Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus-host interactions.

Exposure to polycyclic aromatic hydrocarbons (PAHs) in polluted air influences the composition of the skin microbiome, which in turn is associated with altered skin phenotypes. However, the interactions between PAH exposure and viromes are unclear. This study aims to elucidate how PAH exposure affects the composition and function of skin viruses, their role in shaping the metabolism of bacterial hosts, and the subsequent effects on skin phenotype.

Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.

Background: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants.

Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons.

Background: The effects of air pollutants, particularly polycyclic aromatic hydrocarbons (PAHs), on the skin microbiome remain poorly understood. Thus, to better understand the interplay between air pollutants, microbiomes, and skin conditions, we applied metagenomics and metabolomics to analyze the effects of PAHs in air pollution on the skin microbiomes of over 120 subjects residing in two cities in China with different levels of air pollution.

Results: The skin microbiomes differentiated into two cutotypes (termed 1 and 2) with distinct taxonomic, functional, resistome, and metabolite compositions as well as skin phenotypes that transcended geography and host factors.

City-Scale Meta-Analysis of Indoor Airborne Microbiota Reveals that Taxonomic and Functional Compositions Vary with Building Types.

Currently, there is a lack of understanding on the variations of the indoor airborne microbiotas of different building types within a city, and how operational taxonomic unit (OTU)- and amplicon sequence variant (ASV)-based analyses of the 16S rRNA gene sequences affect interpretation of the indoor airborne microbiota results. Therefore, in this study, the indoor airborne bacterial microbiotas between commercial buildings, residences, and subways within the same city were compared using both OTU- and ASV-based analytic methods. Our findings suggested that indoor airborne bacterial microbiota compositions were significantly different between building types regardless of the bioinformatics method used.

Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city.

Background: Studies of the microbiomes on surfaces in built environment have largely focused on indoor spaces, while outdoor spaces have received far less attention. Piers are engineered infrastructures commonly found in coastal areas, and due to their unique locations at the interface between terrestrial and aquatic ecosystems, pier surfaces are likely to harbor interesting microbiology. In this study, the microbiomes on the metal and concrete surfaces at nine piers located along the coastline of Hong Kong were investigated by metagenomic sequencing.

Multi-omics analysis to decipher the molecular link between chronic exposure to pollution and human skin dysfunction.

Environmental pollution is composed of several factors, namely particulate matter (PM, PM), ozone and Ultra Violet (UV) rays among others and first and the most exposed tissue to these substances is the skin epidermis. It has been established that several skin disorders such as eczema, acne, lentigines and wrinkles are aggravated by exposure to atmospheric pollution. While pollutants can interact with skin surface, contamination of deep skin by ultrafine particles or Polycyclic aromatic hydrocarbons (PAH) might be explained by their presence in blood and hair cortex.

Dysbiosis of the Urinary Bladder Microbiome in Cats with Chronic Kidney Disease.

Although feline urinary tract diseases cause high morbidity and mortality rates, and subclinical bacteriuria is not uncommon, the feline urinary microbiome has not been characterized. We conducted a case-control study to identify the feline urinary bladder microbiome and assess its association with chronic kidney disease (CKD), feline idiopathic cystitis (FIC), and positive urine cultures (PUCs). Of 108 feline urine samples subjected to 16S rRNA gene sequencing, 48 (44.

Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching.

Background: The human skin microbiome has been recently investigated as a potential forensic tool, as people leave traces of their potentially unique microbiomes on objects and surfaces with which they interact. In this metagenomic study of four people in Hong Kong, their homes, and public surfaces in their neighbourhoods, we investigated the stability and identifiability of these microbiota traces on a timescale of hours to days.

Results: Using a Canberra distance-based method of comparing skin and surface microbiomes, we found that a person could be accurately matched to their household in 84% of tests and to their neighbourhood in 50% of tests, and that matching accuracy did not decay for household surfaces over the 10-day study period, although it did for public surfaces.

A global metagenomic map of urban microbiomes and antimicrobial resistance.

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms.

Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome.

Background: As one of the most densely populated microbial communities on Earth, the gut microbiota serves as an important reservoir of antibiotic resistance genes (ARGs), referred to as the gut resistome. Here, we investigated the association of dietary nutritional content with gut ARG diversity and composition, using publicly available shotgun metagenomic sequence data generated from canine and feline fecal samples. Also, based on network theory, we explored ARG-sharing patterns between gut bacterial genera by identifying the linkage structure between metagenomic assemblies and their functional genes obtained from the same data.

Profiling Airborne Microbiota in Mechanically Ventilated Buildings Across Seasons in Hong Kong Reveals Higher Metabolic Activity in Low-Abundance Bacteria.

Metabolically active bacteria within built environments are poorly understood. This study aims to investigate the active airborne bacterial microbiota and compare the total and active microbiota in eight mechanically ventilated buildings over four consecutive seasons using the 16S rRNA gene (rDNA) and the 16S rRNA (rRNA), respectively. The relative abundances of the taxa of presumptive occupants and environmental origins were significantly different between the active and total microbiota.

Airborne Bacteria in Outdoor Air and Air of Mechanically Ventilated Buildings at City Scale in Hong Kong across Seasons.

Studies of the indoor airborne microbiome have mostly been confined to a single location and time point. Here, we characterized, over the course of a year, the geographic variation, building-function dependence, and dispersal characteristics of indoor and outdoor airborne microbiomes (bacterial members only) of eight mechanically ventilated commercial buildings. Based on the Sloan neutral model, airborne microbiomes were randomly dispersed in the respective indoor and outdoor environments and between the two environments during each season.

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.

Neutral Processes Drive Seasonal Assembly of the Skin Mycobiome.

The importance of microorganisms to human skin health has led to a growing interest in the temporal stability of skin microbiota. Here we investigated the dynamics and assembly of skin fungal communities (mycobiomes) with amplicon sequencing of samples collected from multiple sites on 24 healthy Chinese individuals across four seasons (in the order of winter, spring, summer, and autumn in a calendar year). We found a significant difference in community compositions between individuals, and intrapersonal community variation increased over time at all body sites.

Rare Taxa Exhibit Disproportionate Cell-Level Metabolic Activity in Enriched Anaerobic Digestion Microbial Communities.

Microbial communities are composed of populations with vastly different abundances and levels of metabolic and replicative activity, ranging from actively metabolizing and dividing to dormant or nonviable. The 16S rRNA/rDNA ratio is an emerging tool for evaluating cell-level metabolic activity independent of abundance. In this study, we used five long-term enriched model anaerobic digestion (AD) communities to investigate community composition, diversity, structure, and in particular activity based on the rRNA/rDNA ratio.

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.

City-scale distribution and dispersal routes of mycobiome in residences.

Background: Pathogenic and allergenic bacteria and fungi within the indoors can bring detrimental health effects on the occupants. We previously studied the bacterial communities found in households located throughout Hong Kong as well as the skin surfaces of the occupants. As a complementary study, here, we investigated the fungal communities (mycobiome) in the same residences and occupants and identified factors that are important in shaping their diversity, composition, distribution, and dispersal patterns.

Microbiota fingerprints lose individually identifying features over time.

Background: Humans host individually unique skin microbiota, suggesting that microbiota traces transferred from skin to surfaces could serve as forensic markers analogous to fingerprints. While it is known that individuals leave identifiable microbiota traces on surfaces, it is not clear for how long these traces persist. Moreover, as skin and surface microbiota change with time, even persistent traces may lose their forensic potential as they would cease to resemble the microbiota of the person who left them.

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.

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.

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.

Indoor-air microbiome in an urban subway network: diversity and dynamics.

Subway systems are indispensable for urban societies, but microbiological characteristics of subway aerosols are relatively unknown. Previous studies investigating microbial compositions in subways employed methodologies that underestimated the diversity of microbial exposure for commuters, with little focus on factors governing subway air microbiology, which may have public health implications. Here, a culture-independent approach unraveling the bacterial diversity within the urban subway network in Hong Kong is presented.