Hands play a critical role in the exchange of microbiota across one's body, between individuals and with the environment. Hand hygiene practices are used in everyday life to help prevent the spread of disease. All hand hygiene products, irrespective of inclusion of ingredients like antimicrobials or pre/pro/post-biotics, have the potential to alter both the acquired and the innate microbiome of the hand, albeit by different mechanisms. While the intent of hand hygiene is to reduce pathogens on the skin below the infectious dose, this must be balanced with limiting the impact on the hand's resident microbial community, where disruption may contribute to skin irritation or dermatological disease. Most prior studies have focused on pathogen reduction only. With an advancing awareness of its relationship skin health, it is critical to also expand our understanding of the impact of hygiene on the hand's resident microbiota. Here, we explore the impact of various hygiene products and protocols on the hand microbiome. We examine shifts in the microbial community following a single hygiene event, as well as provide an initial exploration into the dynamics of microbial disruption and recovery after multiple exaggerated exposures to ABHS (40 uses in 4 hours). In all explored scenarios, there is an immediate post-hygiene decrease in total microbial biomass and alpha diversity. Furthermore, our data imply that the hand resident microbial community is resilient, with recovery occurring within 3 hours after exaggerated ABHS exposure. Thus, in these exposure scenarios, the benefits of frequent hand hygiene, i.e., pathogen removal, appear appropriately balanced with a low risk of impact on the hand's innate microbiota.

Both the gut microbiome and innate immunity are known to differ across biogeographically diverse human populations. The gut microbiome has been shown to directly influence systemic immunity in animal models.

The COVID-19 pandemic has elevated concern about mask-related skin problems like so-called 'maskne' which is likely rooted in the skin microbiome. We therefore determined if wearing an N95 mask affects the skin microbiome in a 3-day controlled study. On Day 1, subjects (n=10) followed their normal office routine without a mask. On Days 2 and 3, subjects wore an N95 mask (3M Model 8210) from morning to late afternoon (6 hours). The same mask was used both days. Microbiome diversity and composition (16S rRNA amplicon sequencing, V1-V3), stratum corneum (SC) barrier function (TEWL), SC hydration, skin redness and follicular porphyrins were measured on the cheek (masked site) and forehead (control site) each morning and afternoon. At the end of the study, a sample of each mask was collected for microbiome analysis. Mask wearing showed no significant effect on alpha (Shannon) or beta (Brays-Curtis) microbiome diversity. Mask wearing had no significant effect on Cutibacterium acnes relative abundance. Mask wearing corresponded to a small increase in the genus Staphylococcus relative abundance on Day 2 (p=0.03) but not Day 3. There was no significant effect of mask wearing on SC hydration or follicular porphyrins. TEWL and skin redness were elevated (p<0.05) on Day 2 and Day 3 on the masked cheek but not the unmasked forehead; values returned to baseline from Day 2 PM to Day 3 AM. Finally, the mask microbiome reflected that of the subject's skin; the relative abundance of C. acnes on the subject's mask correlated with that on the subject's cheek skin (r2=0.46, p<0.001). In conclusion, wearing an N95 mask for 6 hours per day on two consecutive days under routine office work conditions did not significantly affect the diversity or composition of the skin microbiome and produced only transient changes in visible skin redness and barrier function. Longer term studies with different types of masks under non-office conditions are needed to further understand the influence of mask wearing on the skin microbiome.

In both high- and low-income countries, HIV-negative children born to HIV-positive mothers (HIV exposed, uninfected [HEU]) are more susceptible to severe infection than HIV-unexposed, uninfected (HUU) children, with altered innate immunity hypothesized to be a cause. Both the gut microbiome and systemic innate immunity differ across biogeographically distinct settings, and the two are known to influence each other. And although the gut microbiome is influenced by HIV infection and may contribute to altered immunity, the biogeography of immune-microbiome correlations among HEU children have not been investigated. To address this, we compared the innate response and the stool microbiome of 2-y-old HEU and HUU children from Belgium, Canada, and South Africa to test the hypothesis that region-specific immune alterations directly correlate to differences in their stool microbiomes. We did not detect a universal immune or microbiome signature underlying differences between HEU versus HUU that was applicable to all children. But as hypothesized, population-specific differences in stool microbiomes were readily detected and included reduced abundances of short-chain fatty acid-producing bacteria in Canadian HEU children. Furthermore, we did not identify innate immune-microbiome associations that distinguished HEU from HUU children in any population. These findings suggest that maternal HIV infection is independently associated with differences in both innate immunity and the stool microbiome in a biogeographical population-specific way.

BACKGROUNDThe human skin microbiome is highly personalized, depending on, for example, body site, age, gender, and lifestyle factors. The temporal stability of an individual's skin microbiome-its resiliency and robustness over months and years-is also a personalized feature of the microbiome. The authors measured the temporal stability of the facial skin microbiome in a large cohort of subjects. In addition to measuring microbiome dynamics, they tracked facial skin condition using noninvasive, objective imaging and biophysical measures to identify significant facial features associated with temporal changes in microbiome diversity and composition.METHODSThe authors used 16S ribosomal RNA amplicon sequencing to track cheek and forehead skin microbiome diversity and composition annually over a 2-year period (2017-2019) in 115 healthy adult men and women. Skin metadata included facial features, such as wrinkles, hyperpigmentation, porphyrins, and skin color tone, as well as biophysical parameters for stratum corneum barrier function, pH, hydration, and elasticity.RESULTSAcross the subject population, the facial skin microbiome composition and diversity were relatively stable, showing minor variation over the 2-year period. However, for some subjects, composition, diversity, and relative abundance of specific organisms showed substantial changes from one year to the next, and these changes were associated with changes in stratum corneum barrier function and follicular porphyrins.CONCLUSIONSFor healthy people, facial skin microbiome diversity and composition are relatively stable from year to year. Tracking the temporal changes in the microbiome along with skin phenotypic changes allows for a deeper understanding of the skin microbiome's role in health and disease. These results should be helpful in the design of longer-term intervention trials with microbiome-based skin care treatments.

Background: Allergic disease is the most frequent chronic health issue in children and has been linked to early-life gut microbiome dysbiosis. Many lines of evidence suggest that microbially derived short-chain fatty acids, and particularly butyrate, can promote immune tolerance. Objective: We sought to determine whether bacterial butyrate production in the gut during early infancy is protective against the development of atopic disease in children. Methods: We used shotgun metagenomic analysis to determine whether dysbiosis in butyrate fermentation could be identified in human infants, before their developing allergic disease. Results: We found that the microbiome of infants who went on to develop allergic sensitization later in childhood lacked genes encoding key enzymes for carbohydrate breakdown and butyrate production. Conclusions: Our findings support the importance of microbial carbohydrate metabolism during early infancy in protecting against the development of allergies.

Despite recognition that biogeography and individuality shape the function and composition of the human skin microbiome, we know little about how extrinsic and intrinsic host factors influence its composition. To explore the contributions of these factors to skin microbiome variation, we profiled the bacterial microbiomes of 495 North American subjects (ages, 9 to 78 years) at four skin surfaces plus the oral epithelium using 16S rRNA gene amplicon sequencing. We collected subject metadata, including host physiological parameters, through standardized questionnaires and noninvasive biophysical methods. Using a combination of statistical modeling tools, we found that demographic, lifestyle, and physiological factors collectively explained 12 to 20% of the variability in microbiome composition. The influence of health factors was strongest on the oral microbiome. Associations between host factors and the skin microbiome were generally dominated by operational taxonomic units (OTUs) affiliated with the Clostridiales and Prevotella. A subset of the correlations between microbial features and host attributes were site specific. To further explore the relationship between age and the skin microbiome of the forehead, we trained a Random Forest regression model to predict chronological age from microbial features. Age was associated mostly with two mutually coexcluding Corynebacterium OTUs. Furthermore, skin aging variables (wrinkles and hyperpigmented spots) were independently correlated to these taxa. IMPORTANCE Many studies have highlighted the importance of body site and individuality in shaping the composition of the human skin microbiome, but we still have a poor understanding of how extrinsic (e.g., lifestyle) and intrinsic (e.g., age) factors influence its composition. We characterized the bacterial microbiomes of North American volunteers at four skin sites and the mouth. We also collected extensive subject metadata and measured several host physiological parameters. Integration of host and microbial features showed that the skin microbiome was predominantly associated with demographic, lifestyle, and physiological factors. Furthermore, we uncovered reproducible associations between chronological age, skin aging, and members of the genus Corynebacterium. Our work provides new understanding of the role of host selection and lifestyle in shaping skin microbiome composition. It also contributes to a more comprehensive appreciation of the factors that drive interindividual skin microbiome variation.

Background: Asthma is the most prevalent chronic disease of childhood. Recently, we identified a critical window early in the life of both mice and Canadian infants during which gut microbial changes (dysbiosis) affect asthma development. Given geographic differences in human gut microbiota worldwide, we studied the effects of gut microbial dysbiosis on atopic wheeze in a population living in a distinct developing world environment. Objective: We sought to determine whether microbial alterations in early infancy are associated with the development of atopic wheeze in a nonindustrialized setting. Methods: We conducted a case-control study nested within a birth cohort from rural Ecuador in which we identified 27 children with atopic wheeze and 70 healthy control subjects at 5 years of age. We analyzed bacterial and eukaryotic gut microbiota in stool samples collected at 3 months of age using 16S and 18S sequencing. Bacterial metagenomes were predicted from 16S rRNA data by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States and categorized by function with Kyoto Encyclopedia of Genes and Genomes ontology. Concentrations of fecal short-chain fatty acids were determined by using gas chromatography. Results: As previously observed in Canadian infants, microbial dysbiosis at 3 months of age was associated with later development of atopic wheeze. However, the dysbiosis in Ecuadorian babies involved different bacterial taxa, was more pronounced, and also involved several fungal taxa. Predicted metagenomic analysis emphasized significant dysbiosis-associated differences in genes involved in carbohydrate and taurine metabolism. Levels of the fecal short-chain fatty acids acetate and caproate were reduced and increased, respectively, in the 3-month stool samples of children who went on to have atopic wheeze. Conclusions: Our findings support the importance of fungal and bacterial microbiota during the first 100 days of life on the development of atopic wheeze and provide additional support for considering modulation of the gut microbiome as a primary asthma prevention strategy.

The mammalian gastrointestinal tract harbors a microbial community with metabolic activity critical for host health, including metabolites that can modulate effector functions of immune cells. Mice treated with vancomycin have an altered microbiome and metabolite profile, exhibit exacerbated T helper type 2 cell (Th2) responses, and are more susceptible to allergic lung inflammation. Here we show that dietary supplementation with short-chain fatty acids (SCFAs) ameliorates this enhanced asthma susceptibility by modulating the activity of T cells and dendritic cells (DCs). Dysbiotic mice treated with SCFAs have fewer interleukin-4 (IL4)-producing CD4(+) T cells and decreased levels of circulating immunoglobulin E (IgE). In addition, DCs exposed to SCFAs activate T cells less robustly, are less motile in response to CCL 19 in vitro, and exhibit a dampenedability to transport inhaled allergens to lung draining nodes. Our data thus demonstrate that gut dysbiosis can exacerbate allergic lung inflammation through both Tcell-and DC-dependent mechanisms that are inhibited by SCFAs.

Asthma is a chronic disease of the airways affecting one in ten children in Westernized countries. Recently, our group showed that specific bacterial genera in early life are associated with atopy and wheezing in 1-year-old children. However, little is known about the link between the early life gut microbiome and the diagnosis of asthma in preschool age children. To determine the role of the gut microbiota in preschool age asthma, children up to 4 years of age enrolled in the Canadian Healthy Infant Longitudinal Development (CHILD) study were classified as asthmatic (n=39) or matched healthy controls (n=37). 16S rRNA sequencing and quantitative PCR (qPCR) were used to analyse the composition of the 3-month and 1-year gut microbiome of these children. At 3 months the abundance of the genus, Lachnospira (L), was decreased (P=0.008), whereas the abundance of the species, Clostridium neonatale (C), was increased (P=0.07) in asthmatics. Quartile analysis of stool composition at 3-months revealed a negative association between the ratio of these two bacteria (L/C) and asthma risk by 4 years of age [quartile 1: odds ratio (OR)=15, P=0.02, CI (confidence interval) =1.8-124.7; quartile 2: OR=1.0, ns; quartile 3: OR=0.37, ns]. We conclude that opposing shifts in the relative abundances of Lachnospira and C. neonatale in the first 3 months of life are associated with preschool age asthma, and that the L/C ratio may serve as a potential early life biomarker to predict asthma development.

RATIONALE:The relatively sparse but diverse microbiome in human lungs may become less diverse in chronic obstructive pulmonary disease (COPD). This article examines the relationship of this microbiome to emphysematous tissue destruction, number of terminal bronchioles, infiltrating inflammatory cells, and host gene expression.METHODS:Culture-independent pyrosequencing microbiome analysis was used to examine the V3-V5 regions of bacterial 16S ribosomal DNA in 40 samples of lung from 5 patients with COPD (Global Initiative for Chronic Obstructive Lung Disease [GOLD] stage 4) and 28 samples from 4 donors (controls). A second protocol based on the V1-V3 regions was used to verify the bacterial microbiome results. Within lung tissue samples the microbiome was compared with results of micro-computed tomography, infiltrating inflammatory cells measured by quantitative histology, and host gene expression.MEASUREMENTS AND MAIN RESULTS:Ten operational taxonomic units (OTUs) was found sufficient to discriminate between control and GOLD stage 4 lung tissue, which included known pathogens such as Haemophilus influenzae. We also observed a decline in microbial diversity that was associated with emphysematous destruction, remodeling of the bronchiolar and alveolar tissue, and the infiltration of the tissue by CD4(+) T cells. Specific OTUs were also associated with neutrophils, eosinophils, and B-cell infiltration (P < 0.05). The expression profiles of 859 genes and 235 genes were associated with either enrichment or reductions of Firmicutes and Proteobacteria, respectively, at a false discovery rate cutoff of less than 0.1.CONCLUSIONS:These results support the hypothesis that there is a host immune response to microorganisms within the lung microbiome that appears to contribute to the pathogenesis of COPD.

Background: Previously our group associated early life gut microbial alterations in one-year-old children with risk of active asthma at school age. These early life alterations were characterized by significant reductions in four bacterial genera and a decreased production of microbial derived metabolites. We hypothesize that this early life gut microbial dysbiotic state is also associated with asthma diagnosed in children by three years of age and aim to identify additional bacterial populations that might be contributing to this asthmatic phenotype. Methods: 286 children enrolled in the Canadian Healthy Infant Longitudinal Development (CHILD) study were classified according to the diagnosis of asthma by three years of age. Bacterial 16S rDNA from 3-month and 1-year stool samples from these children was extracted, amplified, and subjected to high throughput Illumina sequencing. Bacterial genera were quantified by quantitative PCR in 16S rDNA samples from all asthmatic children and a subset of controls. An exact logistic regression model was used to assess the effects of potentially confounding variables (i.e. antibiotic exposure, mode of birth). Results: 16S sequence analysis of our sample cohort (286 subjects) identified differentially abundant bacterial populations between asthmatics and controls at 3-months of age. Additionally, qPCR identified significant shifts in the abundance of specific bacterial genera at 3-months and 1-year of age in the asthmatic group when compared to controls. Conclusions: Shifts in the relative abundance of certain gut bacterial populations in early life are associated with asthma diagnosed in children by three years of age.

Asthma is the most prevalent pediatric chronic disease and affects more than 300 million people worldwide. Recent evidence in mice has identified a "critical window" early in life where gut microbial changes (dysbiosis) are most influential in experimental asthma. However, current research has yet to establish whether these changes precede or are involved in human asthma. We compared the gut microbiota of 319 subjects enrolled in the Canadian Healthy Infant Longitudinal Development (CHILD) Study, and show that infants at risk of asthma exhibited transient gut microbial dysbiosis during the first 100 days of life. The relative abundance of the bacterial genera Lachnospira, Veillonella, Faecalibacterium, and Rothia was significantly decreased in children at risk of asthma. This reduction in bacterial taxa was accompanied by reduced levels of fecal acetate and dysregulation of enterohepatic metabolites. Inoculation of germ-free mice with these four bacterial taxa ameliorated airway inflammation in their adult progeny, demonstrating a causal role of these bacterial taxa in averting asthma development. These results enhance the potential for future microbe-based diagnostics and therapies, potentially in the form of probiotics, to prevent the development of asthma and other related allergic diseases in children.

BACKGROUND:Susceptibility to infection as well as response to vaccination varies among populations. To date, the underlying mechanisms responsible for these clinical observations have not been fully delineated. Because innate immunity instructs adaptive immunity, we hypothesized that differences between populations in innate immune responses may represent a mechanistic link to variation in susceptibility to infection or response to vaccination.OBJECTIVE:Determine whether differences in innate immune responses exist among infants from different continents of the world.METHODS:We determined the innate cytokine response following pattern recognition receptor (PRR) stimulation of whole blood from 2-year-old infants across 4 continents (Africa, North America, South America, and Europe).RESULTS:We found that despite the many possible genetic and environmental exposure differences in infants across 4 continents, innate cytokine responses were similar for infants from North America, South America, and Europe. However, cells from South African infants secreted significantly lower levels of cytokines than did cells from infants from the 3 other sites, and did so following stimulation of extracellular and endosomal but not cytosolic PRRs.CONCLUSIONS:Substantial differences in innate cytokine responses to PRR stimulation exist among different populations of infants that could not have been predicted. Delineating the underlying mechanism(s) for these differences will not only aid in improving vaccine-mediated protection but possibly also provide clues for the susceptibility to infection in different regions of the world.

Background Asthma is a chronic inflammatory disease characterized by bronchial hyper-responsiveness [1]. As the most endemic of all childhood diseases, asthma accounts for the majority of hospitalizations and school absences in children [2]. Exciting new research focuses on the involvement of the gut microbiome in asthma development. Murine studies support the hypothesis that the administration of probiotics or antibiotics during post-natal life alters the gut microbiome and ultimately the asthmatic symptoms of these mice [3-5]. This study will translate these findings into humans using stool samples obtained from the Canadian Healthy Infant Longitudinal Development (CHILD) study.

Background Asthma is the most prevalent of all childhood diseases and accounts for the majority of hospitalizations and school absences in children [1]. Current mouse model research has identified the early life gut microbiota as a potential therapeutic target for the prevention of asthma and atopic diseases [2-4]. We hypothesize that the early life gut microbiota could play a similar preventative role against atopic disease development in humans. Methods 1262 children enrolled in the Canadian Healthy Infant Longitudinal Development (CHILD) Study with complete skin prick test and wheeze data at one year were grouped into four clinically relevant phenotypes: atopy + wheeze, atopy only, wheeze only, and control. Bacterial 16S rDNA from 3-month and 1-year stool samples of 319 children in these four phenotypes was extracted, amplified, and subjected to high throughput Illumina sequencing. Quantitative polymerase chain reaction (qPCR) and short chain fatty acid (SCFA) analysis were also conducted on 44 children in the two extreme phenotypes (atopy + wheeze vs. control). Results 16S sequence analysis of our sample cohort (319 subjects) identified bacterial populations that differed in abundance in the atopy + wheeze group at 3-months of age but not at 1-year of age. Additionally, significant changes in the abundance of certain bacterial genera were found in the atopy + wheeze group when compared to controls by qPCR at 3-months of age only. Changes in stool short chain fatty acid production between the atopy + wheeze group and the control group were also observed at 3months of age only. Conclusions Shifts in the relative abundance of certain gut bacterial populations and differences in the levels of stool SCFAs before 3-months of age are associated with atopy and wheeze at one year of age.

BACKGROUND:Resident gut microbiota are now recognized as potent modifiers of host immune responses in various scenarios. Recently, we demonstrated that perinatal exposure to vancomycin, but not streptomycin, profoundly alters gut microbiota and enhances susceptibility to a TH2 model of allergic asthma.OBJECTIVE:Here we sought to further clarify the etiology of these changes by determining whether perinatal antibiotic treatment has a similar effect on the TH1/TH17-mediated lung disease, hypersensitivity pneumonitis.METHODS:Hypersensitivity pneumonitis was induced in C57BL/6 wild-type or recombination-activating gene 1-deficient mice treated perinatally with vancomycin or streptomycin by repeated intranasal administration of Saccharopolyspora rectivirgula antigen. Disease severity was assessed by measuring lung inflammation, pathology, cytokine responses, and serum antibodies. Microbial community analyses were performed on stool samples via 16S ribosomal RNA pyrosequencing and correlations between disease severity and specific bacterial taxa were identified.RESULTS:Surprisingly, in contrast to our findings in an allergic asthma model, we found that the severity of hypersensitivity pneumonitis was unaffected by vancomycin, but increased dramatically after streptomycin treatment. This likely reflects an effect on the adaptive, rather than innate, immune response because the effects of streptomycin were not observed during the early phases of disease and were abrogated in recombination-activating gene 1-deficient mice. Interestingly, Bacteroidetes dominated the intestinal microbiota of streptomycin-treated animals, while vancomycin promoted the expansion of the Firmicutes.CONCLUSIONS:Perinatal antibiotics exert highly selective effects on resident gut flora, which, in turn, lead to very specific alterations in susceptibility to TH2- or TH1/TH17-driven lung inflammatory disease.