Skin microbiota in health and disease: From sequencing to biology

Mapping the microbial landscape and variations based on biological sex, age, and biopsy location in the shoulder skin microbiome

BACKGROUND

The organisms responsible for periprosthetic joint infections (PJIs) of the shoulder are often skin pathogens originating from the patient's own skin flora at the time of surgery. Understanding the normal skin flora around the shoulder is an important step to identify the range of organisms that could be responsible for PJI and to ensure optimization of culture mediums to identify them. This study aimed to provide the first description of the shoulder skin microbiome using high-throughput next-generation sequencing methodology and explore variations by age, biological sex, and biopsy location.

METHODS

Patients undergoing arthroscopic surgery were approached for informed consent to have punch biopsies taken from anterior, lateral, and posterior arthroscopy portal sites. DNA extraction was undertaken followed by illumina sequencing, focusing on the V3-V4 regions of the 16S rRNA gene. Amplicon sequence variants (ASVs) were generated using Deblur workflow and used for taxonomic assignment. Variation in the microbiota community based on age, biological sex, and biopsy location was assessed through alpha and beta diversity metric calculations using phyloseq R package.

RESULTS

Sixty-two patients (24 female, 38 male) aged 18-80 years were recruited, resulting in 186 punch biopsy samples for analysis. Following removal of low-prevalence taxa, 606 ASVs were aggregated at the genus level, resulting in 214 genera across 13 phyla. The top 20 most abundant genera accounted for 73.5% of the overall sequence count. Cutibacterium was the most abundant genus within the study population, followed by Ralstonia, Staphylococcus, Bacteroides, and Streptococcus. Significant differences were observed in beta diversity metrics when comparing by biological sex, which accounted for 3.9%-5.3% of the variation in the microbial community, but not age or biopsy location. Males displayed a greater proportion of gram-positive and aerobic bacteria, whereas females exhibited a greater proportion of gram-negative and stress-tolerant bacteria.

CONCLUSION

This is the first study to look specifically at the microbiome of the cutaneous shoulder and describe the most abundant genera and compositional differences based on age, biological sex, and biopsy location. Biological sex was the only host covariant studied that reached significance in explaining microbiota variation. The top 20 most abundant genera, accounting for 74% of the overall sequence count, would be isolated with standard microbiological culture. As such, this study does not highlight a need to change current culture investigation practice for shoulder PJI, but it serves as an important catalog of skin commensals around the operative site in shoulder surgery.

Skin microbiota variation in Indian families

Background

In India, joint families often encompass members spanning multiple generations cohabiting in the same household, thereby sharing the same ethnicity, genetics, dietary habits, lifestyles, and other living conditions. Such an extended family provides a unique opportunity to evaluate the effect of genetics and other confounding factors like geographical location, diet and age on the skin microbiota within and between families across three generations.

Methods

The present study involved seventy-two individuals from fifteen families from two geographical regions of Maharashtra, India. The 16S rRNA sequencing of V3-V4 regions was performed and the generated taxonomic profiles were used for downstream analysis.

Results

Our study highlights a significant difference in community composition (beta diversity) between families (PERMANOVA; p = 0.001) and geographical locations (p = 0.001). We observed geographical location-wise differences in the relative abundances Staphylococcus in the families from Pune (Wilcoxon test, p = 0.007), and Bacillus in the Ahmednagar families (Wilcoxon test, p = 0.004). When within and between-family comparisons of skin microbiota composition were carried out between different generations (G1-G2, G2-G3, and G1-G3); we observed skin microbiota tended to be more similar within than between families but this difference was not significant.

Conclusion

This study underscores the diversity and commonalities in skin microbiota composition within and between families. Our result suggests that geographical location is significantly associated with the genus composition of skin microbiota, which is quantitatively unique for a family and likely explained by co-habitation.

Efficacy of a Postbiotic Formulation Combined With Microneedling for Mild-to-Moderate Acne: A Self-Control Study

BACKGROUND

Acne vulgaris significantly affects young individuals globally, with its onset associated with an increased prevalence of C acnes, a naturally occurring skin bacterium. In light of the rising concerns regarding antibiotic resistance and the potential for adverse effects, pharmacological interventions may not consistently represent the most suitable option. Nonpharmacological approaches, such as microneedling, offer promising alternative treatment modalities. Furthermore, the integration of postbiotics in skincare formulations for acne management has gained traction recently. Nonetheless, there remains a lack of sufficient evidence to establish the efficacy and safety of postbiotics when combined with microneedling.

OBJECTIVE

To assess the clinical effectiveness of a postbiotic formulation combined with microneedling in mild-to-moderate facial acne vulgaris.

METHODS

Twenty Chinese patients were enrolled, all received one treatment and were monitored 4 weeks posttreatment. The evaluation assessed symptom improvement, treatment safety, and patient satisfaction.

RESULTS

The global acne grading system (GAGS) score decreased more than half based on the baseline. Clinical photographs following treatment revealed improved the skin lesions and brightened skin tone. Statistics from VISIA showed excellent improvement in speckle, pore, red region, and porphyrin. No significant adverse reactions have been reported during the treatment period. Additionally, more than 85% were very satisfied or satisfied with the outcome.

CONCLUSION

Our results showed that the postbiotic formulation combined with microneedling may benefit the restoration of the skin barrier and the equilibrium of skin microbiota. This approach may help mitigate inflammation and address skin lesions, presenting a promising therapeutic avenue for the prevention and management of acne vulgaris.

Chronic Exposure to Petroleum-Derived Hydrocarbons Alters Human Skin Microbiome and Metabolome Profiles: A Pilot Study

Petroleum-derived substances, like industrial oils and grease, are ubiquitous in our daily lives. Comprised of petroleum hydrocarbons (PH), these substances can come into contact with our skin, potentially causing molecular disruptions and contributing to the development of chronic disease. In this pilot study, we employed mass spectrometry-based untargeted metabolomics and 16S rRNA gene sequencing analyses to explore these effects. Superficial skin samples were collected from subjects with and without chronic dermal exposure to PH at two anatomical sites: the fingers (referred to as the hand) and arms (serving as an intersubject variability control). Exposed hands exhibited higher bacterial diversity (Shannon and Simpson indices) and an enrichment of oil-degrading bacteria (ODB), including Dietzia, Paracoccus, and Kocuria. Functional prediction suggested enriched pathways associated with PH degradation in exposed hands vs non-exposed hands, while no differences were observed when comparing the arms. Furthermore, carboxylic acids, glycerophospholipids, organooxygen compounds, phenol ethers, among others, were found to be more abundant in exposed hands. We observed positive correlations among multiple ODB and xenobiotics, suggesting a chemical remodeling of the skin favorable for ODB thriving. Overall, our study offers insights into the complex dysregulation of bacterial communities and the chemical milieu induced by chronic dermal exposure to PH.

Plant Phenolics in the Prevention and Therapy of Acne: A Comprehensive Review

Plants are a rich source of secondary metabolites, among which phenolics are the most abundant. To date, over 8000 various polyphenolic compounds have been identified in plant species, among which phenolic acids, flavonoids, coumarins, stilbenes and lignans are the most important ones. Acne is one of the most commonly treated dermatological diseases, among which acne vulgaris and rosacea are the most frequently diagnosed. In the scientific literature, there is a lack of a detailed scientific presentation and discussion on the importance of plant phenolics in the treatment of the most common specific skin diseases, e.g., acne. Therefore, the aim of this review is to gather, present and discuss the current state of knowledge on the activity of various plant phenolics towards the prevention and treatment of acne, including in vitro, in vivo and human studies. It was revealed that because of their significant antibacterial, anti-inflammatory and antioxidant activities, phenolic compounds may be used in the treatment of various types of acne, individually as well as in combination with commonly used drugs like clindamycin and benzoyl peroxide. Among the various phenolics that have been tested, EGCG, quercetin and nobiletin seem to be the most promising ones; however, more studies, especially clinical trials, are needed to fully evaluate their efficacy in treating acne.

Metagenomic characterisation of canine skin reveals a core healthy skin microbiome

Furthering our knowledge of the skin microbiome is essential to understand health and disease in canines. To date, studies into the canine skin microbiome have focused on 16S rRNA high throughput sequencing however, these lack the granularity of species and strain level taxonomic characterisation and their associated functions. The aim of this study was to provide a comprehensive assessment of the skin microbiome by analysing the skin microbiome of 72 healthy adult colony dogs, across four distinct skin sites and four breeds, using metagenomic sequencing. Our analysis revealed that breed and skin site are drivers of variation, and a core group of taxa and genes are present within the skin microbiome of healthy dogs, comprising 230 taxa and 1219 gene families. We identified 15 species within the core microbiome that are represented by more than one strain. The biosynthesis of secondary metabolites pathway was enriched in the core microbiome suggesting the skin microbiome may play a role in colonisation resistance and protection from invading pathogens. Additionally, we uncovered the novelty of the canine skin microbiome and show that further investigation is required to increase the suitability of current databases for metagenomic sequencing of canine skin samples.

Prokaryotic and eukaryotic skin microbiota modifications triggered by Leishmania infection in localized Cutaneous Leishmaniasis

Cutaneous Leishmaniasis (CL) is a tropical disease characterized by cutaneous ulcers, sometimes with satellite lesions and nodular lymphangitis. Leishmania parasites, transmitted by sandfly vectors, cause this widespread public health challenge affecting millions worldwide. CL's complexity stems from diverse Leishmania species and intricate host interactions. Therefore, this study aims to shed light on the spatial-temporal distribution of Leishmania species and exploring the influence of skin microbiota on disease progression. We analyzed 40 samples from CL patients at three military bases across Colombia. Using Oxford Nanopore's Heat Shock Protein 70 sequencing, we identified Leishmania species and profiled microbiota in CL lesions and corresponding healthy limbs. Illumina sequencing of 16S-rRNA and 18S-rRNA genes helped analyze prokaryotic and eukaryotic communities. Our research uncovered a spatial-temporal overlap between regions of high CL incidence and our sampling locations, indicating the coexistence of various Leishmania species. L. naiffi emerged as a noteworthy discovery. In addition, our study delved into the changes in skin microbiota associated with CL lesions sampled by scraping compared with healthy skin sampled by brushing of upper and lower limbs. We observed alterations in microbial diversity, both in prokaryotic and eukaryotic communities, within the lesioned areas, signifying the potential role of microbiota in CL pathogenesis. The significant increase in specific bacterial families, such as Staphylococcaceae and Streptococcaceae, within CL lesions indicates their contribution to local inflammation. In essence, our study contributes to the ongoing research into CL, highlighting the need for a multifaceted approach to decipher the intricate interactions between Leishmaniasis and the skin microbiota.

Skin Microbial Composition and Genetic Mutation Analysis in Precision Medicine for Epidermolysis Bullosa

Epidermolysis bullosa (EB) is an inherited skin disease representing a spectrum of rare genetic disorders. These conditions share the common trait that causes fragile skin, resulting in the development of blisters and erosions. The inheritance follows an autosomal pattern, and the array of clinical presentations leads to significant physical suffering, considerable morbidity, and mortality. Despite EB having no cure, effectively managing EB remains an exceptional challenge due to its rarity and complexity, occasionally casting a profound impact on the lives of affected individuals. Considering that EB management requires a multidisciplinary approach, this sometimes worsens the condition of patients with EB due to inappropriate handling. Thus, more appropriate and precise treatment management of EB is essentially needed. Advanced technology in medicine and health comes into the bioinformatics era. Including treatment for skin diseases, omics-based approaches aim to evaluate and handle better disease management and treatment. In this work, we review several approaches regarding the implementation of omics-based technology, including genetics, pathogenic mutation, skin microbiomics, and metagenomics analysis for EB. In addition, we highlight recent updates on the potential of metagenomics analysis in precision medicine for EB.

Role of the Microbiota in Skin Neoplasms: New Therapeutic Horizons

The skin and the gut are regularly colonized by a variety of microorganisms capable of interacting with the immune system through their metabolites and influencing the balance between immune tolerance and inflammation. Alterations in the composition and diversity of the skin microbiota have been described in various cutaneous diseases, including skin cancer, and the actual function of the human microbiota in skin carcinogenesis, such as in progression and metastasis, is currently an active area of research. The role of Human Papilloma Virus (HPV) in the pathogenesis of squamous cell carcinoma is well consolidated, especially in chronically immunosuppressed patients. Furthermore, an imbalance between Staphylococcus spp., such as Staphylococcus epidermidis and aureus, has been found to be strongly related to the progression from actinic keratosis to squamous cell carcinoma and differently associated with various stages of the diseases in cutaneous T-cell lymphoma patients. Also, in melanoma patients, differences in microbiota have been related to dissimilar disease course and prognosis and may affect the effectiveness and tolerability of immune checkpoint inhibitors, which currently represent one of the best chances of a cure. From this point of view, acting on microbiota can be considered a possible therapeutic option for patients with advanced skin cancers, even if several issues are still open.

Iron Metabolism of the Skin: Recycling versus Release

The skin protects the body against exogenous stressors. Its function is partially achieved by the permanent regeneration of the epidermis, which requires high metabolic activity and the shedding of superficial cells, leading to the loss of metabolites. Iron is involved in a plethora of important epidermal processes, including cellular respiration and detoxification of xenobiotics. Likewise, microorganisms on the surface of the skin depend on iron, which is supplied by the turnover of epithelial cells. Here, we review the metabolism of iron in the skin with a particular focus on the fate of iron in epidermal keratinocytes. The iron metabolism of the epidermis is controlled by genes that are differentially expressed in the inner and outer layers of the epidermis, establishing a system that supports the recycling of iron and counteracts the release of iron from the skin surface. Heme oxygenase-1 (HMOX1), ferroportin (SLC40A1) and hephaestin-like 1 (HEPHL1) are constitutively expressed in terminally differentiated keratinocytes and allow the recycling of iron from heme prior to the cornification of keratinocytes. We discuss the evidence for changes in the epidermal iron metabolism in diseases and explore promising topics of future studies of iron-dependent processes in the skin.

Glycolipid Biosurfactants in Skincare Applications: Challenges and Recommendations for Future Exploitation

The 21st century has seen a substantial increase in the industrial applications of glycolipid biosurfactant technology. The market value of the glycolipid class of molecules, sophorolipids, was estimated to be USD 409.84 million in 2021, with that of rhamnolipid molecules projected to reach USD 2.7 billion by 2026. In the skincare industry, sophorolipid and rhamnolipid biosurfactants have demonstrated the potential to offer a natural, sustainable, and skin-compatible alternative to synthetically derived surfactant compounds. However, there are still many barriers to the wide-scale market adoption of glycolipid technology. These barriers include low product yield (particularly for rhamnolipids) and potential pathogenicity of some native glycolipid-producing microorganisms. Additionally, the use of impure preparations and/or poorly characterised congeners as well as low-throughput methodologies in the safety and bioactivity assessment of sophorolipids and rhamnolipids challenges their increased utilisation in both academic research and skincare applications. This review considers the current trend towards the utilisation of sophorolipid and rhamnolipid biosurfactants as substitutes to synthetically derived surfactant molecules in skincare applications, the challenges associated with their application, and relevant solutions proposed by the biotechnology industry. In addition, we recommend experimental techniques/methodologies, which, if employed, could contribute significantly to increasing the acceptance of glycolipid biosurfactants for use in skincare applications while maintaining consistency in biosurfactant research outputs.

Dynamic Distribution of Skin Microorganisms in Donkeys at Different Ages and Various Sites of the Body

Considerable evidence suggests that the skin microbiota is not only important and complex in humans and other mammals but also critical for maintaining health and skin homeostasis. To date, studies on the skin microorganisms of donkeys are surprisingly rare. To investigate the dynamic changes in commensal microbial communities on the skins of healthy donkeys throughout the growing period, skin and soil samples were collected from 30 healthy Dezhou donkeys (ranging from 1, 6, 12, 24 to 48 months of age) and their corresponding breeding sheds on the farm. All samples were analysed for high-throughput sequencing of the 16S rRNA and ITS to characterize the skin microbiota of healthy donkeys and compare the differences in skin microbiota among donkeys of different ages. There were notable differences in the proportions of various genera (including bacteria and fungi) between dorsal and abdominal skin with increasing age. The comparison of the skin microbial communities among these groups revealed that Staphylococcus was mainly enriched in the early growing stage (1 and 6 months), while the relative abundance of Streptococcus was higher in both the 1- and 48-month-old age groups. Moreover, some bacteria and commensal fungi, such as Staphylococcus and Trichosporon, were found to be positively correlated between the skin and the environment. This is the first study to investigate the dynamic changes in skin microbiota diversity and composition in donkeys of different ages and at different sites of the body. Furthermore, this study provides insights into the dynamic alterations in skin microbes during a donkey's growth and characterizes the profiles of bacterial and fungal communities across a donkey's body regions (dorsal and abdomen).

Influence of Sex on the Microbiota of the Human Face

The role of the microbiota in health and disease has long been recognized and, so far, the cutaneous microbiota in humans has been widely investigated. The research regarded mainly the microbiota variations between body districts and disease skin states (i.e., atopic dermatitis, psoriasis, acne). In fact, relatively little information is available about the composition of the healthy skin microbiota. The cosmetic industry is especially interested in developing products that maintain and/or improve a healthy skin microbiota. Therefore, in the present work, the authors chose to investigate in detail the structure and composition of the basal bacterial community of the face. Ninety-six cheek samples (48 women and 48 men) were collected in the same season and the same location in central northern Italy. Bacterial DNA was extracted, the 16S rDNA gene was amplified by PCR, the obtained amplicons were subjected to next generation sequencing. The principal members of the community were identified at the genus level, and statistical analyses showed significant variations between the two sexes. This study identified abundant members of the facial skin microbiota that were rarely reported before in the literature and demonstrated the differences between male and female microbiota in terms of both community structure and composition.

Acne Vulgaris, Atopic Dermatitis and Rosacea: The Role of the Skin Microbiota-A Review

The skin harbors a huge number of different microorganisms such as bacteria, fungi and viruses, and it acts as a protective shield to prevent the invasion of pathogens and to maintain the health of the commensal microbiota. Several studies, in fact, have shown the importance of the skin microbiota for healthy skin. However, this balance can be altered by intrinsic and extrinsic factors, leading to the development of skin disease, such as acne vulgaris (AV), atopic dermatitis (AD) and rosacea(RS). Although these diseases are widespread and affect both adolescents and adults, the scientific correlation between these disorders and the skin microbiota and physiological parameters (TEWL, hydration and lipid composition) is still unclear. This review aims to investigate the current literature regarding the correlation between the skin microbiota and its imbalance underlying microbiological aspects, how the skin microbiota changes over the course of the disease and the current possible treatments. The following reported studies show a general imbalance of the bacterial flora. For this reason, more in-depth studies are necessary to explore the different subspecies and strains involved in all three diseases.

New and Upcoming Topical Treatments for Atopic Dermatitis: A Review of the Literature

Atopic dermatitis (AD) is a chronic inflammatory dermatosis with periods of exacerbation and remissions. AD is characterized by intense, persistent pruritus and heterogeneity in clinical symptomatology and severity. Therapeutic goals include the amelioration of cutaneous eruptions, diminishing relapses and eventually the disease burden. To date, topical corticosteroids (TCS) and calcineurin inhibitors (TCI) have yet been deemed the mainstay of topical treatments in AD management. Nevertheless, despite their indisputable efficiency, TCS and TCI are not indicated for continuous long-term use given their safety profile. While research in AD has concentrated predominantly on systemic therapies, more than 30 novel topical compounds are under development. The existing data appear encouraging, with some regimens that are already FDA-approved (ruxolitinib was the most recent in September 2021) and several pharmaceutical pipeline products for mild-to-moderate AD that are in an advanced stage of development, such as tapinarof, difamilast and roflumilast. Larger, long-term studies are still required to evaluate the efficacy and safety of these novel compounds in the long run and weigh their advantages over present treatments. In this review, we aim to provide an overview of the latest knowledge about AD topical treatments, echoing upcoming research trends.

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.

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.

Comparing different sample collection and storage methods for field-based skin microbiome research

OBJECTIVES

The skin, as well as its microbial communities, serves as the primary interface between the human body and the surrounding environment. In order to implement the skin microbiome into human biology research, there is a need to explore the effects of different sample collection and storage methodologies, including the feasibility of conducting skin microbiome studies in field settings.

METHODS

We collected 99 skin microbiome samples from nine infants living in Veracruz, Mexico using a dual-tipped "dry" swab on the right armpit, palm, and forehead and a "wet" swab (0.15 M NaCl and 0.1% Tween 20) on the same body parts on the left side of the body. One swab from each collection method was stored in 95% ethanol while the other was frozen at -20°C. 16S rRNA amplicon sequencing generated data on bacterial diversity and community composition, which were analyzed using PERMANOVA, linear mixed effects models, and an algorithm-based classifier.

RESULTS

Treatment (wet_ethanol, wet_freezer, dry_ethanol, and dry_freezer) had an effect (~10% explanatory power) on the bacterial community diversity and composition of skin samples, although body site exhibited a stronger effect (~20% explanatory power). Within treatments, the collection method (wet vs. dry) affected measures of bacterial diversity to a greater degree than did the storage method (ethanol vs. freezer).

CONCLUSIONS

Our study provides novel information on skin microbiome sample collection and storage methods, suggesting that ethanol storage is suitable for research in resource-limited settings. Our results highlight the need for future study design to account for interbody site microbial variation.