skin. The results show that the combination of classical tape stripping and ORAC assay is a cost-effective and versatile method to evaluate the skin oxidative state and the pro-oxidate and antioxidative effects of topical skin treatments on the iAOC of the skin. Therefore, the model can be considered to be a valuable tool in skin research.

Skin microbiome profile of healthy Cameroonians and Japanese

The commensal microbes of the skin have a significant impact on dermal physiology and pathophysiology. Racial and geographical differences in the skin microbiome are suggested and may play a role in the sensitivity to dermatological disorders, including infectious diseases. However, little is known about the skin microbiome profiles of people living in Central Africa, where severe tropical infectious diseases impose a burden on the inhabitants. This study provided the skin profiles of healthy Cameroonians in different body sites and compared them to healthy Japanese participants. The skin microbiome of Cameroonians was distinguishable from that of Japanese in all skin sites examined in this study. For example, Micrococcus was predominantly found in skin samples of Cameroonians but mostly absent in Japanese skin samples. Instead, the relative abundance of Cutibacterium species was significantly higher in healthy Japanese. Principal coordinate analysis of beta diversity showed that the skin microbiome of Cameroonians formed different clusters from Japanese, suggesting a substantial difference in the microbiome profiles between participants of both countries. In addition, the alpha diversity in skin microbes was higher in Cameroonians than Japanese participants. These data may offer insights into the determinant factors responsible for the distinctness of the skin microbiome of people living in Central Africa and Asia.

Epidermis as a Platform for Bacterial Transmission

The epidermis constitutes a continuous external layer covering the body, offering protection against bacteria, the most abundant living organisms that come into contact with this barrier. The epidermis is heavily colonized by commensal bacterial organisms that help protect against pathogenic bacteria. The highly regulated and dynamic interaction between the epidermis and commensals involves the host’s production of nutritional factors promoting bacterial growth together to chemical and immunological bacterial inhibitors. Signal trafficking ensures the system’s homeostasis; conditions that favor colonization by pathogens frequently foster commensal growth, thereby increasing the bacterial population size and inducing the skin’s antibacterial response, eliminating the pathogens and re-establishing the normal density of commensals. The microecological conditions of the epidermis favors Gram-positive organisms and are unsuitable for long-term Gram-negative colonization. However, the epidermis acts as the most important host-to-host transmission platform for bacteria, including those that colonize human mucous membranes. Bacteria are frequently shared by relatives, partners, and coworkers. The epidermal bacterial transmission platform of healthcare workers and visitors can contaminate hospitalized patients, eventually contributing to cross-infections. Epidermal transmission occurs mostly via the hands and particularly through fingers. The three-dimensional physical structure of the epidermis, particularly the fingertips, which have frictional ridges, multiplies the possibilities for bacterial adhesion and release. Research into the biology of bacterial transmission via the hands is still in its infancy; however, tribology, the science of interacting surfaces in relative motion, including friction, wear and lubrication, will certainly be an important part of it. Experiments on finger-to-finger transmission of microorganisms have shown significant interindividual differences in the ability to transmit microorganisms, presumably due to genetics, age, sex, and the gland density, which determines the physical, chemical, adhesive, nutritional, and immunological status of the epidermal surface. These studies are needed to optimize interventions and strategies for preventing the hand transmission of microorganisms.

Critical thinking and diagnostic reasoning when advanced practitioners assess and treat skin conditions

Advanced clinical practitioner (ACP) roles require a broad range of knowledge of both medical and surgical medicine and the ability to work autonomously in a variety of settings. Despite around half of the UK adult population presenting with a skin condition requiring attention, this is something many ACPs feel unprepared to be consulted on. However, due to the complexity and large number of potential diagnoses, it is imperative that ACPs develop their confidence and knowledge to diagnosis, request investigations and initiate treatment for a patient with a skin complaint. In the first part of this clinical review the authors presented the key elements of history taking, consultation and assessment of the skin. This second clinical review discusses the main differential diagnoses, mimics, common investigations and treatments. This article is designed to support novice ACPs from acute hospital settings to primary care to develop a foundation of understanding in the main diagnosis and treatment options that should be considered following a clinical assessment of patients' skin outside the dermatology setting.

Circulating Antibodies to Skin Bacteria Detected by Serological Lateral Flow Immunoassays Differentially Correlated With Bacterial Abundance

The serological lateral flow immunoassay (LFIA) was used to detect circulating antibodies to skin bacteria. Next-generation sequencing analysis of the skin microbiome revealed a high relative abundance of Cutibacterium acnes but low abundance of Staphylococcus aureus and Corynebacterium aurimucosum on human facial samples. Yet, results from both LFIA and antibody titer quantification in 96-well microplates illustrated antibody titers that were not correspondent, and instead negatively correlated, to their respective abundance with human blood containing higher concentrations of antibodies to both S. aureus and C. aurimucosum than C. acnes. Acne vulgaris develops several unique microbial and cellular features, but its correlation with circulating antibodies to bacteria in the pilosebaceous unit remains unknown. Results here revealed that antibodies to C. acnes and S. aureus were approximately 3-fold higher and 1.5-fold lower, respectively, in acne patients than in healthy subjects. Although the results can be further validated by larger sample sizes, the proof-of-concept study demonstrates a newfound discrepancy between the abundance of skin bacteria and amounts of their corresponding antibodies. And in light of acne-correlated amplified titers of specific anticommensal antibodies, we highlight that profiling these antibodies in the pilosebaceous unit by LFIAs may provide a unique signature for monitoring acne vulgaris.

Evaluation of a new-formula shampoo containing 6% glycyrrhetinic acid complex for scalp seborrheic dermatitis: A pilot study

Background

Scalp seborrheic dermatitis (SD) is a chronic inflammatory dermatosis associated with sebum imbalance and proliferation of Malassezia species. Various antifungal shampoos are commonly used for scalp SD.

Aims

Glycyrrhetinic acid is known to have antioxidative, anti‐inflammatory, and anti‐allergic effects. This study was designed to evaluate the effectiveness of a new‐formula shampoo that contains glycyrrhetinic acid for the treatment of scalp SD.

Patients/Methods

Thirty‐four patients were enrolled and treated with the 6% glycyrrhetinic acid complex shampoo. Efficacy was assessed clinically with Dermatology Life Quality Index (DLQI) and Adherent Scalp Flaking Score (ASFS) by the same dermatologist at baseline, week 2, and week 5. Among the 24 subjects with the most significant clinical improvement, four common microorganisms from scalp samples were analyzed by quantitative polymerase chain reaction (qPCR) at baseline, and week 5.

Results

The DLQI and ASFS at week 2 and week 5 improved significantly relative to baseline. The bacteria profiles showed a significant increase of Cutibacterium acnes and a decrease of Staphylococcus epidermidis at week 5. The fungi profiles showed significant decreases of both Malassezia restricta and Malassezia globosa. The ratio of C. acne to S. epidermidis increased significantly from 0.93 at baseline to 1.55 at week 5. The ratio of M. restricta to M. globosa decreased from 5.02 at baseline to 1.00 at week 5.

Conclusions

The effectiveness of this new regimen was objectively demonstrated at the clinical and microbiological levels. This new formula may alleviate the bacterial and fungal dysbiosis in scalp SD.

Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs

Background

Understanding the influence of methodology on results is an essential consideration in experimental design. In the expanding field of fish microbiology, many best practices and targeted techniques remain to be refined. This study aimed to compare microbial assemblages obtained from Atlantic salmon (Salmo salar) gills by swabbing versus biopsy excision. Results demonstrate the variation introduced by altered sampling strategies and enhance the available knowledge of the fish gill microbiome.

Results

The microbiome was sampled using swabs and biopsies from fish gills, with identical treatment of samples for 16S next generation Illumina sequencing. Results show a clear divergence in microbial communities obtained through the different sampling strategies, with swabbing consistently isolating a more diverse microbial consortia, and suffering less from the technical issue of host DNA contamination associated with biopsy use. Sequencing results from biopsy-derived extractions, however, hint at the potential for more cryptic localisation of some community members.

Conclusions

Overall, results demonstrate a divergence in the obtained microbial community when different sampling methodology is used. Swabbing appears a superior method for sampling the microbiota of mucosal surfaces for broad ecological research in fish, whilst biopsies might be best applied in exploration of communities beyond the reach of swabs, such as sub-surface and intracellular microbes, as well as in pathogen diagnosis. Most studies on the external microbial communities of aquatic organisms utilise swabbing for sample collection, likely due to convenience. Much of the ultrastructure of gill tissue in live fish is, however, potentially inaccessible to swabbing, meaning swabbing might fail to capture the full diversity of gill microbiota. This work therefore also provides valuable insight into partitioning of the gill microbiota, informing varied applications of different sampling methods in experimental design for future research.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02374-0.

Comparison of non-invasive Staphylococcus aureus sampling methods on lesional skin in patients with atopic dermatitis

There is evidence that Staphylococcus aureus colonisation is linked to severity of atopic dermatitis. As no gold standard for S. aureus sampling on atopic dermatitis skin lesions exists, this study compared three commonly used methods. In addition, effectiveness of standard skin disinfection to remove S. aureus colonisation from these inflamed skin lesions was investigated. In 30 atopic dermatitis patients, three different S. aureus sampling methods, i.e. detergent scrubbing, moist swabbing and tape stripping, were performed on naïve and disinfected skin lesions. Two different S. aureus selective media, mannitol salt agar and chromID agar, were used for bacterial growing. Quantifying the S. aureus load varied significantly between the different sampling methods on naïve skin lesions ranging from mean 51 to 1.5 × 10⁴ CFU/cm² (p < 0.001). The qualitative detection on naïve skin was highest with the two detergent-based techniques (86% each), while for tape stripping, this value was 67% (all on chromID agar). In comparison, mannitol salt agar was less sensitive (p < 0.001). The disinfection of the skin lesions led to a significant reduction of the S. aureus load (p < 0.05) but no complete eradication in the case of previously positive swab. The obtained data highlight the importance of the selected sampling method and consecutive S. aureus selection agar plates to implement further clinical studies for the effectiveness of topical anti-staphylococcal antibiotics. Other disinfection regimes should be considered in atopic dermatitis patients when complete de-colonisation of certain skin areas is required, e.g. for surgical procedures.

Comparison of swab types for collection and analysis of microorganisms

The human microbiome has begun to emerge as a potential forensic tool, with varied applications ranging from unique identification to investigative leads that link individuals and/or locations. The relative abundance of the combined DNA of the microbiome, compared to human nuclear DNA, may expand potential sources of biological evidence, especially in cases with transfer or low-copy number DNA samples. This work sought to determine the optimal swab type for the collection and analysis of microorganisms. A bacterium (Proteus mirabilis) was deposited by pipette onto four swab types (cotton, flocked, dental applicators, and dissolvable), and extraction and real-time PCR quantitation of the bacterial DNA were performed, which allowed for absolute microbial DNA recovery and comparison of yields across the four sampling substrates. Flocked swabs had the highest yield (~1240 ng) compared to the cotton swabs (~184 ng), dental applicators (~533 ng), and dissolvable swabs (~430 ng). The collection efficiency was further evaluated for cotton and flocked swabs using dried microbial samples spotted onto non-porous surfaces (treated wood, glass, plastic, and tile). Flocked swabs performed consistently better across wood, glass, and tile, but showed decreased recovery from plastic. The cotton swabs failed in the recovery of P. mirabilis DNA across all surfaces. Knowing the appropriate sampling substrate will be useful as others continue to investigate the use of the microbiome as a forensics tool.

The Clinical Relevance of the Microbiome in Hidradenitis Suppurativa: A Systematic Review

Hidradenitis suppurativa is a chronic disease of the pilosebaceous unit. The name of the condition is a testament to the presumed relationship between the disease and the microbiome. The pathophysiology of hidradenitis suppurativa is, however, complex and believed to be the product of a multifactorial interplay between the interfollicular epithelium, pilosebaceous unit, microbiome, as well as genetic and environmental factors. In this review we assimilate the existing literature regarding the role played by the human microbiome in HS in various contexts of the disease, including the pathophysiologic, therapeutic, and potentially, diagnostic as well prognostic. In conclusion, the role played by the microbiome in HS is extensive and relevant and can have bench-to-bedside applications.

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.

Infection prevention practices and the use of medical tapes

BACKGROUND

Medical tapes are ubiquitous in healthcare and there are currently no guidelines for their storage and use. Tapes cannot be cleaned or disinfected; yet, several clinicians may use a given roll for any number of patients. Reports of tape contamination associated with clinical infection have been published.

PURPOSE

We reviewed the literature reporting microbiological studies, case reports of infections, and nosocomial outbreaks associated with the use of medical tapes and other adhesive devices to assess the prevalence of this problem.

METHODS

We conducted a literature search for cross-contamination due to medical tape use in 6 databases in June 2020 using indexing terms for surgical tape, adhesive agent, adhesives or the keyword for tape. We compiled available evidence on tape contamination as a cause for healthcare-associated infections (HAIs).

MAIN FINDINGS

Forty-two publications reported relevant microbiological studies, case reports of infections, and/or nosocomial outbreaks. Results demonstrated that tape rolls handled with questionable practices can harbor pathogens. Some studies showed the association between contaminated tape and HAIs, which in some cases even led to death.

CONCLUSIONS

The time has come to establish national guidelines to help reduce the risk of cross-contamination from medical tapes. We offer suggested elements for these guidelines. The COVID-19 pandemic brings greater scrutiny to eliminate any avoidable cause of infection transmission.

Association of Skin Microbiome with the Onset and Recurrence of Pressure Injury in Bedridden Elderly People

Pressure injuries have been identified as one of the main health hazards among bedridden elderly people. Bedridden elderly people often stay in the same position for a long time, because they cannot switch positions; thus, the blood flow in the part of the body that is being compressed between the bed and their own weight is continuously blocked. As a result, redness and ulcers occur due to lacking oxygen and nutrients in the skin tissues, and these sites are often infected with microorganisms and, thus, become suppurative wounds, a condition commonly determined as pressure injuries. If left untreated, the pressure injury will recur with microbial infections, often resulting in cellulitis, osteomyelitis, and sepsis. The skin microbiome, in which many types of bacteria coexist, is formed on the skin surface. However, it remains unclear what characteristic of the skin microbiome among the bedridden elderly constitutes the development and severity of pressure injuries and the development of post-pressure injury infections. Thus, in this review article, we outlined the changes in the skin microbiome among the bedridden elderly people and their potential involvement in the onset and recurrence of pressure injuries.

Challenges in exploring and manipulating the human skin microbiome

The skin is the exterior interface of the human body with the environment. Despite its harsh physical landscape, the skin is colonized by diverse commensal microbes. In this review, we discuss recent insights into skin microbial populations, including their composition and role in health and disease and their modulation by intrinsic and extrinsic factors, with a focus on the pathobiological basis of skin aging. We also describe the most recent tools for investigating the skin microbiota composition and microbe-skin relationships and perspectives regarding the challenges of skin microbiome manipulation. Video abstract.

Identifying biases and their potential solutions in human microbiome studies

Advances in DNA sequencing technology have vastly improved the ability of researchers to explore the microbial inhabitants of the human body. Unfortunately, while these studies have uncovered the importance of these microbial communities to our health, they often do not result in similar findings. One possible reason for the disagreement in these results is due to the multitude of systemic biases that are introduced during sequence-based microbiome studies. These biases begin with sample collection and continue to be introduced throughout the entire experiment leading to an observed community that is significantly altered from the true underlying microbial composition. In this review, we will highlight the various steps in typical sequence-based human microbiome studies where significant bias can be introduced, and we will review the current efforts within the field that aim to reduce the impact of these biases. Video abstract.

Tape strips in dermatology research

Tape strips have been used widely in dermatology research as a minimally invasive method to sample the epidermis, avoiding the need for skin biopsies. Most research has focused on epidermal pathology, such as atopic eczema, but there is increasing research into the use of tape strips in other dermatoses, such as skin cancer, and the microbiome. This review summarizes the technique of tape stripping, and discusses which dermatoses have been studied by tape stripping and alternative minimally invasive sampling methods. We review the number of tape strips needed from each patient and the components of the epidermis that can be obtained by tape stripping. With a focus on protein and RNA extraction, we address the techniques used to process tape strips. There is no optimal protocol to extract protein, as this depends on the abundance of the protein studied, its level of expression in the epidermis and its solubility. Many variables can alter the amount of protein obtained from tape strips, which must be standardized to ensure consistency between samples. No study has compared different RNA extraction techniques, but our own experience is that RNA yield is optimized by using 20 tape strips and the use of a cell scraper.

Amplicon-based skin microbiome profiles collected by tape stripping with different adhesive film dressings: a comparative study

Background

Medical film dressings have been used to obtain skin microbiota for skin microbiome studies, although their adhesive force may be so strong that the skin could be injured when applied to those who have fragile skin, such as older people. Several products with less adhesive force are available, although their applicability for skin microbiome studies remains unknown. This study aimed to test whether the dressings with less adhesive force could be used for amplicon-based skin microbiome studies. A set of three different film dressings, with acrylic, urethane, or silicone adhesive, was applied to the back skin of nine healthy young participants. The copy number of the 16S ribosomal RNA (rRNA) gene, microbial compositions, and alpha and beta diversity indices were analyzed by amplicon analysis of the 16S rRNA gene using next-generation sequencing and were compared among the three film dressings.

Results

The dressing with acrylic adhesive yielded the highest copy number of 16S rRNA genes, followed by that with urethane adhesive. The silicone-adhesive dressing yielded a significantly lower copy number of the 16S rRNA gene. The microbial composition of skin microbiota was similar among the three film dressings, although significant differences in the relative abundance of Pseudomonas species and alpha diversity indices were found in the silicone-adhesive dressing. The Bray–Curtis dissimilarity was significantly higher between the acrylic- and silicone-adhesive dressings than between the acrylic- and urethane-adhesive dressings. No adverse effects related to tape stripping were observed for any of the film dressings.

Conclusion

We recommend dressings with acrylic or urethane adhesive for amplicon-based skin microbiome studies. An acrylic adhesive has an advantage in the yield of skin microbiota, and a urethane adhesive should be chosen when applied to fragile skin. The adhesive force of the dressing with silicone adhesive was too weak to be used for collecting skin microbiota.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02122-4.