Significant changes in the skin microbiome mediated by the sport of roller derby

Relative dispersion ratios following fecal microbiota transplant elucidate principles governing microbial migration dynamics

Microorganisms frequently migrate from one ecosystem to another. Yet, despite the potential importance of this process in modulating the environment and the microbial ecosystem, our understanding of the fundamental forces that govern microbial dispersion is still lacking. Moreover, while theoretical models and in-vitro experiments have highlighted the contribution of species interactions to community assembly, identifying such interactions in vivo, specifically in communities as complex as the human gut, remains challenging. To address this gap, here we introduce a robust and rigorous computational framework, termed Relative Dispersion Ratio (RDR) analysis, and leverage data from well-characterized fecal microbiota transplant trials, to rigorously pinpoint dependencies between taxa during the colonization of human gastrointestinal tract. Our analysis identifies numerous pairwise dependencies between co-colonizing microbes during migration between gastrointestinal environments. We further demonstrate that identified dependencies agree with previously reported findings from in-vitro experiments and population-wide distribution patterns. Finally, we explore metabolic dependencies between these taxa and characterize the functional properties that facilitate effective dispersion. Collectively, our findings provide insights into the principles and determinants of community dynamics following ecological translocation, informing potential opportunities for precise community design.

Community assembly of the human piercing microbiome

Predicting how biological communities respond to disturbance requires understanding the forces that govern their assembly. We propose using human skin piercings as a model system for studying community assembly after rapid environmental change. Local skin sterilization provides a 'clean slate' within the novel ecological niche created by the piercing. Stochastic assembly processes can dominate skin microbiomes due to the influence of environmental exposure on local dispersal, but deterministic processes might play a greater role within occluded skin piercings if piercing habitats impose strong selection pressures on colonizing species. Here we explore the human ear-piercing microbiome and demonstrate that community assembly is predominantly stochastic but becomes significantly more deterministic with time, producing increasingly diverse and ecologically complex communities. We also observed changes in two dominant and medically relevant antagonists (Cutibacterium acnes and Staphylococcus epidermidis), consistent with competitive exclusion induced by a transition from sebaceous to moist environments. By exploiting this common yet uniquely human practice, we show that skin piercings are not just culturally significant but also represent ecosystem engineering on the human body. The novel habitats and communities that skin piercings produce may provide general insights into biological responses to environmental disturbances with implications for both ecosystem and human health.

Microbial fingerprints reveal interaction between museum objects, curators, and visitors

Microbial communities reside at the interface between humans and their environment. Whether the microbiome can be leveraged to gain information on human interaction with museum objects is unclear. To investigate this, we selected objects from the Museum für Naturkunde and the Pergamonmuseum in Berlin, Germany, varying in material and size. Using swabs, we collected 126 samples from natural and cultural heritage objects, which were analyzed through 16S rRNA sequencing. By comparing the microbial composition of touched and untouched objects, we identified a microbial signature associated with human skin microbes. Applying this signature to cultural heritage objects, we identified areas with varying degrees of exposure to human contact on the Ishtar gate and Sam'al gate lions. Furthermore, we differentiated objects touched by two different individuals. Our findings demonstrate that the microbiome of museum objects provides insights into the level of human contact, crucial for conservation, heritage science, and potentially provenance research.

Facial Skin Microbiome: Aging-Related Changes and Exploratory Functional Associations with Host Genetic Factors, a Pilot Study

In this exploratory study, we investigate the variation in the facial skin microbiome architecture through aging and their functional association with host genetic factors in a cohort of healthy women, living in the same area and without cutaneous diseases. Notably, facial skin microbiota (SM) samples were collected from a cohort of 15 healthy Caucasian females, firstly divided into three age groups (younger women aged 20–35 years old; middle aged women of 36–52 years old; and older women aged 53–68 years old). Then, the recruited cohort was divided into two groups based on their facial hydration level (dry and normal skin). The facial SM revealed a different composition in the three analyzed aging groups and between normal and dry skins. The middle-aged women also revealed functional variations associated with collagen biosynthesis and oxidative stress damage repair. Otherwise, the association between selected host SNPs (single nucleotide polymorphisms) and the facial SM profile showed significant associations, suggesting a negative correlation with collagen metabolism and ROS damage protection. Finally, the composition and functionality of the facial SM seemed to affect the aging process through the two aging-correlated pathways of host ROS damage repair and collagen metabolism. Our exploratory data could be useful for future studies characterizing the structure, function, and dynamics of the SM in the aging process to design personalized therapeutic agents focusing on potential genomic targets, microbes, and their metabolites.

Effects of short-term experimental manipulation of captive social environment on uropygial gland microbiome and preen oil volatile composition

Introduction

Avian preen oil, secreted by the uropygial gland, is an important source of volatile compounds that convey information about the sender’s identity and quality, making preen oil useful for the recognition and assessment of potential mates and rivals. Although intrinsic factors such as hormone levels, genetic background, and diet can affect preen oil volatile compound composition, many of these compounds are not the products of the animal’s own metabolic processes, but rather those of odor-producing symbiotic microbes. Social behavior affects the composition of uropygial microbial communities, as physical contact results in microbe sharing. We experimentally manipulated social interactions in captive dark-eyed juncos (Junco hyemalis) to assess the relative influence of social interactions, subspecies, and sex on uropygial gland microbial composition and the resulting preen oil odor profiles.

Methods

We captured 24 birds at Mountain Lake Biological Station in Virginia, USA, including birds from two seasonally sympatric subspecies – one resident, one migratory. We housed them in an outdoor aviary in three phases of social configurations: first in same-sex, same-subspecies flocks, then in male-female pairs, and finally in the original flocks. Using samples taken every four days of the experiment, we characterized their uropygial gland microbiome through 16S rRNA gene sequencing and their preen oil volatile compounds via GC-MS.

Results

We predicted that if social environment was the primary driver of uropygial gland microbiome composition, and if microbiome composition in turn affected preen oil volatile profiles, then birds housed together would become more similar over time. Our results did not support this hypothesis, instead showing that sex and subspecies were stronger predictors of microbiome composition. We observed changes in volatile compounds after the birds had been housed in pairs, which disappeared after they were moved back into flocks, suggesting that hormonal changes related to breeding condition were the most important factor in these patterns.

Discussion

Although early life social environment of nestlings and long-term social relationships have been shown to be important in shaping uropygial gland microbial communities, our study suggests that shorter-term changes in social environment do not have a strong effect on uropygial microbiomes and the resulting preen oil volatile compounds.

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 analysis: An emerging forensic investigative tool

Microbial diversity's potential has been investigated in medical and therapeutic studies throughout the last few decades. However, its usage in forensics is increasing due to its effectiveness in circumstances when traditional approaches fail to provide a decisive opinion or are insufficient in forming a concrete opinion. The application of human microbiome may serve in detecting the type of stains of saliva and vaginal fluid, as well as in attributing the stains to the individual. Similarly, the microbiome makeup of a soil sample may be utilised to establish geographic origin or to associate humans, animals, or things with a specific area, additionally microorganisms influence the decay process which may be used in depicting the Time Since death. Further in detecting the traces of the amount and concentration of alcohol, narcotics, and other forensically relevant compounds in human body or visceral tissues as they also affect the microbial community within human body. Beside these, there is much more scope of microbiomes to be explored in terms of forensic investigation, this review focuses on multidimensional approaches to human microbiomes from a forensic standpoint, implying the potential of microbiomes as an emerging tool for forensic investigations such as individual variability via skin microbiomes, reconstructing crime scene, and linking evidence to individual.

Aging Associated Changes in the Adult Human Skin Microbiome and the Host Factors That Affect Skin Microbiome Composition

Understanding changes in the skin microbiome and their relationship to host skin factors during aging remains largely unknown. To better understand this phenomenon, we collected samples for metagenomic and host skin factor analyses from forearm, buttock, and facial skin from 158 Caucasian females at 20-24, 30-34, 40-44, 50-54, 60-64, and 70-74 years of age. Metagenomics analysis was performed using 16S rRNA gene sequencing, while host sebocyte gland area, skin lipids, natural moisturizing factors (NMFs) and anti-microbial peptides (AMPs) measurements were also performed. These analyses demonstrated that skin bacterial diversity increased at all the skin sites with increasing age. Of the bacterial genera with average relative abundance of >1%, only Lactobacillus and Cutibacterium demonstrated a significant change (decrease) in abundance at all sampled skin sites with increasing age. Additional bacterial genera demonstrated significant age and site-specific changes in abundance. Analysis of sebocyte area, NMFs, lipids and AMPs demonstrated an age-related decrease in sebocyte area and increases in NMFs/AMPs/skin lipids, all which correlated with changes in specific bacterial genera. In conclusion, the human skin microbiome undergoes age-associated alterations that may reflect underlying age-related changes in cutaneous biology.

Integrating the human microbiome in the forensic toolkit: Current bottlenecks and future solutions

Over the last few years, advances in massively parallel sequencing technologies (also referred to next generation sequencing) and bioinformatics analysis tools have boosted our knowledge on the human microbiome. Such insights have brought new perspectives and possibilities to apply human microbiome analysis in many areas, particularly in medicine. In the forensic field, the use of microbial DNA obtained from human materials is still in its infancy but has been suggested as a potential alternative in situations when other human (non-microbial) approaches present limitations. More specifically, DNA analysis of a wide variety of microorganisms that live in and on the human body offers promises to answer various forensically relevant questions, such as post-mortem interval estimation, individual identification, and tissue/body fluid identification, among others. However, human microbiome analysis currently faces significant challenges that need to be considered and overcome via future forensically oriented human microbiome research to provide the necessary solutions. In this perspective article, we discuss the most relevant biological, technical and data-related issues and propose future solutions that will pave the way towards the integration of human microbiome analysis in the forensic toolkit.

Priority effects in microbiome assembly

Advances in next-generation sequencing have enabled the widespread measurement of microbiome composition across systems and over the course of microbiome assembly. Despite substantial progress in understanding the deterministic drivers of community composition, the role of historical contingency remains poorly understood. The establishment of new species in a community can depend on the order and/or timing of their arrival, a phenomenon known as a priority effect. Here, we review the mechanisms of priority effects and evidence for their importance in microbial communities inhabiting a range of environments, including the mammalian gut, the plant phyllosphere and rhizosphere, soil, freshwaters and oceans. We describe approaches for the direct testing and prediction of priority effects in complex microbial communities and illustrate these with re-analysis of publicly available plant and animal microbiome datasets. Finally, we discuss the shared principles that emerge across study systems, focusing on eco-evolutionary dynamics and the importance of scale. Overall, we argue that predicting when and how current community state impacts the success of newly arriving microbial taxa is crucial for the management of microbiomes to sustain ecological function and host health. We conclude by discussing outstanding conceptual and practical challenges that are faced when measuring priority effects in microbiomes.

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).

Investigation of Age-Related Changes in the Skin Microbiota of Korean Women

The microbiota of human skin is influenced by host and environmental factors. To determine if chronological age influences the composition of the skin microbiota on the forehead and hands, 73 Korean women were sorted into one of three age groups: (1) 10-29 years (n = 24), (2) 30-49 years (n = 21), and (3) 50-79 years (n = 28). From the 73 women, 146 skin samples (two skin sites per person) were collected. 16S rRNA gene amplicon sequencing was then conducted to analyze the skin microbiota. The overall microbial distribution varied on the forehead but was similar on the hands across the three age groups. In addition, the composition of the skin microbiota differed between the forehead and hands. Commensal microbiota, such as Streptococcus, Staphylococcus, Cutibacterium, and Corynebacterium, which contribute to maintaining skin health via dominant occupation, were affected by increasing age on forehead and hand skin. Alpha diversity indices increased significantly with age on forehead skin. This study indicates that older people may be more susceptible to pathogenic invasions due to an imbalanced skin microbiota resulting from age-related changes. The results of our study may help develop new strategies to rebalance skin microbiota shifted during aging.

Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants

BACKGROUND

Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous microbiota. Given the roles of the skin microbiota have on healthy and undesirable skin phenotypes and the relationships between PAHs and skin properties, we hypothesize that exposure of PAHs may be associated with changes in the cutaneous microbiota. In this study, the skin microbiota of over two hundred Chinese individuals from two cities in China with varying exposure levels of PAHs were characterized by bacterial and fungal amplicon and shotgun metagenomics sequencing.

RESULTS

Skin site and city were strong parameters in changing microbial communities and their assembly processes. Reductions of bacterial-fungal microbial network structural integrity and stability were associated with skin conditions (acne and dandruff). Multivariate analysis revealed associations between abundances of Propionibacterium and Malassezia with host properties and pollutant exposure levels. Shannon diversity increase was correlated to exposure levels of PAHs in a dose-dependent manner. Shotgun metagenomics analysis of samples (n = 32) from individuals of the lowest and highest exposure levels of PAHs further highlighted associations between the PAHs quantified and decrease in abundances of skin commensals and increase in oral bacteria. Functional analysis identified associations between levels of PAHs and abundance of microbial genes of metabolic and other pathways with potential importance in host-microbe interactions as well as degradation of aromatic compounds.

CONCLUSIONS

The results in this study demonstrated the changes in composition and functional capacities of the cutaneous microbiota associated with chronic exposure levels of PAHs. Findings from this study will aid the development of strategies to harness the microbiota in protecting the skin against pollutants. Video Abstract.

Community coalescence: an eco-evolutionary perspective

Community coalescence, the mixing of different communities, is widespread throughout microbial ecology. Coalescence can result in approximately equal contributions from the founding communities or dominance of one community over another. These different outcomes have ramifications for community structure and function in natural communities, and the use of microbial communities in biotechnology and medicine. However, we have little understanding of when a particular outcome might be expected. Here, we integrate existing theory and data to speculate on how a crucial characteristic of microbial communities-the type of species interaction that dominates the community-might affect the outcome of microbial community coalescence. Given the often comparable timescales of microbial ecology and microevolution, we explicitly consider ecological and evolutionary dynamics, and their interplay, in determining coalescence outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Impact of sampling and DNA extraction methods on skin microbiota assessment

The skin microbiota is characterized by high intra- and inter-variability among individuals, due to a multitude of intrinsic and extrinsic parameters such as genetics, lifestyles or pollution. This variability may be heightened due to sampling method as the skin is a multilayer organ and its outermost layer consists of dead cells. In order to investigate this biological variability in a reproducible way, we studied how sampling procedure and DNA extraction methods influence the qualitative and quantitative gathering of bacterial communities. Here, we tested a new sampling procedure that consists in exerting a slight abrasion (scrubbing) on the skin prior to swabbing and extracting DNA in order to remove squames and access deeper ecological niches. Scrubbed and non-scrubbed samples were collected from a panel of six volunteers, and four DNA extraction methods were performed on the samples. The abundance, diversity and structure of the bacterial communities were measured using qPCR technics and 16S rDNA gene-metabarcoding. Bacterial community abundance was significantly impacted by the DNA extraction method (in favor of a method designed for tissues) but not by sampling procedure, as scrubbing does not increase bacterial biomass gathered. Bacterial α- and β-diversities were both affected by DNA extraction methods and sampling procedure. Scrubbing reveals different microbial composition by gathering bacteria living in deeper skin layer, resulting in a lower intra-personal variability. The taxonomic analysis showed that more bacteria belonging to anaerobes groups were present in scrubbed samples. We conclude that DNA extraction methods designed for tissue are not necessarily associated with high qualitative efficiency and slight scrubbing prior DNA extraction reduces intrapersonal variability and give access to a new microbial diversity.

Metabolic phenotyping of the human microbiome

The human microbiome has been identified as having a key role in health and numerous diseases. Trillions of microbial cells and viral particles comprise the microbiome, each representing modifiable working elements of an intricate bioactive ecosystem. The significance of the human microbiome as it relates to human biology has progressed through culture-dependent (for example, media-based methods) and, more recently, molecular (for example, genetic sequencing and metabolomic analysis) techniques. The latter have become increasingly popular and evolved from being used for taxonomic identification of microbiota to elucidation of functional capacity (sequencing) and metabolic activity (metabolomics). This review summarises key elements of the human microbiome and its metabolic capabilities within the context of health and disease.

The impact of lifestyle upon the probability of late bacterial infection after soft-tissue filler augmentation

Purpose: Little is known about the influence of lifestyle-related factors upon the risk of late bacterial infection (LBI) emerging at the site of soft-tissue filler augmentation. The aim of this study was to analyze the impact of some such factors on the risk of LBI by comparing their respective prevalence between two groups of previously healthy women: a group in which infection occurred at a site of cross-linked hyaluronic acid (HA) augmentation and a second group which did not have such an infection.

Patients and methods: The infection group featured 25 women who developed LBI at a site of cross-linked HA augmentation; the control group featured 92 women who did not experience complications during a 24-month period of observation after the same procedure. Data was analyzed statistically using Chi-square tests and logistic regression.

Results: The two groups did not differ significantly in terms of age. However, the frequency of antibiotic therapy, household pet ownership, occupation, hormone replacement therapy or contraception use, and attendance at a swimming pool, sauna, or gym attendance were found to vary with statistical significance, P<0.05.

Conclusions: Women in the control group practiced a more active lifestyle. Antibiotic therapy in the year preceding cross-linked HA augmentation was a factor which rendered a patient predisposed towards the development of LBI. Pet ownership was more prominent among women who did not suffer LBI than within the group in which soft tissue filler-related complications had occurred.

Household composition and the infant fecal microbiome: The INSPIRE study

OBJECTIVES

Establishment and development of the infant gastrointestinal microbiome (GIM) varies cross-culturally and is thought to be influenced by factors such as gestational age, birth mode, diet, and antibiotic exposure. However, there is little data as to how the composition of infants' households may play a role, particularly from a cross-cultural perspective. Here, we examined relationships between infant fecal microbiome (IFM) diversity/composition and infants' household size, number of siblings, and number of other household members.

MATERIALS AND METHODS

We analyzed 377 fecal samples from healthy, breastfeeding infants across 11 sites in eight different countries (Ethiopia, The Gambia, Ghana, Kenya, Peru, Spain, Sweden, and the United States). Fecal microbial community structure was determined by amplifying, sequencing, and classifying (to the genus level) the V1-V3 region of the bacterial 16S rRNA gene. Surveys administered to infants' mothers identified household members and composition.

RESULTS

Our results indicated that household composition (represented by the number of cohabitating siblings and other household members) did not have a measurable impact on the bacterial diversity, evenness, or richness of the IFM. However, we observed that variation in household composition categories did correspond to differential relative abundances of specific taxa, namely: Lactobacillus, Clostridium, Enterobacter, and Klebsiella.

DISCUSSION

This study, to our knowledge, is the largest cross-cultural study to date examining the association between household composition and the IFM. Our results indicate that the social environment of infants (represented here by the proxy of household composition) may influence the bacterial composition of the infant GIM, although the mechanism is unknown. A higher number and diversity of cohabitants and potential caregivers may facilitate social transmission of beneficial bacteria to the infant gastrointestinal tract, by way of shared environment or through direct physical and social contact between the maternal-infant dyad and other household members. These findings contribute to the discussion concerning ways by which infants are influenced by their social environments and add further dimensionality to the ongoing exploration of social transmission of gut microbiota and the "old friends" hypothesis.

Skin Microbiota in Contact Sports Athletes and Selection of Antiseptics for Professional Hygiene

Background

The aim of this study was to assess changes in skin microbiota of wrestlers during training sessions and to determine the sensitivity of hemolytic bacterial isolates to antiseptics.

Methods

The main skin bacterial isolates obtained from the skin of 15 wrestlers were identified by cultivation method, with the following MALDI Biotyper and 16S rRNA gene sequencing methods. The sensitivity of hemolytic isolates to antiseptics (Veltosept-2, Cutasept F, Chlorhexidine, Miramistin, and Hydrogen Peroxide) was evaluated by measuring the size of bacterial growth inhibition zone on agar plates.

Results

Opportunistic bacteria of the species Bacillus cereus, Staphylococcus aureus, S. epidermidis, and S. saprophyticus were the most commonly found species in skin microbiota of wrestlers before and after training sessions. Representatives of all these species mostly had a hemolytic activity. An alcohol-containing antiseptic Veltosept-2 showed the strongest inhibitory effect on the bacterial isolates of athletes' skin microbiota most frequently detected in this study.

Conclusions

The general increase in the bacterial colonization of wrestlers' skin, as well as the presence of hemolytic forms of opportunistic bacteria in cutaneous microbiota, indicates dysbiotic changes and a decrease in the protective features of the host organism. Veltosept-2 application can reduce the incidence of skin infections in contact sports athletes with the highest efficiency.

Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons

The mammalian gut microbiome plays a profound role in the physiology, metabolism, and overall health of its host. However, biologists have only a nascent understanding of the forces that drive inter-individual heterogeneity in gut microbial composition, especially the role of host social environment. Here we used 178 samples from 78 wild yellow baboons (Papio cynocephalus) living in two social groups to test how host social context, including group living, social interactions within groups, and transfer between social groups (e.g., dispersal) predict inter-individual variation in gut microbial alpha and beta diversity. We also tested whether social effects differed for prevalent "core" gut microbial taxa, which are thought to provide primary functions to hosts, versus rare "non-core" microbes, which may represent relatively transient environmental acquisitions. Confirming prior studies, we found that each social group harbored a distinct gut microbial community. These differences included both non-core and core gut microbial taxa, suggesting that these effects are not solely driven by recent gut microbial exposures. Within social groups, close grooming partners had more similar core microbiomes, but not non-core microbiomes, than individuals who rarely groomed each other, even controlling for kinship and diet similarity between grooming partners. Finally, in support of the idea that the gut microbiome can be altered by current social context, we found that the longer an immigrant male had lived in a given social group, the more closely his gut microbiome resembled the gut microbiomes of the group's long-term residents. Together, these results reveal the importance of a host's social context in shaping the gut microbiome and shed new light onto the microbiome-related consequences of male dispersal.

Individual and household attributes influence the dynamics of the personal skin microbiota and its association network

BACKGROUND

Numerous studies have thus far characterized the temporal dynamics of the skin microbiota of healthy individuals. However, there is no information regarding the dynamics of different microbial association network properties. Also, there is little understanding of how living conditions, specifically cohabitation and household occupancy, may be associated with the nature and extent (or degree) of cutaneous microbiota change within individuals over time. In this study, the dynamics of the skin microbiota, and its association networks, on the skin of urban residents over four seasons were characterized.

RESULTS

Similar to western cohorts, the individuals of this cohort show different extents of variations in relative abundance of common skin colonizers, concomitant with individual- and household-associated changes in differential abundances of bacterial taxa. Interestingly, the individualized nature of the skin microbiota extends to various aspects of microbial association networks, including co-occurring and excluding taxa, as well as overall network structural properties. Household occupancy is correlated with the extent of variations in relative abundance of Propionibacterium, Acinetobacter, and Bacillus over multiple skin sites. In addition, household occupancy is also associated with the extent of temporal changes in microbial diversity and composition within a resident's skin.

CONCLUSIONS

This is the first study investigating the potential roles household occupancy has on the extent of change in one's cutaneous microbiota and its association network structures. In particular, we show that relationships between the skin microbiota of a resident, his/her cohabitants, and those of non-cohabitants over time are highly personal and are possibly governed by living conditions and nature of interactions between cohabitants within households over 1 year. This study calls for increased awareness to personal and lifestyle factors that may govern relationships between the skin microbiota of one individual and those of cohabitants, and changes in the microbial association network structures within a person over time. The current study will act as a baseline for future assessments in comparing against temporal dynamics of microbiota from individuals with different skin conditions and for identifying residential factors that are beneficial in promoting the dynamics of the skin microbiota associated with health.

Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands

Bacteria live all around us, and we are constantly exposed to them during our everyday lives. Modern standards of hygiene aim to limit exposure to fecal bacteria, and yet bacteria rapidly colonize the gut in early life and following antibacterial treatment. Exposures to fecal and oral microbes provide risk of disease, but are also necessary since commensal microbes play important roles in health. This work establishes that bacteria of both fecal and oral origins are commonly found on hands. It also establishes that the uniqueness of fecal and oral bacterial communities across people can allow for determination of the likely individual from whom the fecal and oral bacteria came. These techniques allow for understanding the hands as a vector for microbial transmission within families and across populations, which has important implications for public health.

Modern hygienic practices are applied to avoid exposure to pathogens that spread via fecal-oral transmission. Despite this, the gastrointestinal tract is quickly colonized by fecal microbes. The hands are an important vector for the transmission of microbes, but the frequency at which fecal and oral microbes exist on hands and the source of those microbes have not been extensively described. Using data from a previous study that characterized the fecal, oral, and skin microbiota from 73 families, we found a significant incidence of fecal and oral microbes on hands. Of palms, 48.9% had fecal signal and 67.2% had oral signal. Fecal, oral, and forehead microbes were tracked to family members and an individual’s own palms far more often than to unrelated individuals and showed relationships with age, gender, and parental status. For instance, oral microbes that were specifically sourced to the same individual (oneself) were most common on infant palms; mothers had more infant-child-sourced and oral-sourced microbes on their palms than nonparents. Fecal microbes on palms more often sourced to members of the family than unrelated individuals, but more often to other members of the family than oneself. This study supports that the hands are an important vector for the transfer of fecal and oral microbes within families.

IMPORTANCE Bacteria live all around us, and we are constantly exposed to them during our everyday lives. Modern standards of hygiene aim to limit exposure to fecal bacteria, and yet bacteria rapidly colonize the gut in early life and following antibacterial treatment. Exposures to fecal and oral microbes provide risk of disease, but are also necessary since commensal microbes play important roles in health. This work establishes that bacteria of both fecal and oral origins are commonly found on hands. It also establishes that the uniqueness of fecal and oral bacterial communities across people can allow for determination of the likely individual from whom the fecal and oral bacteria came. These techniques allow for understanding the hands as a vector for microbial transmission within families and across populations, which has important implications for public health.

New microbiological challenges for the sugar industry with focus on thermophilic acidophilic bacteria

The potential occurrence of guaiacol producing Alicyclobacillus in sugar products and in the sugar production process was evaluated. Final product testing revealed that granulated sugar products showed random background contamination while liquid sugar products were free from guaiacol producing bacteria. Contamination tracing in the sugar factory process showed that beet soil is a primary contamination route to a sugar factory. The bacteria were completely eliminated in the juice purification at all evaluated factories. Random re-contamination was observed in wash syrups from the A-station. Environmental contamination from air and surfaces could not be observed while 20% of human test subjects showed skin contamination of guaiacol producing bacteria. A successful elimination of guaiacol producing bacteria from sugar products was concluded to be unfeasible due to random re-contamination events in the sugar production process. It is suggested that the goal must be to evaluate realistic technical solutions located at the last step of the supply chain. Thermal and non-thermal treatment techniques are available and among those UV-treatment appears to be a promising elimination technique for TAB (thermophilic acidophilic bacteria) and GP-TAB.

Characterization of hygiene habits and environments in children's care homes

OBJECTIVE

Identify the hygiene habits of children and caregivers in order to prevent and control infectious diseases in care environments in Bogotá, Colombia, as well as characterize the surface bacteria in these environments.

METHOD

Instruments were designed, validated and applied to evaluate healthy habits, with samples taken from surfaces in kitchens, bathrooms, halls, mats, and tools in 230 locations. Th e isolated bacteria were classifi ed using automated methodologies.

RESULTS

A total of 699 bacteria were isolated, with the largest growth percentage found in kitchens (36%). Th ese results are contrary to what was observed, where most of the kitchens appeared to be clean. In the survey, 93% of the caregivers reported washing their hands before handling food, and 23% said they used personal protection items when handling food.

CONCLUSION

There is a need for monitoring and interventions in hygiene and care habits in environments that care for children.

Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities

The emergence of high-throughput sequencing technologies has deepened our understanding of complex microbial communities and greatly facilitated the study of as-yet uncultured microbes and viruses. Studies of complex microbial communities require high-quality data to generate valid results. Here, we detail current methods of microbial and viral community sample acquisition, DNA extraction, sample preparation, and sequencing on Illumina high-throughput platforms. While using appropriate analytical tools is important, it must not overshadow the need for establishing a proper experimental design and obtaining sufficient numbers of samples for statistical purposes. Researchers must also take care to sample biologically relevant sites and control for potential confounding factors (e.g., contamination).

Statistical analysis of co-occurrence patterns in microbial presence-absence datasets

Drawing on a long history in macroecology, correlation analysis of microbiome datasets is becoming a common practice for identifying relationships or shared ecological niches among bacterial taxa. However, many of the statistical issues that plague such analyses in macroscale communities remain unresolved for microbial communities. Here, we discuss problems in the analysis of microbial species correlations based on presence-absence data. We focus on presence-absence data because this information is more readily obtainable from sequencing studies, especially for whole-genome sequencing, where abundance estimation is still in its infancy. First, we show how Pearson's correlation coefficient (r) and Jaccard's index (J)-two of the most common metrics for correlation analysis of presence-absence data-can contradict each other when applied to a typical microbiome dataset. In our dataset, for example, 14% of species-pairs predicted to be significantly correlated by r were not predicted to be significantly correlated using J, while 37.4% of species-pairs predicted to be significantly correlated by J were not predicted to be significantly correlated using r. Mismatch was particularly common among species-pairs with at least one rare species (<10% prevalence), explaining why r and J might differ more strongly in microbiome datasets, where there are large numbers of rare taxa. Indeed 74% of all species-pairs in our study had at least one rare species. Next, we show how Pearson's correlation coefficient can result in artificial inflation of positive taxon relationships and how this is a particular problem for microbiome studies. We then illustrate how Jaccard's index of similarity (J) can yield improvements over Pearson's correlation coefficient. However, the standard null model for Jaccard's index is flawed, and thus introduces its own set of spurious conclusions. We thus identify a better null model based on a hypergeometric distribution, which appropriately corrects for species prevalence. This model is available from recent statistics literature, and can be used for evaluating the significance of any value of an empirically observed Jaccard's index. The resulting simple, yet effective method for handling correlation analysis of microbial presence-absence datasets provides a robust means of testing and finding relationships and/or shared environmental responses among microbial taxa.

Captive bottlenose dolphins and killer whales harbor a species-specific skin microbiota that varies among individuals

Marine animals surfaces host diverse microbial communities, which play major roles for host’s health. Most inventories of marine animal surface microbiota have focused on corals and fishes, while cetaceans remain overlooked. The few studies focused on wild cetaceans, making difficult to distinguish intrinsic inter- and/or intraspecific variability in skin microbiota from environmental effects. We used high-throughput sequencing to assess the skin microbiota from 4 body zones of 8 bottlenose dolphins (Tursiops truncatus) and killer whales (Orcinus orca), housed in captivity (Marineland park, France). Overall, cetacean skin microbiota is more diverse than planktonic communities and is dominated by different phylogenetic lineages and functions. In addition, the two cetacean species host different skin microbiotas. Within each species, variability was higher between individuals than between body parts, suggesting a high individuality of cetacean skin microbiota. Overall, the skin microbiota of the assessed cetaceans related more to the humpback whale and fishes’ than to microbiotas of terrestrial mammals.

Environmental influences on the skin microbiome of humans and cattle in rural Madagascar

Background and objectives

The skin harbors a dynamic community of microorganisms, where contact with humans, other animals and the environment can alter microbial communities. Most research on the human skin microbiome features Western populations living in hygienic conditions, yet these populations have vastly different patterns of environmental contact than the majority of people on Earth, including those living in developing countries.

Methodology

We studied skin microbial communities of humans and cattle (zebu) in rural Madagascar to investigate how zebu ownership affects microbial composition of the human skin, and to characterize non-Western human and zebu skin communities more generally. A portion of the 16S rRNA gene was sequenced from samples of zebu backs and human ankles, forearms, hands and armpits. Analyses were conducted in QIIME, R and LEfSe.

Results

Human and zebu samples varied in microbial community composition, yet we did not find evidence for a shared microbial signature between an individual and his zebu. Microbial communities differed across human body sites, with ankles reflecting increased diversity and greater similarity to samples from zebu, likely due to extensive shared contact with soil by humans and zebu.

Conclusions and implications

Cattle ownership had, at best, weak effects on the human skin microbiome. We suggest that components of human biology and lifestyles override the microbial signature of close contact with zebu, including genetic factors and human–human interaction, irrespective of zebu ownership. Understanding ecological drivers of microbial communities will help determine ways that microbial transfer and community composition change as populations adopt Western lifestyles, and could provide insights into zoonotic disease transmission.

The skin microbiome: impact of modern environments on skin ecology, barrier integrity, and systemic immune programming

Skin barrier structure and function is essential to human health. Hitherto unrecognized functions of epidermal keratinocytes show that the skin plays an important role in adapting whole-body physiology to changing environments, including the capacity to produce a wide variety of hormones, neurotransmitters and cytokine that can potentially influence whole-body states, and quite possibly, even emotions. Skin microbiota play an integral role in the maturation and homeostatic regulation of keratinocytes and host immune networks with systemic implications. As our primary interface with the external environment, the biodiversity of skin habitats is heavily influenced by the biodiversity of the ecosystems in which we reside. Thus, factors which alter the establishment and health of the skin microbiome have the potential to predispose to not only cutaneous disease, but also other inflammatory non-communicable diseases (NCDs). Indeed, disturbances of the stratum corneum have been noted in allergic diseases (eczema and food allergy), psoriasis, rosacea, acne vulgaris and with the skin aging process. The built environment, global biodiversity losses and declining nature relatedness are contributing to erosion of diversity at a micro-ecological level, including our own microbial habitats. This emphasises the importance of ecological perspectives in overcoming the factors that drive dysbiosis and the risk of inflammatory diseases across the life course.

Cleanliness in context: reconciling hygiene with a modern microbial perspective

The concept of hygiene is rooted in the relationship between cleanliness and the maintenance of good health. Since the widespread acceptance of the germ theory of disease, hygiene has become increasingly conflated with sterilization. In reviewing studies across the hygiene literature (most often hand hygiene), we found that nearly all studies of hand hygiene utilize bulk reduction in bacterial load as a proxy for reduced transmission of pathogenic organisms. This treatment of hygiene may be insufficient in light of recent microbial ecology research, which has demonstrated that humans have intimate and evolutionarily significant relationships with a diverse assemblage of microorganisms (our microbiota). The human skin is home to a diverse and specific community of microorganisms, which include members that exist across the ecological spectrum from pathogen through commensal to mutualist. Most evidence suggests that the skin microbiota is likely of direct benefit to the host and only rarely exhibits pathogenicity. This complex ecological context suggests that the conception of hygiene as a unilateral reduction or removal of microbes has outlived its usefulness. As such, we suggest the explicit definition of hygiene as "those actions and practices that reduce the spread or transmission of pathogenic microorganisms, and thus reduce the incidence of disease."

The role of microbiota, and probiotics and prebiotics in skin health

During the past decade, scientists have made great strides in understanding the microbiome's role in human health. Today, the microbiome has become key in scientific research, therapeutic development, medical treatment, and as a news feature in the media. Most studies have focused on the microbiome of our gut, but recently researchers have turned their attention to other microbiomes, including that of the skin. These studies of gut and skin microbiomes are yielding very informative results, new treatment strategies, and the development of new prebiotic and probiotic products for the treatment of many skin conditions.

Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis

BACKGROUND

Patients with atopic dermatitis (AD) are prone to skin infections, with microbes such as Staphylococcus aureus suspected of contributing to pathogenesis. Bleach baths might improve AD by reducing skin microbial burden.

OBJECTIVE

We sought to characterize the microbiota of lesional and nonlesional skin in young children with AD and control subjects and compare changes after treatment with a topical corticosteroid (TCS) alone or TCS + dilute bleach bath.

METHODS

In a randomized, placebo-controlled, single-blinded clinical trial in 21 children with AD and 14 healthy children, lesional and nonlesional AD skin was examined at baseline and after 4-week treatment with TCS alone or TCS plus bleach bath. Microbial DNA was extracted for quantitative polymerase chain reaction of predominant genera and 16S rRNA sequencing.

RESULTS

At baseline, densities of total bacteria and Staphylococcus, including Staphylococcus aureus, were significantly higher at the worst AD lesional site than nonlesional (P = .001) or control (P < .001) skin; bacterial communities on lesional and nonlesional AD skin significantly differed from each other (P = .04) and from control (P < .001). After TCS + bleach bath or TCS alone, bacterial compositions on lesional skin normalized (P < .0001), resembling nonlesional skin, with microbial diversity restored to control skin levels.

LIMITATIONS

The 4-week time period and/or the twice-weekly baths may not have been sufficient for additional impact on the cutaneous microbiome. More detailed sequencing may allow better characterization of the distinguishing taxa with bleach bath treatment.

CONCLUSIONS

Treatment with a TCS cream suffices to normalize the cutaneous microbiota on lesional AD; after treatment, bacterial communities on lesional skin resemble nonlesional skin but remain distinct from control.

Performing Skin Microbiome Research: A Method to the Madness

Growing interest in microbial contributions to human health and disease has increasingly led investigators to examine the microbiome in both healthy skin and cutaneous disorders, including acne, psoriasis, and atopic dermatitis. The need for common language, effective study design, and validated methods is critical for high-quality standardized research. Features, unique to skin, pose particular challenges when conducting microbiome research. This review discusses microbiome research standards and highlights important factors to consider, including clinical study design, skin sampling, sample processing, DNA sequencing, control inclusion, and data analysis.

Shaping of cutaneous function by encounters with commensals

The skin is the largest organ in the human body and provides the first line of defence against environmental attack and pathogen invasion. It harbor multiple commensal microbial communities at different body sites, which play important roles in sensing the environment, protecting against colonization and infection of pathogens, and guiding the host immune system in response to foreign invasions. The skin microbiome is largely variable between individuals and body sites, with several core commensal members commonly shared among individuals at the healthy state. These microbial commensals are essential to skin health and can potentially lead to disease when their abundances and activities change due to alterations in the environment or in the host. While recent advances in sequencing technologies have enabled a large number of studies to characterize the taxonomic composition of the skin microbiome at various body sites and under different physiological conditions, we have limited understanding of the microbiome composition and dynamics at the strain level, which is highly important to many microbe-related diseases. Functional studies of the skin microbial communities and the interactions among community members and with the host are currently scant, warranting future investigations. In this review, we summarize the recent findings on the skin microbiome, highlighting the roles of the major commensals, including bacteria, fungi and bacteriophages, in modulating skin functions in health and disease. Functional studies of the skin microbiota at the metatranscriptomic and proteomic levels are also included to illustrate the interactions between the microbiota and the host skin.

Diversity and evolution of the primate skin microbiome

Skin microbes play a role in human body odour, health and disease. Compared with gut microbes, we know little about the changes in the composition of skin microbes in response to evolutionary changes in hosts, or more recent behavioural and cultural changes in humans. No studies have used sequence-based approaches to consider the skin microbe communities of gorillas and chimpanzees, for example. Comparison of the microbial associates of non-human primates with those of humans offers unique insights into both the ancient and modern features of our skin-associated microbes. Here we describe the microbes found on the skin of humans, chimpanzees, gorillas, rhesus macaques and baboons. We focus on the bacterial and archaeal residents in the axilla using high-throughput sequencing of the 16S rRNA gene. We find that human skin microbial communities are unique relative to those of other primates, in terms of both their diversity and their composition. These differences appear to reflect both ancient shifts during millions of years of primate evolution and more recent changes due to modern hygiene.

Skin fungal community and its correlation with bacterial community of urban Chinese individuals

BACKGROUND

High-throughput sequencing has led to increased insights into the human skin microbiome. Currently, the majority of skin microbiome investigations are limited to characterizing prokaryotic communities, and our understanding of the skin fungal community (mycobiome) is limited, more so for cohorts outside of the western hemisphere. Here, the skin mycobiome across healthy Chinese individuals in Hong Kong are characterized.

RESULTS

Based on a curated fungal reference database designed for skin mycobiome analyses, previously documented common skin colonizers are also abundant and prevalent in this cohort. However, genera associated with local terrains, food, and medicine are also detected. Fungal community composition shows interpersonal (Bray-Curtis ANOSIM = 0.398) and household (Bray-Curtis ANOSIM = 0.134) clustering. Roles of gender and age on diversity analyses are test- and site-specific, and, contrary to bacteria, the effect of household on fungal community composition dissimilarity between samples is insignificant. Site-specific, cross-domain positive and negative correlations at both community and operational taxonomic unit levels may uncover potential relationships between fungi and bacteria on skin.

CONCLUSIONS

The studied Chinese population presents similar major fungal skin colonizers that are also common in western populations, but local outdoor environments and lifestyles may also contribute to mycobiomes of specific cohorts. Cohabitation plays an insignificant role in shaping mycobiome differences between individuals in this cohort. Increased understanding of fungal communities of non-western cohorts will contribute to understanding the size of the global skin pan-mycobiome, which will ultimately help understand relationships between environmental exposures, microbial populations, and the health of global humans.

The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review

Recent high-throughput sequencing technology has led to an expansion of knowledge regarding the microbial communities (microbiome) across various built environments (BEs). The microbiome of the BE is dependent upon building factors and conditions that govern how outdoor microbes enter and persist in the BE. Additionally, occupants are crucial in shaping the microbiome of the BE by releasing human-associated microorganisms and resuspending microbes on floors and surfaces. Therefore, both the outdoors and occupants act as major sources of microorganisms found in the BE. However, most characterizations of the microbiome of the BE have been conducted in the Western world. Notably, outdoor locations and population groups present geographical variations in outdoor and human microbiomes, respectively. Given the influences of the outdoor and human microbiomes on BE microbiology, and the geographical variations in outdoor and human microbiomes, it is likely that the microbiomes of BEs also vary by location. The summation of microbiomes between BEs contribute to a potential BE pan-microbiome, which will both consist of microbes that are ubiquitous in indoor environments around the world, and microbes that appear to be endemic to particular geographical locations. Importantly, the BE pan-microbiome can potentially question the global application of our current views on indoor microbiology. In this review, we first provide an assessment on the roles of building and occupant properties on shaping the microbiome of the BE. This is then followed by a description of geographical variations in the microbiomes of the outdoors and humans, the two main sources of microbes in BEs. We present evidence of differences in microbiomes of BEs around the world, demonstrating the existence of a global pan-microbiome of the BE that is larger than the microbiome of any single indoor environment. Finally, we discuss the significance of understanding the BE pan-microbiome and identifying universal and location-specific relationships between building and occupant characteristics and indoor microbiology. This review highlights the much needed efforts towards determining the pan-microbiome of the BE, thereby identifying general and location-specific links between the microbial communities of the outdoors, human, and BE ecosystems, ultimately improving the health, comfort, and productivity of occupants around the world.

The Human Microbiome and Public Health: Social and Ethical Considerations

Rapid advances in human microbiome research point to an increasing range of health outcomes related to the composition of an individual's microbiome. To date, much research has focused on individual health, with a paucity of attention to public health implications. This is a critical oversight owing to the potentially shared nature of the human microbiome across communities and vertical and horizontal mechanisms for transferring microbiomes among humans. We explored some key ethical and social implications of human microbiome research for public health. We focused on (1) insights from microbiome research about damage to individual and shared microbiomes from prevalent societal practices, and (2) ethical and social implications of novel technologies developed on the basis of emerging microbiome science.

The Microbiota of the Human Skin

The aim of this chapter is to sum up important progress in the field of human skin microbiota research that was achieved over the last years.The human skin is one of the largest and most versatile organs of the human body. Owing to its function as a protective interface between the largely sterile interior of the human body and the highly microbially contaminated outer environment, it is densely colonized with a diverse and active microbiota. This skin microbiota is of high importance for human health and well-being. It is implicated in several severe skin diseases and plays a major role in wound infections. Many less severe, but negatively perceived cosmetic skin phenomena are linked with skin microbes, too. In addition, skin microorganisms, in particular on the human hands, are crucial for the field of hygiene research. Notably, apart from being only a potential source of disease and contamination, the skin microbiota also contributes to the protective functions of the human skin in many ways. Finally, the analysis of structure and function of the human skin microbiota is interesting from a basic, evolutionary perspective on human microbe interactions.Key questions in the field of skin microbiota research deal with (a) a deeper understanding of the structure (species inventory) and function (physiology) of the healthy human skin microbiota in space and time, (b) the distinction of resident and transient skin microbiota members,

Phylogenetic approaches to microbial community classification

BACKGROUND

The microbiota from different body sites are dominated by different major groups of microbes, but the variations within a body site such as the mouth can be more subtle. Accurate predictive models can serve as useful tools for distinguishing sub-sites and understanding key organisms and their roles and can highlight deviations from expected distributions of microbes. Good classification depends on choosing the right combination of classifier, feature representation, and learning model. Machine-learning procedures have been used in the past for supervised classification, but increased attention to feature representation and selection may produce better models and predictions.

RESULTS

We focused our attention on the classification of nine oral sites and dental plaque in particular, using data collected from the Human Microbiome Project. A key focus of our representations was the use of phylogenetic information, both as the basis for custom kernels and as a way to represent sets of microbes to the classifier. We also used the PICRUSt software, which draws on phylogenetic relationships to predict molecular functions and to generate additional features for the classifier. Custom kernels based on the UniFrac measure of community dissimilarity did not improve performance. However, feature representation was vital to classification accuracy, with microbial clade and function representations providing useful information to the classifier; combining the two types of features did not yield increased prediction accuracy. Many of the best-performing clades and functions had clear associations with oral microflora.

CONCLUSIONS

The classification of oral microbiota remains a challenging problem; our best accuracy on the plaque dataset was approximately 81 %. Perfect accuracy may be unattainable due to the close proximity of the sites and intra-individual variation. However, further exploration of the space of both classifiers and feature representations is likely to increase the accuracy of predictive models.

Host genetic variation impacts microbiome composition across human body sites

BACKGROUND

The composition of bacteria in and on the human body varies widely across human individuals, and has been associated with multiple health conditions. While microbial communities are influenced by environmental factors, some degree of genetic influence of the host on the microbiome is also expected. This study is part of an expanding effort to comprehensively profile the interactions between human genetic variation and the composition of this microbial ecosystem on a genome- and microbiome-wide scale.

RESULTS

Here, we jointly analyze the composition of the human microbiome and host genetic variation. By mining the shotgun metagenomic data from the Human Microbiome Project for host DNA reads, we gathered information on host genetic variation for 93 individuals for whom bacterial abundance data are also available. Using this dataset, we identify significant associations between host genetic variation and microbiome composition in 10 of the 15 body sites tested. These associations are driven by host genetic variation in immunity-related pathways, and are especially enriched in host genes that have been previously associated with microbiome-related complex diseases, such as inflammatory bowel disease and obesity-related disorders. Lastly, we show that host genomic regions associated with the microbiome have high levels of genetic differentiation among human populations, possibly indicating host genomic adaptation to environment-specific microbiomes.

CONCLUSIONS

Our results highlight the role of host genetic variation in shaping the composition of the human microbiome, and provide a starting point toward understanding the complex interaction between human genetics and the microbiome in the context of human evolution and disease.

The Microbiome: The Trillions of Microorganisms That Maintain Health and Cause Disease in Humans and Companion Animals

The microbiome is the complex collection of microorganisms, their genes, and their metabolites, colonizing the human and animal mucosal surfaces, digestive tract, and skin. It is now well known that the microbiome interacts with its host, assisting in digestion and detoxification, supporting immunity, protecting against pathogens, and maintaining health. Studies published to date have demonstrated that healthy individuals are often colonized with different microbiomes than those with disease involving various organ systems. This review covers a brief history of the development of the microbiome field, the main objectives of the Human Microbiome Project, and the most common microbiomes inhabiting the human respiratory tract, companion animal digestive tract, and skin in humans and companion animals. The main changes in the microbiomes in patients with pulmonary, gastrointestinal, and cutaneous lesions are described.

Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups

Many studies have characterized microbiomes of western individuals. However, studies involving non-westerners are scarce. This study characterizes the skin microbiomes of Chinese individuals. Skin-associated genera, including Propionibacterium, Corynebacterium, Staphylococcus, and Enhydrobacter were prevalent. Extensive inter-individual microbiome variations were detected, with core genera present in all individuals constituting a minority of genera detected. Species-level analyses presented dominance of potential opportunistic pathogens in respective genera. Host properties including age, gender, and household were associated with variations in community structure. For all sampled sites, skin microbiomes within an individual is more similar than that of different co-habiting individuals, which is in turn more similar than individuals living in different households. Network analyses highlighted general and skin-site specific relationships between genera. Comparison of microbiomes from different population groups revealed race-based clustering explained by community membership (Global R = 0.968) and structure (Global R = 0.589), contributing to enlargement of the skin pan-microbiome. This study provides the foundation for subsequent in-depth characterization and microbial interactive analyses on the skin and other parts of the human body in different racial groups, and an appreciation that the human skin pan-microbiome can be much larger than that of a single population.