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

Zhou, You / Leung, Marcus H Y / Tong, Xinzhao / Lee, Justin Y Y / Lee, Patrick K H

Environmental science & technology

2021 Volume 55, Issue 22, Page(s) 15051–15062

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 ... ...

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.
MeSH term(s)	Bacteria/genetics ; Cities ; Housing ; Microbiota ; RNA, Ribosomal, 16S/genetics
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2021-11-05
Publishing country	United States
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.1c03941
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching.

Wilkins, David / Tong, Xinzhao / Leung, Marcus H Y / Mason, Christopher E / Lee, Patrick K H

Microbiome

2021 Volume 9, Issue 1, Page(s) 129

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 ... ...

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.
MeSH term(s)	Bayes Theorem ; Hong Kong ; Humans ; Metagenomics ; Microbiota/genetics
Language	English
Publishing date	2021-06-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-021-01082-1
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Article: City-Scale Meta-Analysis of Indoor Airborne Microbiota Reveals that Taxonomic and Functional Compositions Vary with Building Types

Zhou, You / Leung, Marcus H. Y. / Tong, Xinzhao / Lee, Justin Y. Y. / Lee, Patrick K. H.

Environmental science & technology. 2021 Nov. 05, v. 55, no. 22

2021

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.
Keywords	biochemical pathways ; bioinformatics ; environmental science ; genes ; meta-analysis ; microorganisms ; technology
Language	English
Dates of publication	2021-1105
Size	p. 15051-15062.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5851
DOI	10.1021/acs.est.1c03941
Database	NAL-Catalogue (AGRICOLA)

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

Leung, Marcus H Y / Tong, Xinzhao / Shen, Zhiyong / Du, Shicong / Bastien, Philippe / Appenzeller, Brice M R / Betts, Richard J / Mezzache, Sakina / Bourokba, Nasrine / Cavusoglu, Nukhet / Aguilar, Luc / Misra, Namita / Clavaud, Cécile / Lee, Patrick K H

Microbiome

2023 Volume 11, Issue 1, Page(s) 124

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 ... ...

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.
MeSH term(s)	Polycyclic Aromatic Hydrocarbons ; Skin/chemistry ; Air Pollutants/analysis ; Biodegradation, Environmental ; Microbiota/genetics ; Environmental Monitoring
Chemical Substances	Polycyclic Aromatic Hydrocarbons ; Air Pollutants
Language	English
Publishing date	2023-06-01
Publishing country	England
Document type	Video-Audio Media ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-023-01564-4
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Article ; Online: Microbiota fingerprints lose individually identifying features over time.

Wilkins, David / Leung, Marcus H Y / Lee, Patrick K H

Microbiome

2017 Volume 5, Issue 1, Page(s) 1

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 ... ...

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.
MeSH term(s)	Air Microbiology ; DNA Fingerprinting ; Data Accuracy ; Family Characteristics ; Forensic Sciences/methods ; Humans ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; Skin/microbiology ; Surface Properties ; Time Factors
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2017-01-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-016-0209-7
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Article ; Online: 6.08 Indoor Microbiome and Airborne Pathogens

Leung, Marcus H.Y. / Tong, Xinzhao / Lee, Patrick K.H.

Comprehensive Biotechnology

Abstract: Abstract Individuals spend a majority of their time in indoor or built environments (BEs), where they are exposed to a diverse community of co-existing microorganisms. These microorganisms constitute the BE microbiome. While predominantly consisting of ... ...

Abstract	Abstract Individuals spend a majority of their time in indoor or built environments (BEs), where they are exposed to a diverse community of co-existing microorganisms. These microorganisms constitute the BE microbiome. While predominantly consisting of commensal microorganisms, the BE microbiome also contains pathogens that may be transmitted to and between indoor occupants. Therefore, characterization of the BE microbiome and understanding how different factors affect the BE microbiome will enable building scientists to assess health risks associated with indoor microbial exposure and manipulate BE conditions to maximize the health and well-being of occupants. We provide an overview of various aspects of the BE microbiome, including the importance of understanding the indoor microbiome from ecological and clinical perspectives, the history behind BE microbiome research, current laboratory, statistical, and bioinformatic methodologies and considerations in BE microbiome research, the different BE microbiome components and factors that shape this microbiome, the risks of pathogen transmission within BEs, and future directions in BE microbiome research. Some of the most recent and cutting-edge research works are described here, with the aim of providing a comprehensive and up-to-date account of the key findings within the field of indoor microbiology.
Keywords	covid19
Publisher	Elsevier; PMC
Document type	Article ; Online
DOI	10.1016/b978-0-444-64046-8.00477-8
Database	COVID19

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Article ; Online: Indoor Microbiome and Airborne Pathogens

Leung, Marcus H.Y. / Tong, Xinzhao / Lee, Patrick K.H.

Comprehensive Biotechnology

Abstract: Individuals spend a majority of their time in indoor or built environments (BEs), where they are exposed to a diverse community of co-existing microorganisms. These microorganisms constitute the BE microbiome. While predominantly consisting of commensal ... ...

Abstract	Individuals spend a majority of their time in indoor or built environments (BEs), where they are exposed to a diverse community of co-existing microorganisms. These microorganisms constitute the BE microbiome. While predominantly consisting of commensal microorganisms, the BE microbiome also contains pathogens that may be transmitted to and between indoor occupants. Therefore, characterization of the BE microbiome and understanding how different factors affect the BE microbiome will enable building scientists to assess health risks associated with indoor microbial exposure and manipulate BE conditions to maximize the health and well-being of occupants. We provide an overview of various aspects of the BE microbiome, including the importance of understanding the indoor microbiome from ecological and clinical perspectives, the history behind BE microbiome research, current laboratory, statistical, and bioinformatic methodologies and considerations in BE microbiome research, the different BE microbiome components and factors that shape this microbiome, the risks of pathogen transmission within BEs, and future directions in BE microbiome research. Some of the most recent and cutting-edge research works are described here, with the aim of providing a comprehensive and up-to-date account of the key findings within the field of indoor microbiology.
Keywords	covid19
Publisher	Elsevier; PMC
Document type	Article ; Online
DOI	10.1016/b978-0-444-64046-8.00477-8
Database	COVID19

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

Tong, Xinzhao / Leung, Marcus H Y / Shen, Zhiyong / Lee, Justin Y Y / Mason, Christopher E / Lee, Patrick K H

Microbiome

2021 Volume 9, Issue 1, Page(s) 213

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 ... ...

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.
MeSH term(s)	Bacteria/genetics ; Metagenome ; Metagenomics ; Microbiota/genetics ; Proteobacteria/genetics
Language	English
Publishing date	2021-11-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-021-01166-y
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Article ; Online: Erratum: Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups.

Leung, Marcus H Y / Wilkins, David / Lee, Patrick K H

Scientific reports

2016 Volume 6, Page(s) 21355

Language	English
Publishing date	2016-02-25
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep21355
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Article ; Online: The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review.

Leung, Marcus H Y / Lee, Patrick K H

Microbiome

2016 Volume 4, Issue 1, Page(s) 21

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 ... ...

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.
MeSH term(s)	Air Microbiology ; Air Pollutants/analysis ; Air Pollution, Indoor/analysis ; Bacteria/classification ; Bacteria/genetics ; Base Sequence ; Environment ; Geography ; High-Throughput Nucleotide Sequencing ; Humans ; Intestines/microbiology ; Microbiota/genetics ; Mouth/microbiology ; Sequence Analysis, DNA ; Skin/microbiology
Chemical Substances	Air Pollutants
Language	English
Publishing date	2016--24
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-016-0165-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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