Age and Mothers: Potent Influences of Children's Skin Microbiota

Preclinical Atopic Dermatitis Skin in Infants: An Emerging Research Area

Whereas clinically apparent atopic dermatitis (AD) can be confirmed by validated diagnostic criteria, the preclinical phenotype of infants who eventually develop AD is less well-characterized. Analogous to unaffected or nonlesional skin in established AD, clinically normal-appearing skin in infants who will develop clinical AD has distinct changes. Prospective studies have revealed insights into this preclinical AD phenotype. In this study, we review the structural, immunologic, and microbiome nature of the preclinical AD phenotype. Determination of markers that predict the development of AD will facilitate targeting of interventions to prevent the development or reduce the severity of AD in infants.

Early life microbiome influences on development of the mucosal innate immune system

The gut microbiota is well known to possess immunomodulatory capacities, influencing a multitude of cellular signalling pathways to maintain host homeostasis. Although the formation of the immune system initiates before birth in a sterile environment, an emerging body of literature indicates that the neonatal immune system is influenced by a first wave of external stimuli that includes signals from the maternal microbiota. A second wave of stimulus begins after birth and must be tightly regulated during the neonatal period when colonization of the host occurs concomitantly with the maturation of the immune system, requiring a fine adjustment between establishing tolerance towards the commensal microbiota and preserving inflammatory responses against pathogenic invaders. Besides integrating cues from commensal microbes, the neonatal immune system must also regulate responses triggered by other environmental signals, such as dietary antigens, which become more complex with the introduction of solid food during the weaning period. This "window of opportunity" in early life is thought to be crucial for the proper development of the immune system, setting the tone of subsequent immune responses in adulthood and modulating the risk of developing chronic and metabolic inflammatory diseases. Here we review the importance of host-microbiota interactions for the development and maturation of the immune system, particularly in the early-life period, highlighting the known mechanisms involved in such communication. This discussion is focused on recent data demonstrating microbiota-mediated education of innate immune cells and its role in the development of lymphoid tissues.

The Skin Microbiome and its Significance for Dermatologists

The skin is a physical and immunological barrier to the external environment. Its large surface area is colonized by diverse communities of microorganisms, including bacteria, viruses, fungi, and Demodex species mites. These microorganisms and their genetic material together create the skin microbiome. Physiologic and anatomic properties of skin sites create biogeographical habitats (dry, moist, and sebaceous) where distinct microbiota communities reside. Although, in general, the composition of these habitats is maintained from person to person, the skin microbiome of an individual also has unique microbial features. Dysbiosis occurs when the normal abundance, composition, or location of the microbiota is changed, most notably there is a decrease in flora diversity. Certain skin diseases, including atopic dermatitis, rosacea, and psoriasis are associated with cutaneous dysbiosis, and even disruption of the gut microbiota. Studies have shown that current treatments for these dermatologic conditions can alter/stabilize the skin microbiome, and there is emerging research detailing the impact of prebiotics, probiotics, and postbiotics on these conditions. Although clinical guidelines do not currently exist, clinical studies support the safety and possible benefits of using topical prebiotics and postbiotics and oral probiotics for a variety of skin conditions. Until such guidelines exist, utilizing carefully designed clinical studies to inform clinical practice is recommended.

A genome catalog of the early-life human skin microbiome

BACKGROUND

Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents.

RESULTS

Here we use deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who are part of the VITALITY trial in Australia as well as 67 maternally matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9483 prokaryotic genomes from 1056 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 21%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also find evidence for microbial sharing at the community, bacterial species, and strain levels between mothers and infants.

CONCLUSIONS

Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and development in early life.

An update on the current understanding of the infant skin microbiome and research challenges

Multiple factors contribute to establishment of skin microbial communities in early life, with perturbations in these ecosystems impacting health. This review provides an update on methods used to profile the skin microbiome and how this is helping enhance our understanding of infant skin microbial communities, including factors that influence composition and disease risk. We also provide insights into new interventional studies and treatments in this area. However, it is apparent that there are still research bottlenecks that include overreliance on high-income countries for skin microbiome 'surveys', many studies still focus solely on the bacterial microbiota, and also technical issues related to the lower microbial biomass of skin sites. These points link to pertinent open-research questions, such as how the whole infant skin microbiome interacts and how microbial-associated functions shape infant skin health and immunity.

Effects of Investigational Moisturizers on the Skin Barrier and Microbiome following Exposure to Environmental Aggressors: A Randomized Clinical Trial and Ex Vivo Analysis

The skin microbiota barrier participates in skin barrier function in addition to the physical, chemical, and immunological protective barriers, and is affected by environmental aggressors and skincare regimens. To better understand the exact effects of real-life environmental conditions on the skin and determine the protective methods, this study investigates the effects of three topical cosmetic moisturizers (water gel moisturizers with/without yeast extract (Moisturizers K and C) and a thick-emulsion cream moisturizer (Moisturizer L)) on clinical and skin microbiome endpoints in the presence of environmental aggressors during an 8-week, randomized controlled, triple-blind clinical trial with 110 participants, and molecular- as well as biomarker-level endpoints on ex vivo skin explants after exposure to simulate urban environmental conditions. The results show that all moisturizers are well-tolerated and improve skin barrier function and surface moisture content from the baseline, and the improvement is maintained at the last analysis point (3 days after trial completion). Compared with the untreated control areas (samples taken from the upper chest), treatment with Moisturizer K prevented a reduction in bacterial and fungal richness, and increased the change ratio of the relative abundance of commensal bacteria, such as Staphylococcus epidermidis and Ralstonia, at the treated sites (samples taken from the forehead). Moreover, Moisturizer K-treated ex vivo skin explants had higher levels of caspase 14 (a marker of skin barrier function), collagen I, and elastin (structure components), and lower levels of aryl hydrocarbon receptor (AHR; activated by air pollutants) and interleukin-6 (IL-6) than those in explants treated with other moisturizers and in the untreated areas of the skin. These results suggest that a skin postbiotic moisturizer with yeast extract supports the regulation of the skin's microbiome balance and may provide a holistic barrier (involving skin microbiome, physical, chemical, and immune barriers) to protect the skin against environmental aggressors.

Skin maturation from birth to 10 years of age: Structure, function, composition and microbiome

Infant and adult skin physiology differ in many ways; however, limited data exist for older children. To further investigate the maturation processes of healthy skin during childhood. Skin parameters were recorded in 80 participants of four age groups: babies (0-2 years), young children (3-6 years), older children (7-<10 years) and adults (25-40 years). Overall, skin barrier function continues to mature, reaching adult levels of transepidermal water loss (TEWL), lipid compactness, stratum corneum (SC) thickness and corneocyte size by the age of about 6 years. Higher levels of lactic acid and lower levels of total amino acids in the SC of babies and young children further indicate higher cell turnover rates. In all age groups, TEWL and skin surface hydration values remain higher on the face compared with the arm. Skin becomes darker and contains higher levels of melanin with increasing age. The composition of skin microbiome of the dorsal forearm in all children groups is distinct from that in adults, with Firmicutes predominating in the former and Proteobacteria in the latter. Skin physiology, along with the skin microbiome, continues to mature during early childhood in a site-specific manner.

An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs

The human skin microbiome represents a variety of complex microbial ecosystems that play a key role in host health. Molecular methods to study these communities have been developed but have been largely limited to low-throughput quantification and short amplicon-based sequencing, providing limited functional information about the communities present. Shotgun metagenomic sequencing has emerged as a preferred method for microbiome studies as it provides more comprehensive information about the species/strains present in a niche and the genes they encode. However, the relatively low bacterial biomass of skin, in comparison to other areas such as the gut microbiome, makes obtaining sufficient DNA for shotgun metagenomic sequencing challenging. Here we describe an optimised high-throughput method for extraction of high molecular weight DNA suitable for shotgun metagenomic sequencing. We validated the performance of the extraction method, and analysis pipeline on skin swabs collected from both adults and babies. The pipeline effectively characterised the bacterial skin microbiota with a cost and throughput suitable for larger longitudinal sets of samples. Application of this method will allow greater insights into community compositions and functional capabilities of the skin microbiome.

Compositional Variations between Adult and Infant Skin Microbiome: An Update

Human skin and its commensal microbiome form the first layer of protection to the outside world. A dynamic microbial ecosystem of bacteria, fungi and viruses, with the potential to respond to external insult, the skin microbiome has been shown to evolve over the life course with an alteration in taxonomic composition responding to altered microenvironmental conditions on human skin. This work sought to investigate the taxonomic, diversity and functional differences between infant and adult leg skin microbiomes. A 16S rRNA gene-based metataxonomic analysis revealed significant differences between the infant and adult skin groups, highlighting differential microbiome profiles at both the genus and species level. Diversity analysis reveals differences in the overall community structure and associated differential predicted functional profiles between the infant and adult skin microbiome suggest differing metabolic processes are present between the groups. These data add to the available information on the dynamic nature of skin microbiome during the life course and highlight the predicted differential microbial metabolic process that exists on infant and adult skin, which may have an impact on the future design and use of cosmetic products that are produced to work in consort with the skin microbiome.

Sample Collection, DNA Extraction, and Library Construction Protocols of the Human Microbiome Studies in the International Human Phenome Project

The human microbiome plays a crucial role in human health. In the past decade, advances in high-throughput sequencing technologies and analytical software have significantly improved our knowledge of the human microbiome. However, most studies concerning the human microbiome did not provide repeatable protocols to guide the sample collection, handling, and processing procedures, which impedes obtaining valid and timely microbial taxonomic and functional results. This protocol provides detailed operation methods of human microbial sample collection, DNA extraction, and library construction for both the amplicon sequencing-based measurements of the microbial samples from the human nasal cavity, oral cavity, and skin, as well as the shotgun metagenomic sequencing-based measurements of the human stool samples among adult participants. This study intends to develop practical procedure standards to improve the reproducibility of microbiota profiling of human samples.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-023-00097-y.

A genome catalog of the early-life human skin microbiome

Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents. Here we used ultra-deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who were part of the VITALITY trial in Australia as well as 67 maternally-matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9,194 bacterial genomes from 1,029 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 25%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also found evidence for vertical transmission at the microbial community, individual skin bacterial species and strain levels between mothers and infants. Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and transmission in early life.

Skin barrier immunology from early life to adulthood

Our skin has a unique barrier function, which is imperative for the body's protection against external pathogens and environmental insults. Although interacting closely and sharing many similarities with key mucosal barrier sites, such as the gut and the lung, the skin also provides protection for internal tissues and organs and has a distinct lipid and chemical composition. Skin immunity develops over time and is influenced by a multiplicity of different factors, including lifestyle, genetics, and environmental exposures. Alterations in early life skin immune and structural development may have long-term consequences for skin health. In this review, we summarize the current knowledge on cutaneous barrier and immune development from early life to adulthood, with an overview of skin physiology and immune responses. We specifically highlight the influence of the skin microenvironment and other host intrinsic, host extrinsic (e.g. skin microbiome), and environmental factors on early life cutaneous immunity.

The dynamic balance of the skin microbiome across the lifespan

For decades research has centered on identifying the ideal balanced skin microbiome that prevents disease and on developing therapeutics to foster this balance. However, this single idealized balance may not exist. The skin microbiome changes across the lifespan. This is reflected in the dynamic shifts of the skin microbiome's diverse, inter-connected community of microorganisms with age. While there are core skin microbial taxa, the precise community composition for any individual person is determined by local skin physiology, genetics, microbe-host interactions, and microbe-microbe interactions. As a key interface with the environment, the skin surface and its appendages are also constantly exchanging microbes with close personal contacts and the environment. Hormone fluctuations and immune system maturation also drive age-dependent changes in skin physiology that support different microbial community structures over time. Here, we review recent insights into the factors that shape the skin microbiome throughout life. Collectively, the works summarized within this review highlight how, depending on where we are in lifespan, our skin supports robust microbial communities, while still maintaining microbial features unique to us. This review will also highlight how disruptions to this dynamic microbial balance can influence risk for dermatological diseases as well as impact lifelong health.

The Skin Microbiome: Current Landscape and Future Opportunities

Our skin is the largest organ of the body, serving as an important barrier against the harsh extrinsic environment. Alongside preventing desiccation, chemical damage and hypothermia, this barrier protects the body from invading pathogens through a sophisticated innate immune response and co-adapted consortium of commensal microorganisms, collectively termed the microbiota. These microorganisms inhabit distinct biogeographical regions dictated by skin physiology. Thus, it follows that perturbations to normal skin homeostasis, as occurs with ageing, diabetes and skin disease, can cause microbial dysbiosis and increase infection risk. In this review, we discuss emerging concepts in skin microbiome research, highlighting pertinent links between skin ageing, the microbiome and cutaneous repair. Moreover, we address gaps in current knowledge and highlight key areas requiring further exploration. Future advances in this field could revolutionise the way we treat microbial dysbiosis associated with skin ageing and other pathologies.

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

OBJECTIVE

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

METHODS

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

RESULTS

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

CONCLUSION

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

How do the skin barrier and microbiome adapt to the extra-uterine environment after birth? Implications for the clinical practice

The multiple protective functions of the skin derive from the interactions between epithelial skin and immune cells as well as the commensal microbiota. Developed in the last trimester of intra-uterine life, the skin barrier adapts dynamically after birth. Specific differences in the structure and physiology have been disclosed between infant and adult skin. The stratum corneum of infants is thinner and structured by thicker corneocytes with a more anisotropic surface in comparison to adult skin. Lower levels of the natural moisturizing factor and its constituents, together with the increased protease activity in the epidermis result in dry baby skin and ongoing adaptation of the desquamation to the extra-uterine environment. Infant epidermis is characterized by an accelerated proliferation rate and clinically competent permeability barrier in term neonates, despite the higher baseline values of transepidermal water loss in infants. The skin surface of newborns is less acidic, which could increase susceptibility to diaper and atopic dermatitis. Immediately after birth, skin is colonized by commensal bacteria-a process dependent on the mode of delivery and of major importance for the maturation of the immune system. Skin bacterial diversity and dysbiosis have been related to different pathology such as atopic and seborrheic dermatitis. This paper focuses on the ongoing structural, functional and biochemical adaptation of the human skin barrier after birth. We discuss the interactions on the 'skin barrier/ microbiota/ immune system' axis and their role in the development of competent functional integrity of the epidermal barrier.

Infant Mode of Delivery Shapes the Skin Mycobiome of Prepubescent Children

Characterizing the skin mycobiome is necessary to define its association with the host immune system, particularly in children. In this study, we describe the skin mycobiome on the face, ventral forearm, and calf of 72 prepubescent children (aged 1 to 10 years) and their mothers, based on internal transcribed spacer (ITS) amplicon sequencing. The age and delivery mode at birth are the most influential factors shaping the skin mycobiome. Compared with that of the vaginally born children, the skin mycobiome of caesarean-born children is assembled by predominantly deterministic niche-based processes and exhibits a more fragile microbial network at all three sampling sites. Moreover, vaginal delivery leads to clearer intra- and interindividual specialization of fungal structures with increasing age; this phenomenon is not observed in caesarean-born children. The maternal correlation with children also differs based on the mode of delivery; specifically, the mycobiomes of vaginally born children at younger ages are more strongly correlated with vagina-associated fungal genera (Candida and Rhodotorula), whereas those of caesarean-delivered children at elder age include more skin-associated and airborne fungal genera (Malassezia and Alternaria). Based on this ecological framework, our results suggest that the delivery mode is significantly associated with maturation of the skin fungal community in children. IMPORTANCE Human skin is permanently colonized by microbes starting at birth. The hygiene hypothesis suggests that a lack of early-life immune imprinting weakens the body's resilience against atopic disorders later in life. To better understand fungal colonization following early-life periods affected by interruption, we studied the skin mycobiomes of 73 children and their mothers. Our results suggest a differentiation of the skin mycobiomes between caesarean-born and vaginally born children. Caesarean-born children exhibit a mycobiome structure with more fitted deterministic niche-based processes, a fragile network, and an unchanged microbial dissimilarity over time. In vaginally born children, this dissimilarity increases with age. The results indicate that initial microbial colonization has a long-term impact on a child's skin mycobiome. We believe that these findings will inspire further investigations of the "hygiene hypothesis" in the human microbiome, especially in providing novel insights into influences on the development of the early-life microbiome.

Ecological Processes and Human Behavior Provide a Framework for Studying the Skin Microbial Metacommunity

Metacommunity theory dictates that a microbial community is supported both by local ecological processes and the dispersal of microbes between neighboring communities. Studies that apply this perspective to human-associated microbial communities are thus far limited to the gut microbiome. Yet, the skin serves as the primary barrier between the body and the external environment, suggesting frequent opportunities for microbial dispersal to the variable microbial communities that are housed across skin sites. This paper applies metacommunity theory to understand the dispersal of microbes to the skin from the physical and social environment, as well as between different skin sites on an individual's body. This includes highlighting the role of human behavior in driving microbial dispersal, as well as shaping physiological properties of skin that underscore local microbial community dynamics. By leveraging data from research on the skin microbiomes of amphibians and other animals, this paper provides recommendations for future research on the skin microbial metacommunity, including generating testable predictions about the ecological underpinnings of the skin microbiome.

Microbiome-Immune Interactions in Allergy and Asthma

The human microbiota has been established as a key regulator of host health, in large part owing to its constant interaction with and impact on host immunity. A range of environmental exposures spanning from the prenatal period through adulthood are known to affect the composition and molecular productivity of microbiomes across mucosal and dermal tissues with short- and long-term consequences for host immune function. Here we review recent findings in the field that provide insights into how microbial-immune interactions promote and sustain immune dysfunction associated with allergy and asthma. We consider both early life microbiome perturbation and the molecular underpinnings of immune dysfunction associated with subsequent allergy and asthma development in childhood, as well as microbiome features that relate to phenotypic attributes of allergy and asthma in older patients with established disease.

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.

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.

Dynamics of vaginal microbiome in female beagles at different ages

Age-related changes in human vaginal microbiota composition have been reported, and such changes might be influenced by humidity, external stimuli, hormone levels, drug to use, and other factors. However, there is no report about the vaginal microbiota composition of female beagles at different ages. To investigate the effects of aging on the vaginal microbiota independent of other effects, we analyzed the vaginal microbiomes of 23 beagles at a wide range of ages from 1 year to 7 years old (except the 3rd year), 1-2 y were categorized into youth stage (YS), 4-5 y were categorized into middle stage (MS), and 6-7 y were categorized into elderly stage (ES) based on age. Samples were collected by scraping the vaginal mucosa of YS (n = 8), MS (n = 5) and ES (n = 10), and analyzed by 16S-rRNA gene high-throughput-sequencing. The diversity of the vaginal microbiome in female beagles was found to continuously change with age. We also found associations between age and specific members and functions of the vaginal microbiome. The metabolism of terpenoids and polyketide and the cell motility are significantly enhanced with age. Our results suggest that the proportion of Tenericutes might be a biomarker which could distinguish between YS and others.

Early life host-microbe interactions in skin

Our skin is the interface through which we mediate lifelong interactions with our surrounding environment. Initial development of the skin's epidermis, adnexal structures, and barrier function is necessary for normal cutaneous microbial colonization, immune development, and prevention of disease. Early life microbial exposures can have unique and long-lasting impacts on skin health. The identity of neonatal skin microbes and the context in which they are first encountered, i.e., through a compromised skin barrier or in conjunction with cutaneous inflammation, can have additional short- and long-term health consequences. Here, we discuss key attributes of infant skin and endogenous and exogenous factors that shape its relationship to the early life cutaneous microbiome, with a focus on their clinical implications.

Predominance of Staphylococcus correlates with wound burden and disease activity in dystrophic epidermolysis bullosa: a prospective case-control study

Recessive dystrophic epidermolysis bullosa (RDEB) is characterized by skin blistering and wounds. To uncover changes in skin and mucosal microbiome related to age and disease progression, and microbiome impact on clinical and inflammatory laboratory parameters, swabs from wounded and unwounded skin, oral mucosa and stool samples of 28 children with RDEB and 28 healthy controls were subjected to 16S-rRNA gene sequencing. Skin microbiome of RDEB patients showed significantly reduced alpha diversity compared to healthy controls and early, age-dependent predominance of Staphylococcus aureus first in wounds, then in unwounded skin. These findings were more pronounced in severe disease with higher abundances of Staphylococcus aureus compared to intermediate disease. Staphylococcus aureus abundance correlated significantly with both acute and chronic wound burden. Changes in oral mucosal and gut microbiome were discrete with no significant differences in alpha diversity. Our findings show that children with RDEB experience skin microbiome changes early in life. Longitudinal studies should confirm that dysbiosis starts in wounds and later extends to unwounded skin. The predominance of Staphylococcus aureus significantly correlates with wound burden and disease activity, and to some extent with systemic inflammation.

Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care

The microbiome, as a community of microorganisms and their structural elements, genomes, metabolites/signal molecules, has been shown to play an important role in human health, with significant beneficial applications for gut health. Skin microbiome has emerged as a new field with high potential to develop disruptive solutions to manage skin health and disease. Despite an incomplete toolbox for skin microbiome analyses, much progress has been made towards functional dissection of microbiomes and host-microbiome interactions. A standardized and robust investigation of the skin microbiome is necessary to provide accurate microbial information and set the base for a successful translation of innovations in the dermo-cosmetic field. This review provides an overview of how the landscape of skin microbiome research has evolved from method development (multi-omics/data-based analytical approaches) to the discovery and development of novel microbiome-derived ingredients. Moreover, it provides a summary of the latest findings on interactions between the microbiomes (gut and skin) and skin health/disease. Solutions derived from these two paths are used to develop novel microbiome-based ingredients or solutions acting on skin homeostasis are proposed. The most promising skin and gut-derived microbiome interventional strategies are presented, along with regulatory, safety, industrial, and technical challenges related to a successful translation of these microbiome-based concepts/technologies in the dermo-cosmetic industry.

Skin Microbiota and Clinical Associations in Netherton Syndrome

Netherton syndrome (NS) is a rare, life-threatening syndrome caused by serine protease inhibitor Kazal-type 5 gene (SPINK5) mutations, resulting in skin barrier defect, bacterial skin infections, and allergic sensitization in early childhood. Recent data on adult patients with NS suggest that the presence of Staphylococcus aureus further promotes barrier disruption and skin inflammation. We analyzed the skin microbiota by shotgun sequencing in 12 patients with NS from eight Finnish families with healthy family controls as the reference and correlated the findings with allergen-specific IgE prevalence, immune cell phenotype, and infection history of the patients. Compared with healthy family controls, skin microbiome diversity and normal skin site variability were measurably decreased in patients with NS. No correlation was found between allergic sensitization and skin microbiota as such, but low circulating CD57+ and/or CD8+ T cells significantly correlated with lower microbial diversity and less abundance of S. aureus (P < 0.05). S. aureus was the most prevalent species in patients with NS but also Streptococcus agalactiae was abundant in four patients. The genomic DNA relative abundance of S. aureus secreted virulence peptides and proteases PSMα, staphopain A, and staphopain B were increased in most of the samples of patients with NS, and their abundance was significantly (P < 0.05) associated with recurrent childhood skin infections, confirming the clinical relevance of S. aureus dominance in the NS skin microbiome.

Interrelationships between Skin Structure, Function, and Microbiome of Pregnant Females and Their Newborns: Study Protocol for a Prospective Cohort Study

Background

Pregnancy leads to several skin changes, but evidence about structural and functional skin changes is scarce. Findings on skin structure and function in children in their first year reveal rapid skin maturation, but evidence indicates that in particular, water holding and transport mechanisms are different from adults. Important questions include whether maternal cutaneous properties predict infant skin condition, and if so, how. This is especially relevant for the skin's microbiome because it closely interacts with the host and is assumed to play a role in many skin diseases. Therefore, the study objective is to explore characteristics of skin and hair of pregnant women and their newborns during pregnancy and in the first six months after delivery and their associations.

Methods

The study has an observational longitudinal design. We are recruiting pregnant females between 18 and 45 years using advertisement campaigns in waiting areas of gynecologists and hospital's outpatient services. A final sample size of n = 100 women is the target. We perform noninvasive, standardized skin, hair, and skin microbiome measurements. We establish the baseline visit during pregnancy until at the latest four weeks before delivery. We schedule follow-up visits four weeks and six months after birth for mothers and their newborns. We will calculate descriptive statistical methods using frequencies and associations over time depending on scale levels of the measurements. Discussion. The majority of previous studies that have investigated infants' skin microbiome and its associations used cross-sectional designs and focused on selected characteristics in small samples. In our longitudinal study, we will characterize a broad range of individual and environmental characteristics of mothers and their newborns to evaluate interrelationships with skin parameters and their changes over time. Considering the combination of these multiple variables and levels will allow for a deeper understanding of the complex interrelationship of the newborn's skin maturation. This trial is registered with ClinicalTrials.gov (Identifier: NCT04759924).

Analysis of the Bacterial Flora of Sensitive Facial Skin Among Women in Guangzhou

Background

Sensitive skin (SS) is easily irritated by various environmental stimuli, and epidemiological surveys surprisingly find that self-perceived SS is widespread worldwide.

Objective

To investigate whether SS is linked to changes in the skin bacterial population using 16S rRNA sequencing and bioinformatic analysis.

Patients and Methods

According to both the Huaxi SS Questionnaire and Lactic Acid Stimulation Test, 60 female volunteers in Guangzhou were classified into normal skin (NS) and SS groups. Skin barrier parameters were assessed by the CK skin tester. The DNA of the bacterial flora on the facial skin surface was extracted and was subjected to 16S rRNA sequencing.

Results

The skin hydration was significantly lower in the SS group compared to the NS group (P =0.032). Based on 16S rRNA sequencing and bioinformatic analysis, the number of operational taxonomic units (OTUs) significantly decreased in the SS group (P =0.0235, SS vs NS). The relative abundance of Neisseriaceae in SS group decreased significantly (P <0.05, SS vs NS), while that of Neisseria (within the Neisseriaceae family) increased significantly (P <0.05, SS vs NS).

Conclusion

SS is accompanied by a decrease in species diversity and richness, which may be relevant to the weakening of the microbial barrier (due to the increase of Neisseria or the decrease of Neisseriaceae). Thus, corresponding treatment for Neisseriaceae may be a new idea in the treatment of SS.

Nationality and body location alter human skin microbiome

Skin microbiomes function directly in human health and are affected by various external and internal factors. However, few studies have showed the variation of human skin microbiota at multiple body sites in individuals of different national origin living in the same environment. Here, using 16S rRNA sequencing, we investigated the diversity and function of skin microbiomes in different body locations of Chinese and Pakistani individuals from a single college in China. Body location and nationality significantly affected community structures, while season and gender only impacted community member. Due to different lifestyles and likely genetic characteristics of the hosts, Proteobacteria was more abundant in Pakistanis than in Chinese individuals. There were significant differences in the Shannon diversity of skin microorganisms among different skin sites of Chinese individuals, but not in Pakistanis. PICRUSt prediction indicated that gene functions involved in carbohydrate metabolism, lipid metabolism, and xenobiotics biodegradation and metabolism were higher in bacteria collected from Pakistanis than those from Chinese individuals, but the amino acid metabolism of skin microorganisms in Chinese people was higher. The relative abundances of potential pathogenic bacteria also differed in different body locations, providing a foundation for studying skin-associated bacterial diseases. Through a meta-analysis of 233 human skin samples from eight elevational sites in western China, we found that skin microbial diversity first decreased and then increased with increasing altitude. Network analysis showed positive correlation between altitude and Lactobacillus, Chryseobacterium, or Acinetobacter. Our results uncover the variation of human skin microbiota allowing future explorations of potential significance for human health. KEY POINTS: • Body location and nationality affect skin microbiota diversity and function. • Proteobacteria was more abundant in Pakistanis than in Chinese. • Skin microbial diversity first decreased and then increased with elevated altitude.

Human Skin Microbiome: Impact of Intrinsic and Extrinsic Factors on Skin Microbiota

The skin is the largest organ of the human body and it protects the body from the external environment. It has become the topic of interest of researchers from various scientific fields. Microorganisms ensure the proper functioning of the skin. Of great importance, are the mutual relations between such microorganisms and their responses to environmental impacts, as dysbiosis may contribute to serious skin diseases. Molecular methods, used for microorganism identification, allow us to gain a better understanding of the skin microbiome. The presented article contains the latest reports on the skin microbiota in health and disease. The review discusses the relationship between a properly functioning microbiome and the body's immune system, as well as the impact of internal and external factors on the human skin microbiome.

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.

Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences

Alterations in the human microbiome have been observed in a variety of conditions such as asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial intelligence with rich microbiome datasets can offer an improved understanding of the microbiome's role in human health. To gain actionable insights it is essential to consider both the predictive power and the transparency of the models by providing explanations for the predictions. We combine the collection of leg skin microbiome samples from two healthy cohorts of women with the application of an explainable artificial intelligence (EAI) approach that provides accurate predictions of phenotypes with explanations. The explanations are expressed in terms of variations in the relative abundance of key microbes that drive the predictions. We predict skin hydration, subject's age, pre/post-menopausal status and smoking status from the leg skin microbiome. The changes in microbial composition linked to skin hydration can accelerate the development of personalized treatments for healthy skin, while those associated with age may offer insights into the skin aging process. The leg microbiome signatures associated with smoking and menopausal status are consistent with previous findings from oral/respiratory tract microbiomes and vaginal/gut microbiomes respectively. This suggests that easily accessible microbiome samples could be used to investigate health-related phenotypes, offering potential for non-invasive diagnosis and condition monitoring. Our EAI approach sets the stage for new work focused on understanding the complex relationships between microbial communities and phenotypes. Our approach can be applied to predict any condition from microbiome samples and has the potential to accelerate the development of microbiome-based personalized therapeutics and non-invasive diagnostics.

Characterization of the human skin resistome and identification of two microbiota cutotypes

BACKGROUND

The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity.

RESULTS

In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp, are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures. Of note, the abundance of ARGs was significantly higher in Chinese than Americans, while multidrug-resistant bacteria ("superbugs") existed on the skin of both Americans and Chinese. A detailed analysis of microbial signatures identified Moraxella osloensis as a species specific for Chinese skin. Importantly, Moraxella osloensis proved to be a signature species for one of two robust patterns of microbial networks present on Chinese skin, with Cutibacterium acnes indicating the second one. Each of such "cutotypes" was associated with distinct patterns of data-driven marker genes, functional modules, and host skin properties. The two cutotypes markedly differed in functional modules related to their metabolic characteristics, indicating that host-dependent trophic chains might underlie their development.

CONCLUSIONS

The development of the iHSMGC will facilitate further studies on the human skin microbiome. In the present study, it was used to further characterize the human skin resistome. It also allowed to discover the existence of two cutotypes on the human skin. The latter finding will contribute to a better understanding of the interpersonal complexity of the skin microbiome. Video abstract.

Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States

This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis).

Daily practices put humans in close contact with the surrounding environment, and differences in these practices have an impact on human physiology, development, and health. There is mounting evidence that the microbiome represents an interface that mediates interactions between the human body and the environment. In particular, the skin microbiome serves as the primary interface with the external environment and aids in host immune function by contributing as the first line of defense against pathogens. Despite these important connections, we have only a basic understanding of how the skin microbiome is first established, or which environmental factors contribute to its development. To this end, this study compared the skin bacterial communities of infants (n = 47) living in four populations in Mexico and the United States that span the socioeconomic gradient, where we predicted that variation in physical and social environments would shape the infant skin microbiome. Results of 16S rRNA bacterial gene sequencing on 119 samples (armpit, hand, and forehead) showed that infant skin bacterial diversity and composition are shaped by population-level factors, including those related to socioeconomic status and household composition, and vary by skin site and infant age. Differences in infant-environment interactions, including with other people, appear to vary across the populations, likely influencing infant microbial exposures and, in turn, the composition of infant skin bacterial communities. These findings suggest that variation in microbial exposures stemming from the local environment in infancy can impact the establishment of the skin microbiome across body sites, with implications for developmental and health outcomes.

IMPORTANCE This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis).

Skin Microbiome as Years Go By

The skin microbial communities, i.e., the microbiota, play a major role in skin barrier function so must remain dynamic to adapt to the changes in the niche environment that occur across the different body sites throughout the human lifespan. This review provides an overview of the major alterations occurring in the skin microbiome (microbial and genomic components) during the various stages of life, beginning with its establishment in the first weeks of life through to what is known about the microbiome in older populations. Studies that have helped identify the factors that most influence skin microbiome function, structure, and composition during the various life stages are highlighted, and how alterations affecting the delicate balance of the microbiota communities may contribute to variations in normal physiology and lead to skin disease is discussed. This review underlines the importance of improving our understanding of the skin microbiome in populations of all ages to gain insights into the pathophysiology of skin diseases and to allow better monitoring and targeted treatment of more vulnerable populations.

Dynamics of Skin Mycobiome in Infants

Understanding the microbial community structure of the human skin is important for treating cutaneous diseases; however, little is known regarding skin fungal communities (mycobiomes). The aim of the present study was to investigate the features of and variations in skin fungal communities during infancy in 110 subjects less than 6 months of age. Skin samples were obtained from the back, antecubital fossa, and volar forearm, while physiological parameters including transepidermal water loss, pH, surface moisture, and deep layer hydration were evaluated. Skin fungal diversity decreased after the first three months of life. Differences in fungal community composition were greater among individual infants than among the three skin sites in the same individual. Inter- and intra-individual variation were similar and lower, respectively, than the variability between two samples obtained 12 weeks apart, from the same site in the same subject, suggesting low stability of fungal communities on infant skin. Skin physiological parameters showed little correlation with skin fungal community structure. Additionally, Malassezia was the most represented genus (36.43%) and M. globosa was the most abundant species in Malassezia with its abundance decreasing from 54.06% at 0–2 months to 34.54% at 5–6 months. These findings provide a basis for investigating the causative fungi-skin interactions associated with skin diseases.

Impact of the early-life skin microbiota on the development of canine atopic dermatitis in a high-risk breed birth cohort

Canine atopic dermatitis (CAD) is a prevalent inflammatory skin disease of dogs worldwide. Certain breeds such as the West Highland White Terriers (WHWT) are predisposed to suffer from CAD. Microbial dysbiosis is known to play a significant role in the pathogenesis of the disease, which is similar to its human counterpart, atopic dermatitis (AD). To date, no large cohort-study has been conducted in a predisposed dog breed to study the impact of the early-life microbiota on the development of CAD, as well as the possible implication of factors such as hygiene and access to the outdoors. In this study skin samples of 143 WHWT, including 109 puppies up to three weeks old and 34 parent dogs, from 17 breeders, were subjected to 16S rRNA gene and ITS2 amplicon sequencing to disclose the bacterial and fungal oral and skin microbiota, respectively. The oral samples served as a control group to confirm differences between haired and mucosal surfaces. The cutaneous microbiota differed between sample sites and age of the dogs. The season of sampling, geographical origin as well as hygiene status of the household and the access to the outdoors shaped the skin microbiota of the puppies significantly. However, we found that the individual early-life microbiota did not predispose for the later development of CAD.

A Mother's Touch: Emerging Roles in Development of the Cutaneous Microbiome

Skin-associated bacteria constitute a large proportion of the human microbiome and influence host immunity. The healthy cutaneous microbiome adopts site-specific composition, weeks to months postpartum. Zhu et al. (2019) expand the scope of pediatric data, tracking infant skin microflora changes by site, through childhood, and establish new associations with delivery mode and maternal microbiome.