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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. ENVIRONMENTAL SCIENCE & TECHNOLOGY 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] [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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Sun X, Hu YH, Wang J, Fang C, Li J, Han M, Wei X, Zheng H, Luo X, Jia Y, Gong M, Xiao L, Song Z. Efficient and stable metabarcoding sequencing data using a DNBSEQ-G400 sequencer validated by comprehensive community analyses. GIGABYTE 2021; 2021:gigabyte16. [PMID: 36824325 PMCID: PMC9632034 DOI: 10.46471/gigabyte.16] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/18/2021] [Indexed: 11/09/2022] Open
Abstract
Metabarcoding is a widely used method for fast characterization of microbial communities in complex environmental samples. However, the selction of sequencing platform can have a noticeable effect on the estimated community composition. Here, we evaluated the metabarcoding performance of a DNBSEQ-G400 sequencer developed by MGI Tech using 16S and internal transcribed spacer (ITS) markers to investigate bacterial and fungal mock communities, as well as the ITS2 marker to investigate the fungal community of 1144 soil samples, with additional technical replicates. We show that highly accurate sequencing of bacterial and fungal communities is achievable using DNBSEQ-G400. Measures of diversity and correlation from soil metabarcoding showed that the results correlated highly with those of different machines of the same model, as well as between different sequencing modes (single-end 400 bp and paired-end 200 bp). Moderate, but significant differences were observed between results produced with different sequencing platforms (DNBSEQ-G400 and MiSeq); however, the highest differences can be caused by selecting different primer pairs for PCR amplification of taxonomic markers. These differences suggested that care is needed while jointly analyzing metabarcoding data from differenet experiments. This study demonstrated the high performance and accuracy of DNBSEQ-G400 for short-read metabarcoding of microbial communities. Our study also produced datasets to allow further investigation of microbial diversity.
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Affiliation(s)
| | - Yue-Hua Hu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | | | - Chao Fang
- BGI-Shenzhen, Shenzhen 518083, China.,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiguang Li
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Mo Han
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Haotian Zheng
- BGI-Shenzhen, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Xiaoqing Luo
- BGI-Shenzhen, Shenzhen 518083, China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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Size resolved characteristics of urban and suburban bacterial bioaerosols in Japan as assessed by 16S rRNA amplicon sequencing. Sci Rep 2020; 10:12406. [PMID: 32699373 PMCID: PMC7376176 DOI: 10.1038/s41598-020-68933-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/03/2020] [Indexed: 02/01/2023] Open
Abstract
To study the size-resolved characteristics of airborne bacterial community composition, diversity, and abundance, outdoor aerosol samples were analysed by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing with Illumina MiSeq. The samples were collected using size-resolved samplers between August and October 2016, at a suburban site in Toyama City and an urban site in Yokohama City, Japan. The bacterial communities were found to be dominated by Actinobacteria, Firmicutes, and Proteobacteria. At the genus level, we found a high abundance of human skin-associated bacteria, such as Propionibacterium, Staphylococcus, and Corynebacterium, in the urban site. Whereas, a high abundance of bacteria associated with soil and plants, such as Methylobacterium and Sphingomonas, was observed in the suburban site. Furthermore, our data revealed a shift in the bacterial community structure, diversity, and abundance of total bacteria at a threshold of 1.1-µm diameter. Interestingly, we observed that Legionella spp., the causal agents of legionellosis in humans, were mainly detected in > 2.1 µm coarse particles. Our data indicate that local environmental factors including built environments could influence the outdoor airborne bacterial community at each site. These results provide a basis for understanding the size-resolved properties of bacterial community composition, diversity, and abundance in outdoor aerosol samples and their potential influence on human health.
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Abstract
Airborne microorganisms are very difficult to assess accurately under field conditions owing to differences in the sample collection efficiency of the selected sampler and variations in DNA extraction efficiencies. Consequently, bioaerosol abundance and biodiversity can be underestimated, making it more difficult to link specific bioaerosol components to diseases and human health risk. Owing to the low biomass in air samples, it remains a challenge to obtain a representative microbiological sample to recover sufficient DNA for downstream analyses. Improved sampling methods are particularly crucial, especially for investigating viral communities, owing to the extremely low biomass of viral particles in the air compared with other environments. Without detailed information about sampling, characterization and enumeration techniques, interpretation of exposure level is very difficult. Despite this, bioaerosol research has been enhanced by molecular tools, especially next-generation sequencing approaches that have allowed faster and more detailed characterization of air samples.
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Li H, Zhou XY, Yang XR, Zhu YG, Hong YW, Su JQ. Spatial and seasonal variation of the airborne microbiome in a rapidly developing city of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 665:61-68. [PMID: 30772579 DOI: 10.1016/j.scitotenv.2019.01.367] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/21/2019] [Accepted: 01/28/2019] [Indexed: 05/04/2023]
Abstract
Exposure to airborne microbes (AM) can affect the human microbiome and has various consequences for human health. Investigating the profiles of AM and the potential bacterial pathogens within, along with the factors influencing their community, is pivotal for understanding the impact of AM on human health. In this study, we collected AM during spring and summer from 11 sites with various levels of urbanization in the city of Xiamen, China. Bacterial community compositions of the AM were determined based on 16S rRNA gene amplicon sequencing. Firmicutes and Proteobacteria were the predominating phyla in the airborne bacterial communities, and a higher (P < 0.05) diversity of AM was found during the summer as compared to the spring. Significant differences in the community structure of the AM and the potential bacterial pathogens within airborne microbes were observed among the seasons and the sites with different levels of urbanization. Increases and/or decreases in the abundance of Bacillus and Acinetobacter could explain a major part of the variations in the AM community compositions. The proportion of potential bacterial pathogens during the summer was significantly higher (P < 0.01) than in the spring, and the relative abundance of several bacterial pathogens (i.e. Burkholderia multivoran, Enterococcus faecium and Streptococcus thermophilus) related to human diseases (39.8% of total pathogens on average) increased with increasing urbanization levels, suggesting that urbanization can increase the AM-associated human health risk.
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Affiliation(s)
- Hu Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Xin-Yuan Zhou
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China; State Key Laboratory of Urban and Regional Ecology Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - You-Wei Hong
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China.
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Espenshade J, Thijs S, Gawronski S, Bové H, Weyens N, Vangronsveld J. Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study. Front Microbiol 2019; 10:675. [PMID: 31024477 PMCID: PMC6460055 DOI: 10.3389/fmicb.2019.00675] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/18/2019] [Indexed: 12/20/2022] Open
Abstract
The aerial surfaces of plants harbor diverse communities of microorganisms. The rising awareness concerning the potential roles of these phyllosphere microbiota for airborne pollutant remediation and plant growth promotion, advocates for a better understanding of their community structure and dynamics in urban ecosystems. Here, we characterized the epiphytic microbial communities on leaves of Platanus × hispanica trees in the city centre of Hasselt (Belgium), and the nearby forest area of Bokrijk, Genk (Belgium). We compared the influences of season, site, and air pollutants concentration variations on the tree’s phyllosphere microbiome by determining the intra- and inter-individual variation in leaf bacterial communities. High-throughput amplicon sequencing of the 16S rRNA gene revealed large variation in the bacterial community structure and diversity throughout the years but also allowed to discriminate an environment effect on community assembly. Partial drivers for this environment effect on composition can be correlated with the huge differences in ultrafine particulate matter (UFP) and black carbon on the leaves. A change in bacterial community composition was noted for trees growing in the city center compared to the natural site, and also more human-associated genera were found colonizing the leaves from the city center. These integrated results offer an original and first insight in the Platanus phyllomicrobiota, which can offer new opportunities to use phyllosphere microorganisms to enhance air pollution degradation.
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Affiliation(s)
- Jordan Espenshade
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Sofie Thijs
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Stanislaw Gawronski
- Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Hannelore Bové
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium.,Centre for Surface Chemistry and Catalysis, KU Leuven, Leuven, Belgium
| | - Nele Weyens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Department of Plant Physiology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Lublin, Poland
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Leung MH, Tong X, Lee PK. Indoor Microbiome and Airborne Pathogens. COMPREHENSIVE BIOTECHNOLOGY 2019. [PMCID: PMC7151935 DOI: 10.1016/b978-0-444-64046-8.00477-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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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] [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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