Nationality and body location alter human skin microbiome

Composition and diversity of 16S rRNA based skin bacterial microbiome in healthy horses

Characterization of microbiota structure on the skin of healthy horses is important for further development of modulation strategies to ensure optimal bacterial composition for physiological processes. This requirement is also supported by the relatively high incidence of dermatological diseases in horses and thus the need to manage them therapeutically. The taxonomic analysis of skin samples (n = 30) from five different body parts of clinically healthy Shetlands ponies females (neck, back, abdomen, pastern, muzzle) kept under homogeneous conditions (in open stalls with paddock, feed with dry hay, green grass ad libitum and granulated feed) was performed using amplification of V3-V4 region of the 16S rRNA gene. Results indicate that bacteria associated with healthy equine skin represent 18 phyla, 29 classes and 119 families. The most abundant phyla were Proteobacteria (30.8 ± 9.1%) followed by Actinobacteriota (20.4 ± 7.6%), Firmicutes (19.5 ± 10.1%), Bacteroidota (8.5 ± 5.0%) and Deinococcota (7.2 ± 14.8%). Among 229 genera identified, Corynebacterium (7.4 ± 6.5%) was the most abundant genus in skin sites of horses, followed by Deinococcus (7.1 ± 14.9%) and Macrococcus (5.0 ± 8.2%). Indices for the richness and diversity of species within bacterial populations for five regions of horses skin revealed no significant variations observed for species richness (Chao1, p-value 0.2001) but significant result for species evenness (Shannon, p-value 0.0049) with maximum on the neck and minimum on the back skin site. The clustering was seen across samples from different skin sites but also across samples collected from individual horses.

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.

Therapeutic textiles: A promising approach for human skin dysbiosis?

The close interaction between skin and clothing has become an attractive cornerstone for the development of therapeutic textiles able to alleviate skin disorders, namely those correlated to microbiota dysregulation. Skin microbiota imbalance is known in several skin diseases, including atopic dermatitis (AD), psoriasis, seborrheic dermatitis, rosacea, acne and hidradenitis suppurative (HS). Such microbiota dysregulation is usually correlated with inflammation, discomfort and pruritus. Although conventional treatments, that is, the administration of steroids and antibiotics, have shown some efficacy in treating and alleviating these symptoms, there are still disadvantages that need to be overcome. These include their long-term usage with side effects negatively impacting resident microbiota members, antibiotic resistance and the elevated rate of recurrence. Remarkably, therapeutic textiles as a non-pharmacological measure have emerged as a promising strategy to treat, alleviate the symptoms and control the severity of many skin diseases. This systematic review showcases for the first time the effects of therapeutic textiles on patients with skin dysbiosis, focusing on efficacy, safety, adverse effects and antimicrobial, antioxidant and anti-inflammatory properties. The main inclusion criteria were clinical trials performed in patients with skin dysbiosis who received treatment involving the use of therapeutic textiles. Although there are promising outcomes regarding clinical parameters, safety and adverse effects, there is still a lack of information about the impact of therapeutic textiles on the skin microbiota of such patients. Intensive investigation and corroboration with clinical trials are needed to strengthen, define and drive the real benefit and the ideal biomedical application of therapeutic textiles.

An overview of the bacterial microbiome of public transportation systems-risks, detection, and countermeasures

When we humans travel, our microorganisms come along. These can be harmless but also pathogenic, and are spread by touching surfaces or breathing aerosols in the passenger cabins. As the pandemic with SARS-CoV-2 has shown, those environments display a risk for infection transmission. For a risk reduction, countermeasures such as wearing face masks and distancing were applied in many places, yet had a significant social impact. Nevertheless, the next pandemic will come and additional countermeasures that contribute to the risk reduction are needed to keep commuters safe and reduce the spread of microorganisms and pathogens, but also have as little impact as possible on the daily lives of commuters. This review describes the bacterial microbiome of subways around the world, which is mainly characterized by human-associated genera. We emphasize on healthcare-associated ESKAPE pathogens within public transport, introduce state-of-the art methods to detect common microbes and potential pathogens such as LAMP and next-generation sequencing. Further, we describe and discuss possible countermeasures that could be deployed in public transportation systems, as antimicrobial surfaces or air sterilization using plasma. Commuting in public transport can harbor risks of infection. Improving the safety of travelers can be achieved by effective detection methods, microbial reduction systems, but importantly by hand hygiene and common-sense hygiene guidelines.

Similarity of Chinese and Pakistani oral microbiome

Oral microbiota is vital for human health and can be affected by various factors (i.e. diets, ethnicity). However, few studies have compared oral microbiota of individuals from different nationalities in the same environment. Here, we explored the assembly and interaction of oral microbial communities of Chinese and Pakistanis in one university. Firmicutes and Proteobacteria were the predominant microorganisms in the oral cavity of Chinese and Pakistanis. Streptococcus and Neisseria were the dominant genera of China, while Streptococcus and Haemophilus were the dominant genera of Pakistanis. In addition, the oral community membership and structure were not influenced by season, Chinese/Pakistani student and gender, reflecting the stability of the human oral microbiome. The beta diversity of oral microbiomes between Chinese and Pakistanis significantly differed in winter, but not in spring. The alpha diversity of Chinese students and Pakistani students was similar. Moreover, oral microbial community of both Chinese and Pakistani students was mainly driven by stochastic processes. The microbial network of Chinese was more complexity and stability than that of Pakistanis. Our study uncovers the characteristics of human oral microbiota, which is of great significance for oral and human health.

Clinical effect of Pediococcus acidilactici PMC48 on hyperpigmented skin

BACKGROUND

The excessive production and accumulation of melanin in the epidermal skin layer can result in skin hyperpigmentation and darkening. Current technologies for regulating melanin are based on inhibiting melanin biosynthesis. They have low effectiveness and safety issues.

AIMS

This study aimed to evaluate the potential role of Pediococcus acidilactici PMC48 as a probiotic strain in medicines and cosmetics for skin treatment.

MATERIALS AND METHODS

Meanwhile, our research team has reported that P. acidilactici PMC48 strain isolated from sesame leaf kimchi can directly decompose the already synthesized melanin. It can also inhibit melanin biosynthesis. In the present study, we investigated the skin-whitening effect of this strain by arranging an 8-week clinical trial with 22 participants. PMC48 was applied to each participant's artificially UV-induced tanned skin in the clinical trial. Its whitening effect was investigated based on visual evaluation, skin brightness, and melanin index.

RESULTS

PMC48 showed a significant effect on the artificially induced pigmented skin. The color intensity of the tanned skin was decreased by 47.647%, and skin brightness was increased by 8.098% after the treatment period. PMC48 also significantly decreased the melanin index by 11.818%, indicating its tyrosinase inhibition capacity. Also, PMC48 improved skin moisture content level by 20.943%. Additionally, 16S rRNA-based amplicon sequencing analysis showed a distinct increase in Lactobacillaceae in the skin by up to 11.2% at the family level without affecting other skin microbiota. Furthermore, it showed no toxicity in in vitro or in vivo analyses.

DISCUSSION

These results indicate that P. acidilactici PMC48 is a promising probiotic strain that can be used to develop medicines and cosmetic products to solve skin-related problems.

CONCLUSIONS

These results demonstrate that P. acidilactici PMC48 can be a potential probiotic for the cosmetic industry against different skin disorders.

Microbiome in a ground-based analog cabin of China Space Station during a 50-day human occupation

Dead-corner areas in space station that untouched by the clean-up campaign often experience microorganisms outbreaks, but the microbiome of these areas has never been studied. In this study, the microbiome in a ground-based analog ``Tianhe'' core module of China Space Station was first investigated during a 50-day three-crew occupation. Dead-corner areas were receiving attention by adopting a new sampling method. Results indicate that the astronauts occupation did not affect the dominant bacteria community, but affected a small proportion. Due to the frequent activity of astronauts in the work and sleep areas, the biomarkers in these two areas are common human skin surface and gut microorganisms, respectively. For areas that astronaut rarely visits, the biomarkers in which are common environmental microbial groups. Fluorescence counting showed that 70.12-84.78% of bacteria were alive, with a quantity of 104-105 cells/100 cm2. With the occupation time extension, the number of microorganisms increased. At the same sampling time, there was no significant bioburden difference in various locations. The cultivable bioburden ranged from 101 to 104 colony forming unit (CFU)/100 cm2, which are the following eight genera Penicillium, Microsphaeropsis, Stachybotrys, Humicola, Cladosporium, Bacillus, Planomicrobium, and Acinetobacter. Chryseomicrobium genus may be a key focus for future microbial prevention and control work.

Spatial diversity of the skin bacteriome

The bacterial communities of the human skin impact its physiology and homeostasis, hence elucidating the composition and structure of the healthy skin bacteriome is paramount to understand how bacterial imbalance (i.e., dysbiosis) may lead to disease. To obtain an integrated view of the spatial diversity of the skin bacteriome, we surveyed from 2019 to 2023 five skin regions (belly button, behind ears, between toes, calves and forearms) with different physiological characteristics (dry, moist and sebaceous) in 129 healthy adults (579 samples - after data cleaning). Estimating bacterial diversity through 16S rRNA metataxonomics, we identified significant (p < 0.0001) differences in the bacterial relative abundance of the four most abundant phyla and 11 genera, alpha- and beta-diversity indices and predicted functional profiles (36 to 400 metabolic pathways) across skin regions and microenvironments. No significant differences, however, were observed across genders, ages, and ethnicities. As previously suggested, dry skin regions (forearms and calves) were more even, richer, and functionally distinct than sebaceous (behind ears) and moist (belly button and between toes) regions. Within skin regions, bacterial alpha- and beta-diversity also varied significantly for some of the years compared, suggesting that skin bacterial stability may be region and subject dependent. Our results, hence, confirm that the skin bacteriome varies systematically across skin regions and microenvironments and provides new insights into the internal and external factors driving bacterial diversity.

Characteristics of bacterial community and ARG profiles in the surface and air environments in a spacecraft assembly cleanroom

Understanding the microbial communities and antibiotic resistance genes (ARGs) in spacecraft assembly cleanrooms is crucial for spacecraft microbial control and astronaut safety. However, there have been few reports of ARG profiles and their relationship with microbiomes in such environments. In the present study, we assessed the bacterial community and ARGs in the air dust and surface environments of a typical spacecraft assembly cleanroom. Our results show a significant difference in bacterial composition between surfaces and air dust, as they belong to two distinct ecostates. Bacillus and Acinetobacter were significantly enriched in the air samples. Bacterial community network analysis revealed lower topological parameters and robustness of bacterial networks in the air samples. We also observed different distribution patterns of some typical ARGs between surface and air dust samples. Notably, the ermB gene exhibited a relatively high copy number and was enriched in the surface environment, compared to that in the air. Overall, our study provides insight into the complex microbial community and the distribution and transfer of ARGs in spacecraft assembly cleanrooms, and offers important input for developing control strategies against ARGs.

Haze Exposure Changes the Skin Fungal Community and Promotes the Growth of Talaromyces Strains

Haze pollution has been a public health issue. The skin microbiota, as a component of the first line of defense, is disturbed by environmental pollutants, which may have an impact on human health. A total of 74 skin samples from healthy students were collected during haze and nonhaze days in spring and winter. Significant differences of skin fungal community composition between haze and nonhaze days were observed in female and male samples in spring and male samples in winter based on unweighted UniFrac distance analysis. Phylogenetic diversity whole-tree indices and observed features were significantly increased during haze days in male samples in winter compared to nonhaze days, but no significant difference was observed in other groups. Dothideomycetes, Capnodiales, Mycosphaerellaceae, etc. were significantly enriched during nonhaze days, whereas Trichocomaceae, Talaromyces, and Pezizaceae were significantly enriched during haze days. Thus, five Talaromyces strains were isolated, and an in vitro culture experiment revealed that the growth of representative Talaromyces strains was increased at high concentrations of particulate matter, confirming the sequencing results. Furthermore, during haze days, the fungal community assembly was better fitted to a niche-based assembly model than during nonhaze days. Talaromyces enriched during haze days deviated from the neutral assembly process. Our findings provided a comprehensive characterization of the skin fungal community during haze and nonhaze days and elucidated novel insights into how haze exposure influences the skin fungal community. IMPORTANCE Skin fungi play an important role in human health. Particulate matter (PM), the main haze pollutant, has been a public environmental threat. However, few studies have assessed the effects of air pollutants on skin fungi. Here, haze exposure influenced the diversity and composition of the skin fungal community. In an in vitro experiment, a high concentration of PM promoted the growth of Talaromyces strains. The fungal community assembly is better fitted to a niche-based assembly model during haze days. We anticipate that this study may provide new insights on the role of haze exposure disturbing the skin fungal community. It lays the groundwork for further clarifying the association between the changes of the skin fungal community and adverse health outcomes. Our study is the first to report the changes in the skin fungal community during haze and nonhaze days, which expands the understanding of the relationship between haze and skin fungi.

The impact of bioactive textiles on human skin microbiota

In order to support the elevated market demand for the development of textiles with specific benefits for a healthy and safe lifestyle, several bioactive textiles with defined properties, including antimicrobial, antioxidant, anti-inflammatory, anti-odor, and anti-repellent, anti-ultraviolet (UV) radiation, have been proposed. Antimicrobial textiles, particularly, have received special interest considering the search for smart, protective textiles that also impact health and well-being. Although the incorporation of antimicrobials into textile material has been well succeeded, the addition of such components in textile clothing can influence the balance of the skin microbiota of the wearer. While most antimicrobial textiles have demonstrated good biocompatibility and antimicrobial performance against bacteria, fungi, and viruses, some problems such as textile biodegradation, odor, and dissemination of unwanted microorganisms might arise. However, little is known about the impact of such antimicrobial textile-products on human skin microbiota. To address this issue, the present review, for the first time, gives an overview about the main effects of antimicrobial textiles, i.e., antibacterial, antifungal, and antiviral, on skin microbiota while driving future investigation to elucidate their putative clinical relevance and possible applications according to their impact on skin microbiota. This knowledge may open doors for the development of more microbiota friendly textiles or antimicrobial textile-products able to target specific populations of the skin microbiota aiming to alleviate skin disorders, malodor, and allergies by avoiding the growth and spread of pathogenic microorganisms.

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.

Heavy rainfall accelerates the temporal turnover but decreases the deterministic processes of buried gravesoil bacterial communities

The influences of global climatic change require an understanding of changes in soil microbial communities under precipitation. However, little is known about how soil ("gravesoil") microbial communities associated with corpse decay respond to precipitation. Here, we explored the variations of temporal turnover and assembly in gravesoil bacterial communities in the Qinghai-Tibet Plateau ecosystem via controlled rainfall simulation experiments. In our experiments, rainfall intensity was set to 2.5 and 5 mm/3 days to simulate moderate and heavy rainfall, respectively, and sampling was conducted on the 4th, 11th, 18th, 32nd, 46th and 60th day. Our results showed precipitation significantly altered bacterial abundances and community structures. Analysis of time-decay relationships revealed that precipitation resulted in a divergent succession of gravesoil bacterial community structure and abundance changes of dominant phyla, such as Chloroflexi. Moreover, in the experimental groups, our results suggested that moderate rainfall increased the deterministic processes in the initial and mid periods, whereas heavy rainfall decreased these processes of gravesoil microbial community assembly in every period compared with those in the control group. The dispersal capacity induced by stochastic processes of gravesoil microbial communities decreased over time under moderate rainfall, whereas it initially increased and then decreased under heavy rainfall. This study highlights the influence of heavy rainfall on bacterial communities during corpse decay, which can provide some inferences for predicting changes in soil microbial communities under global climatic change.

Microbial Interplay in Skin and Chronic Wounds

Purpose of Review

Microbial infections in chronic wounds can often lead to lower-limb amputation, decrease in quality of life, and increase in mortality rate, and there is an unmet need to distinguish between pathogens and colonisers in these chronic wounds. Hence, identifying the composition of healthy skin microbiota, microbes associated with chronic wound and healing processes, and microbial interactions and host response in healing wounds vs. non-healing wounds can help us in formulating innovative individual-centric treatment protocols.

Recent Findings

This review highlights various metabolites and biomarkers produced by microbes that have been identified to modulate these interactions, particularly those involved in host–microbe and microbe–microbe communication. Further, considering that many skin commensals demonstrate contextual pathogenicity, we provide insights into promising initiatives in the wound microbiome research.

Summary

The skin microbiome is highly diverse and variable, and considering its importance remains to be a hotspot of medical investigations and research to enable us to prevent and treat skin disorders and chronic wound infections. This is especially relevant now considering that non-healing and chronic wounds are highly prevalent, generally affecting lower extremities as seen in diabetic foot ulcers, venous leg ulcers, and pressure ulcers. Pathogenic bacteria are purported to have a key role in deferring healing of wounds. However, the role of skin microflora in wound progression has been a subject of debate. In this review, we discuss biomarkers associated with chronic wound microenvironment along with the relevance of skin microflora and their metabolites in determining the chronicity of wounds.

Effect of Solar Radiation on Skin Microbiome: Study of Two Populations

Here, we examined the skin microbiome of two groups of healthy volunteers living on the Mediterranean coast with different exposures to sun radiation. One group, exposed to the sun in the summer, was compared with a group covered with clothing throughout the year. The seasonal effects on the skin microbiome of three body sites were determined before and after summer. Surprisingly, at the phyla level, there were no significant differences in microbiome diversity between the groups. Furthermore, within each group, there were no significant seasonal differences in high-abundance species at any of the sampling sites. These results suggest that the skin microbiome, developed over years, remains stable even after several months of exposure to summer weather, direct sunlight and humidity. However, in the group exposed to the sun during the summer months, there were significant differences in low-abundance species in sun-exposed areas of the skin (the inner and outer arm). These subtle changes in low-abundance species are interesting, and their effect on skin physiology should be studied further.

Shotgun metagenomic sequencing reveals skin microbial variability from different facial sites

Biogeography (body site) is known to be one of the main factors influencing the composition of the skin microbial community. However, site-associated microbial variability at a fine-scale level was not well-characterized since there was a lack of high-resolution recognition of facial microbiota across kingdoms by shotgun metagenomic sequencing. To investigate the explicit microbial variance in the human face, 822 shotgun metagenomic sequencing data from Han Chinese recently published by our group, in combination with 97 North American samples from NIH Human Microbiome Project (HMP), were reassessed. Metagenomic profiling of bacteria, fungi, and bacteriophages, as well as enriched function modules from three facial sites (forehead, cheek, and the back of the nose), was analyzed. The results revealed that skin microbial features were more alike in the forehead and cheek while varied from the back of the nose in terms of taxonomy and functionality. Analysis based on biogeographic theories suggested that neutral drift with niche selection from the host could possibly give rise to the variations. Of note, the abundance of porphyrin-producing species, i.e., Cutibacterium acnes, Cutibacterium avidum, Cutibacterium granulosum, and Cutibacterium namnetense, was all the highest in the back of the nose compared with the forehead/cheek, which was consistent with the highest porphyrin level on the nose in our population. Sequentially, the site-associated microbiome variance was confirmed in American populations; however, it was not entirely consistent. Furthermore, our data revealed correlation patterns between Propionibacterium acnes bacteriophages with genus Cutibacterium at different facial sites in both populations; however, C. acnes exhibited a distinct correlation with P. acnes bacteriophages in Americans/Chinese. Taken together, in this study, we explored the fine-scale facial site-associated changes in the skin microbiome and provided insight into the ecological processes underlying facial microbial variations.

Determining Informative Microbial Single Nucleotide Polymorphisms for Human Identification

The skin microbiome is a highly abundant and relatively stable source of DNA that may be utilized for human identification (HID). In this study, a set of single nucleotide polymorphisms (SNPs) with a high mean estimated Wright's fixation index (F_ST) (>0.1) and widespread abundance (found in ≥75% of samples compared) were selected from a diverse set of markers in the hidSkinPlex panel. The least absolute shrinkage and selection operator (LASSO) was used in a novel machine learning framework to generate a SNP panel and predict the human host from skin microbiome samples collected from the hand, manubrium, and foot. The framework was devised to emulate a new unknown person introduced to the algorithm and to match samples from that person against a population database. Unknown samples were classified with 96% accuracy (Matthews correlation coefficient [MCC], 0.954) in the test (n = 225 samples) data set. A final panel of informative SNPs was determined for HID (hidSkinPlex+) using all 51 individuals sampled at three body sites in triplicate. The hidSkinPlex+ panel comprises 365 SNPs and yielded prediction accuracy for the correct host of 95% (MCC = 0.949). The accuracy of the hidSkinPlex+ panel may be somewhat overestimated due to using 26 individuals from the training data set for the selection of the final panel. However, this accuracy still provides an indication of performance when tested on new samples. IMPORTANCE One of the fundamental goals in forensic genetics is to identify the source of biological evidence. Methods for detecting human DNA have advanced and can be quite sensitive, but not all DNA samples are amenable to current methods. However, the human skin microbiome is a source of DNA with high copy numbers, and it has the potential for high discriminatory power. The hidSkinPlex panel has been used for HID; however, some aspects of it could be improved. Missing information is ambiguous, as it is unclear if marker drop-out is a by-product of a low-template sample or if the reasons for not observing a marker are biological. Such ambiguity may confound methods for HID, and as such, an improved marker set (hidSkinPlex+) was designed that is considerably smaller and more robust to drop-out (365 SNPs contained in 135 markers) yet still can be used to accurately predict the human host.