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Leung MHY, Tong X, Shen Z, Du S, Bastien P, Appenzeller BMR, Betts RJ, Mezzache S, Bourokba N, Cavusoglu N, Aguilar L, Misra N, Clavaud C, Lee PKH. Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons. Microbiome 2023; 11:124. [PMID: 37264459 DOI: 10.1186/s40168-023-01564-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/01/2023] [Indexed: 06/03/2023]
Abstract
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. High PAH exposure was linked to dry skin and cutotype 2, which was enriched with species with potential biodegradation functions and had reduced correlation network structure integrity. The positive correlations identified between dominant taxa, key functional genes, and metabolites in the arginine biosynthesis pathway in cutotype 1 suggest that arginine from bacteria contributes to the synthesis of filaggrin-derived natural moisturizing factors (NMFs), which provide hydration for the skin, and could explain the normal skin phenotype observed. In contrast, no correlation with the arginine biosynthesis pathway was observed in cutotype 2, which indicates the limited hydration functions of NMFs and explains the observed dry skin phenotype. In addition to dryness, skin associated with cutotype 2 appeared prone to other adverse conditions such as inflammation. CONCLUSIONS This study revealed the roles of PAHs in driving skin microbiome differentiation into cutotypes that vary extensively in taxonomy and metabolic functions and may subsequently lead to variations in skin-microbe interactions that affect host skin health. An improved understanding of the roles of microbiomes on skin exposed to air pollutants can aid the development of strategies that harness microbes to prevent undesirable skin conditions. Video Abstract.
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Affiliation(s)
- Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Zhiyong Shen
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Shicong Du
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | | | - Brice M R Appenzeller
- Human Biomonitoring Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | | | | | | | | | - Luc Aguilar
- L'Oréal Research and Innovation, Aulnay-Sous-Bois, France
| | - Namita Misra
- L'Oréal Research and Innovation, Aulnay-Sous-Bois, France
| | - Cécile Clavaud
- L'Oréal Research and Innovation, Aulnay-Sous-Bois, France
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
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2
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Archer SDJ, Lee KC, Caruso T, Alcami A, Araya JG, Cary SC, Cowan DA, Etchebehere C, Gantsetseg B, Gomez-Silva B, Hartery S, Hogg ID, Kansour MK, Lawrence T, Lee CK, Lee PKH, Leopold M, Leung MHY, Maki T, McKay CP, Al Mailem DM, Ramond JB, Rastrojo A, Šantl-Temkiv T, Sun HJ, Tong X, Vandenbrink B, Warren-Rhodes KA, Pointing SB. Contribution of soil bacteria to the atmosphere across biomes. Sci Total Environ 2023; 871:162137. [PMID: 36775167 DOI: 10.1016/j.scitotenv.2023.162137] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/20/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The dispersion of microorganisms through the atmosphere is a continual and essential process that underpins biogeography and ecosystem development and function. Despite the ubiquity of atmospheric microorganisms globally, specific knowledge of the determinants of atmospheric microbial diversity at any given location remains unresolved. Here we describe bacterial diversity in the atmospheric boundary layer and underlying soil at twelve globally distributed locations encompassing all major biomes, and characterise the contribution of local and distant soils to the observed atmospheric community. Across biomes the diversity of bacteria in the atmosphere was negatively correlated with mean annual precipitation but positively correlated to mean annual temperature. We identified distinct non-randomly assembled atmosphere and soil communities from each location, and some broad trends persisted across biomes including the enrichment of desiccation and UV tolerant taxa in the atmospheric community. Source tracking revealed that local soils were more influential than distant soil sources in determining observed diversity in the atmosphere, with more emissive semi-arid and arid biomes contributing most to signatures from distant soil. Our findings highlight complexities in the atmospheric microbiota that are relevant to understanding regional and global ecosystem connectivity.
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Affiliation(s)
- Stephen D J Archer
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Kevin C Lee
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Tancredi Caruso
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Antonio Alcami
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Jonathan G Araya
- Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - S Craig Cary
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Claudia Etchebehere
- Biological Research Institute Clemente Estable, Ministry of Education, Montevideo, Uruguay
| | | | - Benito Gomez-Silva
- Departamento Biomédico and CeBiB, Universidad de Antofagasta, Antofagasta, Chile
| | - Sean Hartery
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, New Zealand; Canadian High Arctic Research Station, Cambridge Bay, Nunavut, Canada
| | - Mayada K Kansour
- Department of Biological Sciences, Kuwait University, Kuwait City, Kuwait
| | - Timothy Lawrence
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Charles K Lee
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Matthias Leopold
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Australia
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Teruya Maki
- Department of Life Sciences, Kindai University, Osaka, Japan
| | | | - Dina M Al Mailem
- Department of Biological Sciences, Kuwait University, Kuwait City, Kuwait
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa; Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Henry J Sun
- Desert Research Institute, Las Vegas, NV, USA
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China; Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Bryan Vandenbrink
- Canadian High Arctic Research Station, Cambridge Bay, Nunavut, Canada
| | | | - Stephen B Pointing
- Yale-NUS College, National University of Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore; Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa, Japan.
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Zhou Y, Leung MHY, Tong X, Lee JYY, Lee PKH. City-Scale Meta-Analysis of Indoor Airborne Microbiota Reveals that Taxonomic and Functional Compositions Vary with Building Types. Environ Sci Technol 2021; 55:15051-15062. [PMID: 34738808 DOI: 10.1021/acs.est.1c03941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
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. The processes of ecological drift and random dispersal consistently played significant roles in the assembly of the indoor microbiota across building types. Abundant taxa tended to be more centralized in the correlation network of each building type, highlighting their importance. Taxonomic changes between the microbiotas of different building types were also linked to changes in their inferred metabolic function capabilities. Overall, the results imply that customized strategies are necessary to manage indoor airborne bacterial microbiotas for each building type or even within each specific building.
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Affiliation(s)
- You Zhou
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
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Tong X, Leung MHY, Shen Z, Lee JYY, Mason CE, Lee PKH. Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city. Microbiome 2021; 9:213. [PMID: 34724986 PMCID: PMC8562002 DOI: 10.1186/s40168-021-01166-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/20/2021] [Indexed: 05/25/2023]
Abstract
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. The roles played by different physical attributes and environmental factors in shaping the taxonomic composition and functional traits of the pier surface microbiomes were determined. Metagenome-assembled genomes were reconstructed and their putative biosynthetic gene clusters were characterized in detail. RESULTS Surface material was found to be the strongest factor in structuring the taxonomic and functional compositions of the pier surface microbiomes. Corrosion-related bacteria were significantly enriched on metal surfaces, consistent with the pitting corrosion observed. The differential enrichment of taxa mediating biodegradation suggests differences between the metal and concrete surfaces in terms of specific xenobiotics being potentially degraded. Genome-centric analysis detected the presence of many novel species, with the majority of them belonging to the phylum Proteobacteria. Genomic characterization showed that the potential metabolic functions and secondary biosynthetic capacity were largely correlated with taxonomy, rather than surface attributes and geography. CONCLUSIONS Pier surfaces are a rich reservoir of abundant novel bacterial species. Members of the surface microbial communities use different mechanisms to counter the stresses under oligotrophic conditions. A better understanding of the outdoor surface microbiomes located in different environments should enhance the ability to maintain outdoor surfaces of infrastructures. Video Abstract.
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Affiliation(s)
- Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Zhiyong Shen
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
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5
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Misra N, Clavaud C, Guinot F, Bourokba N, Nouveau S, Mezzache S, Palazzi P, Appenzeller BMR, Tenenhaus A, Leung MHY, Lee PKH, Bastien P, Aguilar L, Cavusoglu N. Multi-omics analysis to decipher the molecular link between chronic exposure to pollution and human skin dysfunction. Sci Rep 2021; 11:18302. [PMID: 34526566 PMCID: PMC8443591 DOI: 10.1038/s41598-021-97572-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/03/2021] [Indexed: 12/24/2022] Open
Abstract
Environmental pollution is composed of several factors, namely particulate matter (PM2.5, PM10), 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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Affiliation(s)
- Namita Misra
- Research and Innovation, L'Oréal SA, Aulnay Sous Bois, France.
| | - Cécile Clavaud
- Research and Innovation, L'Oréal SA, Aulnay Sous Bois, France
| | - Florent Guinot
- Research and Innovation, L'Oréal SA, Aulnay Sous Bois, France
| | | | | | - Sakina Mezzache
- Research and Innovation, L'Oréal SA, Aulnay Sous Bois, France
| | - Paul Palazzi
- Human Biomonitoring Research Unit, Luxembourg Institute of Health, Strassen, Luxemburg
| | - Brice M R Appenzeller
- Human Biomonitoring Research Unit, Luxembourg Institute of Health, Strassen, Luxemburg
| | - Arthur Tenenhaus
- CentraleSupelec Laboratoire des Signaux et Systemes, Université Paris-Saclay, CNRS, Gif-sur-Yvette, France
- Brain and Spine Institute, Paris, France
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | | | - Luc Aguilar
- Research and Innovation, L'Oréal SA, Aulnay Sous Bois, France
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6
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Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 2021; 184:3376-3393.e17. [PMID: 34043940 PMCID: PMC8238498 DOI: 10.1016/j.cell.2021.05.002] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/05/2021] [Accepted: 04/29/2021] [Indexed: 01/14/2023]
Abstract
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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Affiliation(s)
- David Danko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniela Bezdan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Evan E Afshin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Chandrima Bhattacharya
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniel J Butler
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Kern Rei Chng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Daisy Donnellan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Katelyn Jackson
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Katerina Kuchin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Mikhail Karasikov
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Abigail Lyons
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Lauren Mak
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dmitry Meleshko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Harun Mustafa
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Beth Mutai
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Kenya Medical Research Institute - Kisumu, Kisumu, Kenya
| | - Russell Y Neches
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Amanda Ng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | | | | | - Eileen Png
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Krista A Ryon
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jorge L Sanchez
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Heba Shaaban
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Maria A Sierra
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dominique Thomas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Ben Young
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Omar O Abudayyeh
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Josue Alicea
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Malay Bhattacharyya
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India
| | | | - Eduardo Castro-Nallar
- Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Ana M Cañas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Aspassia D Chatziefthimiou
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Youping Deng
- University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Christelle Desnues
- Aix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Emmanuel Dias-Neto
- Medical Genomics group, A.C.Camargo Cancer Center, São Paulo - SP, Brazil
| | - Marius Dybwad
- Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, Kyiv, Ukraine; Kyiv Academic University, Kyiv, Ukraine
| | - Dennis Gankin
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | | | - David C Green
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Iman Hajirasouliha
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jaden J A Hastings
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Santiago, Chile; Wellcome Sanger Institute, Hinxton, UK
| | | | - Andre Kahles
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; Kyiv Academic University, Kyiv, Ukraine; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Frank J Kelly
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Kaymisha Knights
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paweł P Łabaj
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Boku University Viennna, Vienna, Austria
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Per O Ljungdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Gabriella Mason-Buck
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Ken McGrath
- Microba, 388 Queen St, Brisbane City, QLD 4000, Australia
| | - Cem Meydan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Emmanuel F Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | | | - Houtan Noushmehr
- University of São Paulo, Ribeirão Preto Medical School, Ribeirão Preto - SP, Brazil
| | - Manuela Oliveira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria
| | - Orhan Özcan
- Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicolás Rascovan
- Microbial Paleogenomics Unit, Institut Pasteur, CNRS UMR2000, Paris 75015, France
| | - Hugues Richard
- Sorbonne University, Faculty of Science, Institute of Biology Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France; Robert Koch Institute, Berlin, Germany
| | - Gunnar Rätsch
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | - Leming Shi
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Rania Siam
- University of Medicine and Health Sciences, St. Kitts, West Indies and American University in Cairo, Cairo, Egypt
| | - Le Huu Song
- 108 Military Central Hospital, Hanoi, Vietnam; Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
| | | | - Denise Syndercombe Court
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | | | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Klas I Udekwu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; SciLife EVP, Department of Aquatic Sciences Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Santiago, Chile; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Brandon Valentine
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dimitar I Vassilev
- Faculty of Mathematics and Informatics, Sofia University "St. Kliment Ohridski," Sofia, Bulgaria
| | - Elena M Vayndorf
- Institute of Arctic Biology, University of Alaska, Fairbanks, Fairbanks, AK, USA
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Univeristätsklinikum Tübingen, Tübingen, Germany; Faculty of Medicine, Duy Tan University, Da Nang, Vietnam
| | - Jun Wu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | | | - Jifeng Zhu
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Christopher E Mason
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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7
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Wilkins D, Tong X, Leung MHY, Mason CE, Lee PKH. Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching. Microbiome 2021; 9:129. [PMID: 34090519 PMCID: PMC8180031 DOI: 10.1186/s40168-021-01082-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/21/2021] [Indexed: 05/06/2023]
Abstract
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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Affiliation(s)
- David Wilkins
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
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8
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Leung MHY, Tong X, Bøifot KO, Bezdan D, Butler DJ, Danko DC, Gohli J, Green DC, Hernandez MT, Kelly FJ, Levy S, Mason-Buck G, Nieto-Caballero M, Syndercombe-Court D, Udekwu K, Young BG, Mason CE, Dybwad M, Lee PKH. Characterization of the public transit air microbiome and resistome reveals geographical specificity. Microbiome 2021; 9:112. [PMID: 34039416 PMCID: PMC8157753 DOI: 10.1186/s40168-021-01044-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/09/2021] [Indexed: 05/21/2023]
Abstract
BACKGROUND The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized. RESULTS City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes. CONCLUSIONS Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.
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Affiliation(s)
- M H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - X Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - K O Bøifot
- Comprehensive Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - D Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - D J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - D C Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - J Gohli
- Comprehensive Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - D C Green
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - M T Hernandez
- Environmental Engineering Program, College of Engineering and Applied Science, University of Colorado, Boulder, CO, USA
| | - F J Kelly
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - S Levy
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - G Mason-Buck
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - M Nieto-Caballero
- Environmental Engineering Program, College of Engineering and Applied Science, University of Colorado, Boulder, CO, USA
| | - D Syndercombe-Court
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - K Udekwu
- Department of Aquatic Sciences & Assessment, Swedish University of Agriculture, Uppsala, Sweden
| | - B G Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - C E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - M Dybwad
- Comprehensive Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway.
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK.
| | - P K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
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9
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Zhou Y, Leung MHY, Tong X, Lai Y, Tong JCK, Ridley IA, Lee PKH. Profiling Airborne Microbiota in Mechanically Ventilated Buildings Across Seasons in Hong Kong Reveals Higher Metabolic Activity in Low-Abundance Bacteria. Environ Sci Technol 2021; 55:249-259. [PMID: 33346641 DOI: 10.1021/acs.est.0c06201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
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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Affiliation(s)
- You Zhou
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Yonghang Lai
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Jimmy C K Tong
- Building Sustainability Group, Arup, Hong Kong SAR, China
| | - Ian A Ridley
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
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10
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Zhou Y, Lai Y, Tong X, Leung MHY, Tong JCK, Ridley IA, Lee PKH. Airborne Bacteria in Outdoor Air and Air of Mechanically Ventilated Buildings at City Scale in Hong Kong across Seasons. Environ Sci Technol 2020; 54:11732-11743. [PMID: 32852192 DOI: 10.1021/acs.est.9b07623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
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 PM2.5 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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Affiliation(s)
- You Zhou
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Yonghang Lai
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Jimmy C K Tong
- Building Sustainability Group, Arup, Kowloon, Hong Kong SAR, China
| | - Ian A Ridley
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
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11
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Leung MHY, Tong X, Bastien P, Guinot F, Tenenhaus A, Appenzeller BMR, Betts RJ, Mezzache S, Li J, Bourokba N, Breton L, Clavaud C, Lee PKH. Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants. Microbiome 2020; 8:100. [PMID: 32591010 PMCID: PMC7320578 DOI: 10.1186/s40168-020-00874-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/20/2020] [Indexed: 05/25/2023]
Abstract
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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Affiliation(s)
- Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | | | - Florent Guinot
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Arthur Tenenhaus
- CentraleSupelec-L2S-Laboratoire des signaux et systèmes, Brain and Spine Institute, Université Paris-Sud, Orsay, France
| | | | | | | | - Jing Li
- L’Oréal Research and Innovation, Pudong, China
| | | | - Lionel Breton
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Cécile Clavaud
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
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12
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Kim Y, Leung MHY, Kwok W, Fournié G, Li J, Lee PKH, Pfeiffer DU. Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome. Anim Microbiome 2020; 2:4. [PMID: 33500005 PMCID: PMC7807453 DOI: 10.1186/s42523-020-0022-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 01/29/2020] [Indexed: 12/21/2022] Open
Abstract
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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Affiliation(s)
- Younjung Kim
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Wendy Kwok
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Guillaume Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.,School of Data Science, City University of Hong Kong, Hong Kong, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Dirk U Pfeiffer
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.,Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
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13
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Gomez-Silvan C, Leung MHY, Grue KA, Kaur R, Tong X, Lee PKH, Andersen GL. A comparison of methods used to unveil the genetic and metabolic pool in the built environment. Microbiome 2018; 6:71. [PMID: 29661230 PMCID: PMC5902888 DOI: 10.1186/s40168-018-0453-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/28/2018] [Indexed: 05/15/2023]
Abstract
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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Affiliation(s)
- Cinta Gomez-Silvan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Katherine A. Grue
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Current affiliation: Department of Physical Therapy and Rehabilitation Science, University of California, San Francisco, CA USA
| | - Randeep Kaur
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Gary L. Andersen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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14
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Leung MHY, Tong X, Wilkins D, Cheung HHL, Lee PKH. Individual and household attributes influence the dynamics of the personal skin microbiota and its association network. Microbiome 2018; 6:26. [PMID: 29394957 PMCID: PMC5797343 DOI: 10.1186/s40168-018-0412-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 01/19/2018] [Indexed: 05/09/2023]
Abstract
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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Affiliation(s)
- Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong
| | - David Wilkins
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong
| | - Hedwig H. L. Cheung
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong
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Leung MHY, Tong X, Tong JCK, Lee PKH. Airborne bacterial assemblage in a zero carbon building: A case study. Indoor Air 2018; 28:40-50. [PMID: 28767182 DOI: 10.1111/ina.12410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/27/2017] [Indexed: 05/15/2023]
Abstract
Currently, there is little information pertaining to the airborne bacterial communities of green buildings. In this case study, the air bacterial community of a zero carbon building (ZCB) in Hong Kong was characterized by targeting the bacterial 16S rRNA gene. Bacteria associated with the outdoor environment dominated the indoor airborne bacterial assemblage, with a modest contribution from bacteria associated with human skin. Differences in overall community diversity, membership, and composition associated with short (day-to-day) and long-term temporal properties were detected, which may have been driven by specific environmental genera and taxa. Furthermore, time-decay relationships in community membership (based on unweighted UniFrac distances) and composition (based on weighted UniFrac distances) differed depending on the season and sampling location. A Bayesian source-tracking approach further supported the importance of adjacent outdoor air bacterial assemblage in sourcing the ZCB indoor bioaerosol. Despite the unique building attributes, the ZCB microbial assemblage detected and its temporal characteristics were not dissimilar to that of conventional built environments investigated previously. Future controlled experiments and microbial assemblage investigations of other ZCBs will undoubtedly uncover additional knowledge related to how airborne bacteria in green buildings may be influenced by their distinctive architectural attributes.
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Affiliation(s)
- M H Y Leung
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - X Tong
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - J C K Tong
- Building Sustainability Group, Arup, Kowloon, Hong Kong
| | - P K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
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Tong X, Leung MHY, Wilkins D, Lee PKH. City-scale distribution and dispersal routes of mycobiome in residences. Microbiome 2017; 5:131. [PMID: 28978345 PMCID: PMC5628474 DOI: 10.1186/s40168-017-0346-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 09/20/2017] [Indexed: 05/10/2023]
Abstract
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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Affiliation(s)
- Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - David Wilkins
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
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Abstract
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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Affiliation(s)
- David Wilkins
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong, Special Administrative Region of China
| | - Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong, Special Administrative Region of China
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong, Special Administrative Region of China
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Leung MHY, Chan KCK, Lee PKH. Skin fungal community and its correlation with bacterial community of urban Chinese individuals. Microbiome 2016; 4:46. [PMID: 27558504 PMCID: PMC4997687 DOI: 10.1186/s40168-016-0192-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/17/2016] [Indexed: 05/17/2023]
Abstract
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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Affiliation(s)
- Marcus H. Y. Leung
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | | | - Patrick K. H. Lee
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
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Leung MHY, Lee PKH. The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review. Microbiome 2016; 4:21. [PMID: 27216717 PMCID: PMC4877933 DOI: 10.1186/s40168-016-0165-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/11/2016] [Indexed: 05/10/2023]
Abstract
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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Affiliation(s)
- Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, B5423-AC1 Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, B5423-AC1 Hong Kong
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Leung MHY, Wilkins D, Lee PKH. Erratum: Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups. Sci Rep 2016; 6:21355. [PMID: 26914663 PMCID: PMC4767136 DOI: 10.1038/srep21355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Leung MHY, Wilkins D, Lee PKH. Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups. Sci Rep 2015; 5:11845. [PMID: 26177982 PMCID: PMC4503953 DOI: 10.1038/srep11845] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/08/2015] [Indexed: 02/07/2023] Open
Abstract
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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Affiliation(s)
- Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - David Wilkins
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong
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Leung MHY, Oriyo NM, Gillespie SH, Charalambous BM. The adaptive potential during nasopharyngeal colonisation of Streptococcus pneumoniae. Infect Genet Evol 2011; 11:1989-95. [PMID: 21925618 DOI: 10.1016/j.meegid.2011.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 08/31/2011] [Accepted: 09/03/2011] [Indexed: 10/17/2022]
Abstract
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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Affiliation(s)
- Marcus H Y Leung
- Centre for Clinical Microbiology, University College London Medical School, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
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