Publications by authors named "Marcus Leung"

24 Publications

  • Page 1 of 1

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

Sci Rep 2021 Sep 15;11(1):18302. Epub 2021 Sep 15.

Research and Innovation, L'Oréal SA, Aulnay Sous Bois, France.

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. Molecular mechanisms leading to skin dysfunction due to pollution exposure have been poorly explored in humans. In addition to various host skin components, cutaneous microbiome is another target of these environment aggressors and can actively contribute to visible clinical manifestation such as wrinkles and aging. The present study aimed to investigate the association between pollution exposure, skin microbiota, metabolites and skin clinical signs in women from two cities with different pollution levels. Untargeted metabolomics and targeted proteins were analyzed from D-Squame samples from healthy women (n = 67 per city), aged 25-45 years and living for at least 15 years in the Chinese cities of Baoding (used as a model of polluted area) and Dalian (control area with lower level of pollution). Additional samples by swabs were collected from the cheeks from the same population and microbiome was analysed using bacterial 16S rRNA as well as fungal ITS1 amplicon sequencing and metagenomics analysis. The level of exposure to pollution was assessed individually by the analysis of polycyclic aromatic hydrocarbons (PAH) and their metabolites in hair samples collected from each participant. All the participants of the study were assessed for the skin clinical parameters (acne, wrinkles, pigmented spots etc.). Women from the two cities (polluted and less polluted) showed distinct metabolic profiles and alterations in skin microbiome. Profiling data from 350 identified metabolites, 143 microbes and 39 PAH served to characterize biochemical events that correlate with pollution exposure. Finally, using multiblock data analysis methods, we obtained a potential molecular map consisting of multi-omics signatures that correlated with the presence of skin pigmentation dysfunction in individuals living in a polluted environment. Overall, these signatures point towards macromolecular alterations by pollution that could manifest as clinical sign of early skin pigmentation and/or other imperfections.
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http://dx.doi.org/10.1038/s41598-021-97572-1DOI Listing
September 2021

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

mSystems 2021 Aug 27;6(4):e0051021. Epub 2021 Jul 27.

Centre for Companion Animal Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Konggrid.35030.35, Hong Kong SAR.

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 (44.4%) samples reached the 500-sequence rarefaction threshold and were selected for further analysis, suggesting that the feline bladder microbiome is typically sparse. Selected samples included 17 CKD, 9 FIC, 8 PUC cases and 14 controls. Among these, 19 phyla, 145 families, and 218 genera were identified. were the most abundant, followed by . Notably, four major urotypes were identified, including two urotypes predominated by Escherichia or and two others characterized by relatively high alpha diversity, Diverse 1 and Diverse 2. Urotype was associated with disease status ( value of 0.040), with the Escherichia-predominant urotype being present in 53% of CKD cases and in all of the Escherichia coli PUC cases. Reflecting these patterns, the overall microbial composition of CKD cases was more similar to that of E. coli PUC cases than to that of controls ( value of <0.001). Finally, PUC cases had microbial compositions distinct from those of controls as well as CKD and FIC cases, with significantly lower Shannon diversity and Faith's phylogenetic diversity values. Despite the clinical importance of urinary diseases in cats, the presence of resident urine microbes has not been demonstrated in cats, and the role of these microbes as a community in urinary health remains unknown. Here, we have shown that cats with and without urinary tract disease harbor unique microbial communities in their urine. We found no evidence to suggest that the bladder microbiome is implicated in the pathogenesis of feline idiopathic cystitis, a disease similar to bladder pain syndrome/interstitial cystitis in humans. However, cats with chronic kidney disease had dysbiosis of their bladder microbiome, which was predominated by Escherichia and had a community structure similar to that of cats with Escherichia coli cystitis. These findings suggest that chronic kidney disease alters the bladder environment to favor Escherichia colonization, potentially increasing the risk of overt clinical infection.
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http://dx.doi.org/10.1128/mSystems.00510-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8407359PMC
August 2021

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

Microbiome 2021 06 5;9(1):129. Epub 2021 Jun 5.

School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.

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. The time of day at which a skin or surface sample was taken affected matching accuracy, and 160 species across all sites were found to have a significant variation in abundance between morning and evening samples. We hypothesised that daily routines drive a rhythm of daytime dispersal from the pooled public surface microbiome followed by normalisation of a person's microbiome by contact with their household microbial reservoir, and Dynamic Bayesian Networks (DBNs) supported dispersal from public surfaces to skin as the major dispersal route among all sites studied.

Conclusions: These results suggest that in addition to considering the decay of microbiota traces with time, diurnal patterns in microbiome exposure that contribute to the human skin microbiome assemblage must also be considered in developing this as a potential forensic method. Video Abstract.
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http://dx.doi.org/10.1186/s40168-021-01082-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8180031PMC
June 2021

A global metagenomic map of urban microbiomes and antimicrobial resistance.

Cell 2021 Jun 26;184(13):3376-3393.e17. Epub 2021 May 26.

Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.

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. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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http://dx.doi.org/10.1016/j.cell.2021.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8238498PMC
June 2021

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

Anim Microbiome 2020 Feb 7;2(1). Epub 2020 Feb 7.

Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.

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.

Results: In both canine and feline gut microbiota, an increase in protein and a reduction in carbohydrate in the diet were associated with increased ARG diversity. ARG diversity of the canine gut microbiota also increased, but less strongly, after a reduction in protein and an increase in carbohydrate in the diet. The association between ARG and taxonomic composition suggests that diet-induced changes in the gut microbiota may be responsible for changes in ARG composition, supporting the links between protein metabolism and antibiotic resistance in gut microbes. In the analysis of the ARG-sharing patterns, 22 ARGs were shared among 46 genera in the canine gut microbiota, and 11 ARGs among 28 genera in the feline gut microbiota. Of these ARGs, the tetracycline resistance gene tet(W) was shared among the largest number of genera, predominantly among Firmicutes genera. Bifidobacterium, a genus extensively used in the fermentation of dairy products and as probiotics, shared tet(W) with a wide variety of other genera. Finally, genera from the same phylum were more likely to share ARGs than with those from different phyla.

Conclusions: Our findings show that dietary nutritional content, especially protein content, is associated with the gut resistome and suggest future research to explore the impact of dietary intervention on the development of antibiotic resistance in clinically-relevant gut microbes. Our network analysis also reveals that the genetic composition of bacteria acts as an important barrier to the horizontal transfer of ARGs. By capturing the underlying gene-sharing relationships between different bacterial taxa from metagenomes, our network approach improves our understanding of horizontal gene transfer dynamics.
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http://dx.doi.org/10.1186/s42523-020-0022-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7807453PMC
February 2020

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

Environ Sci Technol 2021 01 21;55(1):249-259. Epub 2020 Dec 21.

School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.

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. The Sloan neutral model suggested that ecological drift and random dispersal played a smaller role in the assembly of the active microbiota than the total microbiota. The seasonal nature of the active microbiota was consistent with that of the total microbiota in both indoor and outdoor environments, while only the indoor environment was significantly affected by geography. The relative abundances of the active and total taxa were positively correlated, suggesting that the high-abundance members were also the greatest contributors to the community-level metabolic activity. Based on the rRNA/rDNA ratio, the low-abundance members consistently had a higher taxon-level metabolic activity than the high-abundance members over seasons, suggesting that the low-abundance members may have the ability to survive and thrive in the indoor environment and their impact on the health of occupants cannot be overlooked.
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http://dx.doi.org/10.1021/acs.est.0c06201DOI Listing
January 2021

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

Environ Sci Technol 2020 10 10;54(19):11732-11743. Epub 2020 Sep 10.

School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China.

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. The dominant taxa in the indoor and outdoor environments showed minor variations at each location among seasons. The airborne microbiomes displayed weak seasonality for both indoor and outdoor environments, while a weak geographic variation was found only for the indoor environments. Source tracking results show that outdoor air and occupant skin were major contributors to the indoor airborne microbiomes, but the extent of the contribution from each source varied within and among buildings over the seasons, which suggests variations in local building use. Based on 32 cases of indoor airborne microbiome data, we determined that the indoor/outdoor (I/O) ratio of PM was not a robust indicator of the sources found indoors. Alternatively, the indoor concentration of carbon dioxide was more closely correlated with the major sources of the indoor airborne microbiome in mechanically ventilated environments.
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http://dx.doi.org/10.1021/acs.est.9b07623DOI Listing
October 2020

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

Microbiome 2020 06 26;8(1):100. Epub 2020 Jun 26.

School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.

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.
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http://dx.doi.org/10.1186/s40168-020-00874-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320578PMC
June 2020

Neutral Processes Drive Seasonal Assembly of the Skin Mycobiome.

mSystems 2019 Mar-Apr;4(2). Epub 2019 Mar 26.

School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.

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. Within each season, the frequency of occurrence of most operational taxonomic units (OTUs) was well fitted by a neutral model, highlighting the importance of stochastic forces such as passive dispersal and ecological drift in skin community assembly. Despite the significant richness contributed by neutrally distributed OTUs, skin coassociation networks were dominated by taxa well-adapted to multiple body sites (forehead, forearm, and palm), although hub species were disproportionately rare. Taken together, these results suggest that while skin mycobiome assembly is a predominantly neutral process, taxa that could be under the influence of selective forces (e.g., host selection) are potentially key to the structure of a community network. Fungi are well recognized members of the human skin microbiota and are crucial to cutaneous health. Common cutaneous diseases such as seborrheic dermatitis and dermatophytes are linked to fungal species. Most studies related to skin microbial community dynamics have focused on Western subjects, while non-Western individuals are understudied. In this study, we explore the seasonal changes of the skin mycobiome in a healthy Chinese cohort and identify ecological processes that could possibly give rise to such variations. Our work reveals the dynamic nature of host skin fungal community, highlighting the dominant roles neutral forces play in the seasonal assembly of skin mycobiome. This study provides insight into the microbial ecology of the human skin microbiome and fills a knowledge gap in the literature regarding the dynamics of skin fungal community.
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http://dx.doi.org/10.1128/mSystems.00004-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6435813PMC
March 2019

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

mSystems 2019 Jan-Feb;4(1). Epub 2019 Jan 22.

School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR.

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. We cross-validated the 16S amplicon-based results using two alternative operational taxonomic unit (OTU) formation methods (conventional 97% sequence similarity and 100% sequence similar zero-radius OTUs by UNOISE3) and compared these to metagenome-derived population genomes and metatranscriptomes. Significant positive correlations were observed between microbial total activity and abundance with both the amplicon- and omic-based methods. All three methods revealed disproportionately high transcription/abundance ratios for some rare taxa but lower ratios for most abundant taxa for all the communities, which was further corroborated by the high replication rate (iRep) of most low-abundance population genomes. Variation in microbial activity levels is increasingly being recognized as both an important dimension in community function and a complicating factor in sequencing-based survey methods. This study extends previous reports that rare taxa may contribute disproportionately to community activity in some natural environments, showing that this may also hold in artificially maintained model communities with well-described inputs, outputs, and biochemical functions. These results demonstrate that assessment of activity levels using the rRNA/rDNA ratio is robust across taxonomic unit formation methods and is independently corroborated by omics methods. The results also provide insight into the comparative advantages and disadvantages of different taxonomic unit formation methods in amplicon sequencing studies, showing that UNOISE3 provides comparable microbial diversity, structure, and activity information as the 97% sequence similarity method but potentially loses some phylogenetic diversity and creates more "phantom taxa" (which are present in the RNA pool but not the corresponding DNA pool).
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http://dx.doi.org/10.1128/mSystems.00208-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343076PMC
January 2019

A comparison of methods used to unveil the genetic and metabolic pool in the built environment.

Microbiome 2018 04 16;6(1):71. Epub 2018 Apr 16.

Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.

Background: A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs. biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting.

Results: We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at - 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community.

Conclusions: Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.
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http://dx.doi.org/10.1186/s40168-018-0453-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902888PMC
April 2018

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

Microbiome 2018 02 2;6(1):26. Epub 2018 Feb 2.

School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong.

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.
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http://dx.doi.org/10.1186/s40168-018-0412-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797343PMC
February 2018

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

Microbiome 2017 10 4;5(1):131. Epub 2017 Oct 4.

School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.

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.

Results: We observed that common skin and environmental fungal taxa dominated air, surface, and skin samples. Individual and touch frequency strongly and respectively shaped the fungal community structure on occupant skin and residential surfaces. Cross-domain analysis revealed positive correlations between bacterial and fungal community diversity and composition, especially for skin samples. SourceTracker prediction suggested that some fungi can be transferred bidirectionally between surfaces and skin sites, but bacteria showed a stronger dispersal potential. In addition, we detected a modest but significant association between indoor airborne bacterial composition and geographic distance on a city-wide scale, a pattern not observed for fungi. However, the distance-decay effects were more pronounced at shorter local scale for both communities, and airflow might play a prominent role in driving the spatial variation of the indoor airborne mycobiome.

Conclusions: Our study suggests that occupants exert a weaker influence on surface fungal communities compared to bacterial communities, and local environmental factors, including air currents, appear to be stronger determinants of indoor airborne mycobiome than ventilation strategy, human occupancy, and room type.
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http://dx.doi.org/10.1186/s40168-017-0346-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5628474PMC
October 2017

Microbiota fingerprints lose individually identifying features over time.

Microbiome 2017 01 9;5(1). Epub 2017 Jan 9.

School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong, Special Administrative Region of China.

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. We followed skin and surface microbiota within households for four seasons to determine whether accurate microbiota-based matching of individuals to their households could be achieved across long time delays.

Results: While household surface microbiota traces could be matched to the correct occupant or occupants with 67% accuracy, accuracy decreased substantially when skin and surface samples were collected in different seasons, and particularly when surface samples were collected long after skin samples. Most OTUs persisted on skin or surfaces for less than one season, indicating that OTU loss was the major cause of decreased matching accuracy. OTUs that were more useful for individual identification persisted for less time and were less likely to be deposited from skin to surface, suggesting a trade-off between the longevity and identifying value of microbiota traces.

Conclusions: While microbiota traces have potential forensic value, unlike fingerprints they are not static and may degrade in a way that preferentially erases features useful in identifying individuals.
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http://dx.doi.org/10.1186/s40168-016-0209-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5234115PMC
January 2017

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

Microbiome 2016 08 24;4(1):46. Epub 2016 Aug 24.

B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.

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.
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http://dx.doi.org/10.1186/s40168-016-0192-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4997687PMC
August 2016

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

Microbiome 2016 05 24;4(1):21. Epub 2016 May 24.

School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, B5423-AC1, Hong Kong.

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.
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http://dx.doi.org/10.1186/s40168-016-0165-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877933PMC
May 2016

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

Sci Rep 2015 Jul 16;5:11845. Epub 2015 Jul 16.

School of Energy and Environment, City University of Hong Kong, Hong Kong.

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.
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http://dx.doi.org/10.1038/srep11845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503953PMC
July 2015

Indoor air bacterial communities in Hong Kong households assemble independently of occupant skin microbiomes.

Environ Microbiol 2016 06 11;18(6):1754-63. Epub 2015 Jun 11.

School of Energy and Environment, City University of Hong Kong, Tat Chee Ave, Kowloon, Hong Kong.

More than in any other habitat, humans exert a large influence on microbial communities indoors. Frequent contact between occupant skin and indoor surfaces causes indoor surface microbial communities to be largely assembled from and thus closely resemble occupant skin microbiomes. While indoor air and dust are known to also contain many human-associated taxa, household air communities have not yet been directly compared with occupant skin microbiomes. We sampled microorganisms from air, surfaces and occupant skin in 19 Hong Kong households and used Illumina sequencing of the V4 hypervariable region of the 16S rRNA gene to investigate the dispersal relationships between the bacterial communities at each site. Our results confirmed that indoor surfaces bear the 'bacterial fingerprint' of household occupant skin. However, while air communities contained abundant human-associated taxa and were household specific, air communities in each household did not resemble occupant skin from that household any more than occupant skin from other households. Our results suggest that, at least in Hong Kong, indoor air bacterial communities may be assembled largely from outdoor air and occupant body sites other than skin, and unlike surface communities do not harbour the occupants' skin 'bacterial fingerprint'.
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http://dx.doi.org/10.1111/1462-2920.12889DOI Listing
June 2016

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

Appl Environ Microbiol 2014 Nov 29;80(21):6760-70. Epub 2014 Aug 29.

School of Energy and Environment, City University of Hong Kong, Hong Kong

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. Aerosol samples from multiple subway lines and outdoor locations were collected. Targeting the 16S rRNA gene V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those associated with skin. Overall, subway lines harbored different phylogenetic communities based on α- and β-diversity comparisons, and closer inspection suggests that each community within a line is dependent on architectural characteristics, nearby outdoor microbiomes, and connectedness with other lines. Microbial diversities and assemblages also varied depending on the day sampled, as well as the time of day, and changes in microbial communities between peak and nonpeak commuting hours were attributed largely to increases in skin-associated genera in peak samples. Microbial diversities within the subway were influenced by temperature and relative humidity, while carbon dioxide levels showed a positive correlation with abundances of commuter-associated genera. This Hong Kong data set and communities from previous studies conducted in the United States formed distinct community clusters, indicating that additional work is required to unravel the mechanisms that shape subway microbiomes around the globe.
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http://dx.doi.org/10.1128/AEM.02244-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249038PMC
November 2014

Sequetyping: serotyping Streptococcus pneumoniae by a single PCR sequencing strategy.

J Clin Microbiol 2012 Jul 2;50(7):2419-27. Epub 2012 May 2.

Centre for Clinical Microbiology, University College London Medical School, Royal Free Campus, London, United Kingdom.

The introduction of pneumococcal conjugate vaccines necessitates continued monitoring of circulating strains to assess vaccine efficacy and replacement serotypes. Conventional serological methods are costly, labor-intensive, and prone to misidentification, while current DNA-based methods have limited serotype coverage requiring multiple PCR primers. In this study, a computer algorithm was developed to interrogate the capsulation locus (cps) of vaccine serotypes to locate primer pairs in conserved regions that border variable regions and could differentiate between serotypes. In silico analysis of cps from 92 serotypes indicated that a primer pair spanning the regulatory gene cpsB could putatively amplify 84 serotypes and differentiate 46. This primer set was specific to Streptococcus pneumoniae, with no amplification observed for other species, including S. mitis, S. oralis, and S. pseudopneumoniae. One hundred thirty-eight pneumococcal strains covering 48 serotypes were tested. Of 23 vaccine serotypes included in the study, most (19/22, 86%) were identified correctly at least to the serogroup level, including all of the 13-valent conjugate vaccine and other replacement serotypes. Reproducibility was demonstrated by the correct sequetyping of different strains of a serotype. This novel sequence-based method employing a single PCR primer pair is cost-effective and simple. Furthermore, it has the potential to identify new serotypes that may evolve in the future.
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http://dx.doi.org/10.1128/JCM.06384-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3405617PMC
July 2012

Streptococcus pseudopneumoniae identification by pherotype: a method to assist understanding of a potentially emerging or overlooked pathogen.

J Clin Microbiol 2012 May 29;50(5):1684-90. Epub 2012 Feb 29.

Centre for Clinical Microbiology, University College London Medical School, Royal Free Campus, London, United Kingdom.

The recent identification of Streptococcus pseudopneumoniae (pseudopneumococcus) has complicated classification schemes within members of the "mitis" streptococcal group. Accurate differentiation of this species is necessary for understanding its disease potential and identification in clinical settings. This work described the use of the competence-stimulatory peptide ComC sequence for identification of S. pseudopneumoniae. ComC sequences from clinical sources were determined for 17 strains of S. pseudopneumoniae, Streptococcus pneumoniae, and Streptococcus oralis. An additional 58 ComC sequences from a range of sources were included to understand the diversity and suitability of this protein as a diagnostic marker for species identification. We identified three pherotypes for this species, delineated CSP6.1 (10/14, 79%), CSP6.3 (3/14, 21%), and SK674 (1/14, 7%). Pseudopneumococcal ComC sequences formed a discrete cluster within those of other oral streptococci. This suggests that the comC sequence could be used to identify S. pseudopneumoniae, thus simplifying the study of the pathogenic potential of this organism. To avoid confusion between pneumococcal and pseudopneumococcal pherotypes, we have renamed the competence pherotype CSP6.1, formerly reported as an "atypical" pneumococcus, CSPps1 to reflect its occurrence in S. pseudopneumoniae.
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http://dx.doi.org/10.1128/JCM.00131-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3347113PMC
May 2012

Pneumococcal sepsis and nasopharyngeal carriage.

Curr Opin Pulm Med 2012 May;18(3):222-7

Centre for Clinical Microbiology, University College London Medical School, Royal Free Campus, Rowland Hill Street, London, UK.

Purpose Of Review: Streptococcus pneumoniae (the pneumococcus) remains an important cause of invasive disease including bacteraemia. This review highlights recent findings related to pneumococcal bacteraemia, virulence factors, and multiple colonization, including strain competition, biofilm formation, and competence.

Recent Findings: Countries with no vaccination programmes see vaccine serotypes still prevalent in disease, whereas the emergence of nonvaccine serotypes in nasopharyngeal carriage and invasive disease is seen in countries with conjugate vaccination in place. Co-colonizing strains are being uncovered with more sensitive methods, and may act synergistically or compete with each other for survival. Several factors such as iron uptake, quorum signalling and the luxS gene, involved in colonization and virulence, are discussed. The role of quorum sensing signalling molecules and formation of biofilms are being explored.

Summary: Epidemiological data suggest that the latest serotype-based conjugate vaccines should provide heightened protection, although serotype replacement is now being seen. Much remains to be elucidated about its biology during multiple colonization, when evolution and adaptation to its host take place. The modes of colonization (biofilm, intracellular or surface adherence to the mucosal epithelium), and whether organisms that cause invasive disease have attenuated ability to colonize the nasopharynx remain to be elucidated.
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http://dx.doi.org/10.1097/MCP.0b013e328352103bDOI Listing
May 2012

The adaptive potential during nasopharyngeal colonisation of Streptococcus pneumoniae.

Infect Genet Evol 2011 Dec 10;11(8):1989-95. Epub 2011 Sep 10.

Centre for Clinical Microbiology, University College London Medical School, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom.

Adaptation to host defences and antimicrobials is critical for Streptococcus pneumoniae (the pneumococcus) during colonisation of the nasopharynx--its only ecological habitat. The pneumococcus is highly transformable with the genome between different strains varying widely in both gene content and gene sequence. Thus, mixed strains colonising together will expand the genetic reservoir--"supragenome" for this highly transformable microorganism, increasing its adaptive potential. The extent of the phenotypic and genotypic diversity of strains co-colonising in the nasopharynx was determined. In contrast to most carriage studies, which characterise single colonies, a systematic analysis of up to 20 colonies per colonisation was undertaken in Tanzanian children for 12 months. The serotype was determined by conventional serology and confirmed by DNA-based methods. The antibiotype for penicillin and co-trimoxazole was determined from the minimum inhibitory concentration determined by E-test. As representative of the genotype of strains the sequence types (STs) was determined by multilocus sequence typing (MLST). Of 61 colonisation events studied, seven (11.5%) had strains expressing multiple serotypes, with a maximum of five serotypes detected. Four colonisation events also had co-colonisation of penicillin and/or co-trimoxazole susceptible and non-susceptible pneumococci. Sequence typing revealed that 58% were unique to our cohort. Simultaneous colonisation of up to six STs with two expressing serotype 6B was seen. Re-isolation of either the same or different strains of serotype 6B was seen. Genetically related single-locus and double-locus variants were identified in our cohort that differed by multiple nucleotides. Multiple colony characterisation revealed phenotypic and genetic evidence of microevolution and a greater diversity of pneumococcal strains colonising together than previously observed, thus increasing the potential to adapt in response to the host environment during colonisation.
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http://dx.doi.org/10.1016/j.meegid.2011.09.002DOI Listing
December 2011
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