1
|
Wu J, Hu Y, Perlin MH, Danko D, Lu J, Oliveira M, Werner J, Zambrano MM, Sierra MA, Osuolale OO, Łabaj P, Rascovan N, Hazrin-Chong NH, Jang S, Suzuki H, Nieto-Caballero M, Prithiviraj B, Lee PKH, Chmielarczyk A, Różańska A, Zhao Y, Wang L, Mason CE, Shi T. Landscape of global urban environmental resistome and its association with local socioeconomic and medical status. Sci China Life Sci 2024:10.1007/s11427-023-2504-1. [PMID: 38489008 DOI: 10.1007/s11427-023-2504-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/06/2023] [Indexed: 03/17/2024]
Abstract
Antimicrobial resistance (AMR) poses a critical threat to global health and development, with environmental factors-particularly in urban areas-contributing significantly to the spread of antibiotic resistance genes (ARGs). However, most research to date has been conducted at a local level, leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments. To address this issue, we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples, which were collected by the MetaSUB International Consortium involving diverse urban environments in 60 cities of 27 countries, utilizing a deep-learning based methodology. Our findings demonstrated the strong geographical specificity of urban environmental resistome, and their correlation with various local socioeconomic and medical conditions. We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters (BGCs) across different countries, and discovered that the urban environment represents a rich source of novel antibiotics. Our study provides a comprehensive overview of the global urban environmental resistome, and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.
Collapse
Affiliation(s)
- Jun Wu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yige Hu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, 40292, USA
| | - David Danko
- Weill Cornell Medicine, New York, 10065, USA
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, 10065, USA
| | - Jun Lu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Manuela Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4050-290, Portugal
- Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, 4200-465, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, 4050-290, Portugal
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Wächterstraße 76, 72074, Tübingen, Germany
| | | | - Maria A Sierra
- Weill Cornell Medicine, New York, 10065, USA
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, 10065, USA
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, 340271, Nigeria
| | - Paweł Łabaj
- Maopolska Centre of Biotechnology, Jagiellonian University, Kraków, 30-005, Poland
| | - Nicolás Rascovan
- Aix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, 83041, France
| | - Nur Hazlin Hazrin-Chong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia UKM, 43600, Bangi, Selangor, Malaysia
| | - Soojin Jang
- Institut Pasteur Korea, Seoul, 13488, Republic of Korea
| | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
| | - Marina Nieto-Caballero
- Civil, Environmental and Architectural Department, University of Colorado at Boulder, Boulder, 80303, USA
| | | | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, 999077, China
| | - Agnieszka Chmielarczyk
- Department of Microbiology, Faculty of Medicine, Jagiellonian University, Krakow, 30-005, Poland
| | - Anna Różańska
- Department of Microbiology, Faculty of Medicine, Jagiellonian University, Krakow, 30-005, Poland
| | - Yongxiang Zhao
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning, 530021, China.
| | - Lan Wang
- College of Architecture and Urban Planning, Tongji University, Shanghai, 200092, China.
| | - Christopher E Mason
- Weill Cornell Medicine, New York, 10065, USA.
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, 10065, USA.
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
| |
Collapse
|
2
|
Bao Y, Ruan Y, Wu J, Wang WX, Leung KMY, Lee PKH. Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments. Environ Sci Technol 2024; 58:780-794. [PMID: 38118133 DOI: 10.1021/acs.est.3c08076] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 12/22/2023]
Abstract
Assessing the impacts of cumulative anthropogenic disturbances on estuarine ecosystem health is challenging. Using spatially distributed sediments from the Pearl River Estuary (PRE) in southern China, which are significantly influenced by anthropogenic activities, we demonstrated that metagenomics-based surveillance of benthic microbial communities is a robust approach to assess anthropogenic impacts on estuarine benthic ecosystems. Correlational and threshold analyses between microbial compositions and environmental conditions indicated that anthropogenic disturbances in the PRE sediments drove the taxonomic and functional variations in the benthic microbial communities. An ecological community threshold of anthropogenic disturbances was identified, which delineated the PRE sediments into two groups (H and L) with distinct taxa and functional traits. Group H, located nearshore and subjected to a higher level of anthropogenic disturbances, was enriched with pollutant degraders, putative human pathogens, fecal pollution indicators, and functional traits related to stress tolerance. In contrast, Group L, located offshore and subjected to a lower level of anthropogenic disturbances, was enriched with halotolerant and oligotrophic taxa and functional traits related to growth and resource acquisition. The machine learning random forest model identified a number of taxonomic and functional indicators that could differentiate PRE sediments between Groups H and L. The identified ecological community threshold and microbial indicators highlight the utility of metagenomics-based microbial surveillance in assessing the adverse impacts of anthropogenic disturbances in estuarine sediments, which can assist environmental management to better protect ecosystem health.
Collapse
Affiliation(s)
- Yingyu Bao
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| | - Yuefei Ruan
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Jiaxue Wu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Kenneth M Y Leung
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, 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
| |
Collapse
|
3
|
Yu J, Lee JYY, Tang SN, Lee PKH. Niche differentiation in microbial communities with stable genomic traits over time in engineered systems. ISME J 2024; 18:wrae042. [PMID: 38470313 PMCID: PMC10987969 DOI: 10.1093/ismejo/wrae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/02/2023] [Revised: 02/21/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024]
Abstract
Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models to investigate the niches of microbes in communities and the temporal succession patterns of community compositions. High-quality representative metagenome-assembled genomes revealed that taxonomic, functional, and trait-based compositions were strongly shaped by environmental selection, with replacement processes primarily driving variations in taxonomic and functional compositions. Plant-specific indicators were associated with system environmental conditions and exhibited strong determinism and trajectory directionality over time. The partitioning of microbes in a co-abundance network according to groups of plant-specific indicators, together with significant between-group differences in genomic traits, indicated the occurrence of niche differentiation. The indicators of the treatment plant with rich nutrient input and high substrate removal efficiency exhibited a faster predicted growth rate, lower guanine-cytosine content, smaller genome size, and higher codon usage bias than the indicators of the other plants. In individual plants, taxonomic composition displayed a more rapid temporal succession than functional and trait-based compositions. The succession of taxonomic, functional, and trait-based compositions was correlated with the kinetics of treatment processes in the activated sludge systems. This study provides insights into ecological niches of microbes in engineered systems and succession patterns of their functions and traits, which will aid microbial community management to improve treatment performance.
Collapse
Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Kowloon, 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, Kowloon, Hong Kong SAR, China
| |
Collapse
|
4
|
Hao C, Elias JE, Lee PKH, Lam H. metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering. Microbiome 2023; 11:176. [PMID: 37550758 PMCID: PMC10405559 DOI: 10.1186/s40168-023-01602-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/26/2022] [Accepted: 06/18/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND The high diversity and complexity of the microbial community make it a formidable challenge to identify and quantify the large number of proteins expressed in the community. Conventional metaproteomics approaches largely rely on accurate identification of the MS/MS spectra to their corresponding short peptides in the digested samples, followed by protein inference and subsequent taxonomic and functional analysis of the detected proteins. These approaches are dependent on the availability of protein sequence databases derived either from sample-specific metagenomic data or from public repositories. Due to the incompleteness and imperfections of these protein sequence databases, and the preponderance of homologous proteins expressed by different bacterial species in the community, this computational process of peptide identification and protein inference is challenging and error-prone, which hinders the comparison of metaproteomes across multiple samples. RESULTS We developed metaSpectraST, an unsupervised and database-independent metaproteomics workflow, which quantitatively profiles and compares metaproteomics samples by clustering experimentally observed MS/MS spectra based on their spectral similarity. We applied metaSpectraST to fecal samples collected from littermates of two different mother mice right after weaning. Quantitative proteome profiles of the microbial communities of different mice were obtained without any peptide-spectrum identification and used to evaluate the overall similarity between samples and highlight any differentiating markers. Compared to the conventional database-dependent metaproteomics analysis, metaSpectraST is more successful in classifying the samples and detecting the subtle microbiome changes of mouse gut microbiomes post-weaning. metaSpectraST could also be used as a tool to select the suitable biological replicates from samples with wide inter-individual variation. CONCLUSIONS metaSpectraST enables rapid profiling of metaproteomic samples quantitatively, without the need for constructing the protein sequence database or identification of the MS/MS spectra. It maximally preserves information contained in the experimental MS/MS spectra by clustering all of them first and thus is able to better profile the complex microbial communities and highlight their functional changes, as compared with conventional approaches. tag the videobyte in this section as ESM4 Video Abstract.
Collapse
Affiliation(s)
- Chunlin Hao
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- 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
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| |
Collapse
|
5
|
Liu Y, Lee PKH, Nah T. Emerging investigator series: aqueous photooxidation of live bacteria with hydroxyl radicals under cloud-like conditions: insights into the production and transformation of biological and organic matter originating from bioaerosols. Environ Sci Process Impacts 2023; 25:1150-1168. [PMID: 37376782 DOI: 10.1039/d3em00090g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Live bacteria in clouds are exposed to free radicals such as the hydroxyl radical (˙OH), which is the main driver of many photochemical processes. While the ˙OH photooxidation of organic matter in clouds has been widely studied, equivalent investigations on the ˙OH photooxidation of bioaerosols are limited. Little is known about the daytime encounters between ˙OH and live bacteria in clouds. Here we investigated the aqueous ˙OH photooxidation of four bacterial strains, B. subtilis, P. putida, E. hormaechei B0910, and E. hormaechei pf0910, in microcosms composed of artificial cloud water that mimicked the chemical composition of cloud water in Hong Kong. The survival rates for the four bacterial strains decreased to zero within 6 hours during exposure to 1 × 10-16 M of ˙OH under artificial sunlight. Bacterial cell damage and lysis released biological and organic compounds, which were subsequently oxidized by ˙OH. The molecular weights of some of these biological and organic compounds were >50 kDa. The O/C, H/C, and N/C ratios increased at the initial onset of photooxidation. As the photooxidation progressed, there were few changes in the H/C and N/C, whereas the O/C continued to increase for hours after all the bacterial cells had died. The increase in the O/C was due to functionalization and fragmentation reactions, which increased the O content and decreased the C content, respectively. In particular, fragmentation reactions played key roles in transforming biological and organic compounds. Fragmentation reactions cleaved the C-C bonds of carbon backbones of higher molecular weight proteinaceous-like matter to form a variety of lower molecular weight compounds, including HULIS of molecular weight <3 kDa and highly oxygenated organic compounds of molecular weight <1.2 kDa. Overall, our results provided new insights at the process level into how daytime reactive interactions between live bacteria and ˙OH in clouds contribute to the formation and transformation of organic matter.
Collapse
Affiliation(s)
- Yushuo Liu
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- City University of Hong Kong Shenzhen Research Institute, Nanshan District, Shenzhen, China
| | - 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
| | - Theodora Nah
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- City University of Hong Kong Shenzhen Research Institute, Nanshan District, Shenzhen, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
6
|
Liang Z, Zhou L, Li X, Cuevas RAI, Tang R, Li M, Cheng C, Chu Y, Lee PKH, Lai ACK, Chan CK. Secondary aerosol formation in incense burning particles by O 3 and OH oxidation via single particle mixing state analysis. Sci Total Environ 2023:164942. [PMID: 37329918 DOI: 10.1016/j.scitotenv.2023.164942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/31/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
Incense burning is a common religious activity that emits abundant gaseous and particulate pollutants into the atmosphere. During their atmospheric lifetime, these gases and particles are subjected to oxidation, leading to the formation of secondary pollutants. We examined the oxidation of incense burning plumes under O3 exposure and dark condition using an oxidation flow reactor connected to a single particle aerosol mass spectrometer (SPAMS). Nitrate formation was observed in incense burning particles, mainly attributable to the ozonolysis of nitrogen-containing organic compounds. With UV on, nitrate formation was significantly enhanced, likely due to HNO3/HNO2/NOx uptake triggered by OH chemistry, which is more effective than ozone oxidation. The extent of nitrate formation is insensitive to O3 and OH exposure, possibly due to the diffusion limitation on interfacial uptake. The O3-UV-aged particles are more oxygenated and functionalized than O3-Dark-aged particles. Oxalate and malonate, two typical secondary organic aerosol (SOA) components, were found in O3-UV-aged particles. Our work reveals that nitrate, accompanied by SOA, can rapidly form in incense-burning particles upon photochemical oxidation in the atmosphere, which could deepen our understanding of air pollution caused by religious activities.
Collapse
Affiliation(s)
- Zhancong Liang
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China; City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Liyuan Zhou
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China; City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Xinyue Li
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Rosemarie Ann Infante Cuevas
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China; City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Rongzhi Tang
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China; City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Mei Li
- Institute of Mass Spectrometry and Atmospheric Environment, Guangdong Provincial Engineering Research Center for On-line Source Apportionment System of Air Pollution, Jinan University, Guangzhou 510632, China; Guangdong-Hongkong-Macau Joint Laboratory of Collaborative Innovation for Environmental Quality, Guangzhou 510632, China
| | - Chunlei Cheng
- Institute of Mass Spectrometry and Atmospheric Environment, Guangdong Provincial Engineering Research Center for On-line Source Apportionment System of Air Pollution, Jinan University, Guangzhou 510632, China; Guangdong-Hongkong-Macau Joint Laboratory of Collaborative Innovation for Environmental Quality, Guangzhou 510632, China
| | - Yangxi Chu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Alvin C K Lai
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Chak K Chan
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China; City University of Hong Kong Shenzhen Research Institute, Shenzhen, China; Low-Carbon and Climate Impact Research Centre, City University of Hong Kong, Hong Kong, China.
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Du S, Tong X, Lai ACK, Chan CK, Mason CE, Lee PKH. Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution. Nat Commun 2023; 14:2676. [PMID: 37160974 PMCID: PMC10169181 DOI: 10.1038/s41467-023-38400-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
Viruses in built environments (BEs) raise public health concerns, yet they are generally less studied than bacteria. To better understand viral dynamics in BEs, this study assesses viromes from 11 habitats across four types of BEs with low to high occupancy. The diversity, composition, metabolic functions, and lifestyles of the viromes are found to be habitat dependent. Caudoviricetes species are ubiquitous on surface habitats in the BEs, and some of them are distinct from those present in other environments. Antimicrobial resistance genes are identified in viruses inhabiting surfaces frequently touched by occupants and in viruses inhabiting occupants' skin. Diverse CRISPR/Cas immunity systems and anti-CRISPR proteins are found in bacterial hosts and viruses, respectively, consistent with the strongly coupled virus-host links. Evidence of viruses potentially aiding host adaptation in a specific-habitat manner is identified through a unique gene insertion. This work illustrates that virus-host interactions occur frequently in BEs and that viruses are integral members of BE microbiomes.
Collapse
Affiliation(s)
- Shicong Du
- 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, P. R. China
| | - Alvin C K Lai
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Chak K Chan
- 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.
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Lee JYY, Miao Y, Chau RLT, Hernandez M, Lee PKH. Artificial intelligence-based prediction of indoor bioaerosol concentrations from indoor air quality sensor data. Environ Int 2023; 174:107900. [PMID: 37012194 DOI: 10.1016/j.envint.2023.107900] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 01/16/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
Exposure to bioaerosols in indoor environments, especially public venues that have a high occupancy and poor ventilation, is a serious public health concern. However, it remains challenging to monitor and determine real-time or predict near-future concentrations of airborne biological matter. In this study, we developed artificial intelligence (AI) models using physical and chemical data from indoor air quality sensors and physical data from ultraviolet light-induced fluorescence observations of bioaerosols. This enabled us to effectively estimate the bioaerosol (bacteria-, fungi- and pollen-like particle) and 2.5-µm and 10-µm particulate matter (PM2.5 and PM10) on a real-time and near-future (≤60 min) basis. Seven AI models were developed and evaluated using measured data from an occupied commercial office and a shopping mall. A long short-term memory model required a relatively short training time and gave the highest prediction accuracy of ∼ 60 %-80 % for bioaerosols and ∼ 90 % for PM on the testing and time series datasets from the two venues. This work demonstrates how AI-based methods can leverage bioaerosol monitoring into predictive scenarios that building operators can use for improving indoor environmental quality in near real-time.
Collapse
Affiliation(s)
- Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yanhao Miao
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ricky L T Chau
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Mark Hernandez
- Civil, Environmental and Architectural Engineering Department, Environmental Engineering Program, University of Colorado, Boulder, CO, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong Special Administrative Region, China.
| |
Collapse
|
11
|
Yu J, Tang SN, Lee PKH. Universal Dynamics of Microbial Communities in Full-Scale Textile Wastewater Treatment Plants and System Prediction by Machine Learning. Environ Sci Technol 2023; 57:3345-3356. [PMID: 36795777 DOI: 10.1021/acs.est.2c08116] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The performance of full-scale biological wastewater treatment plants (WWTPs) depends on the operational and environmental conditions of treatment systems. However, we do not know how much these conditions affect microbial community structures and dynamics across systems over time and predictability of the treatment performance. For over a year, the microbial communities of four full-scale WWTPs processing textile wastewater were monitored. During temporal succession, the environmental conditions and system treatment performance were the main drivers, which explained up to 51% of community variations within and between all plants based on the multiple regression models. We identified the universality of community dynamics in all systems using the dissimilarity-overlap curve method, with the significant negative slopes suggesting that the communities containing the same taxa from different plants over time exhibited a similar composition dynamic. The Hubbell neutral theory and the covariance neutrality test indicated that all systems had a dominant niche-based assembly mechanism, supporting that the communities had a similar composition dynamic. Phylogenetically diverse biomarkers for the system conditions and treatment performance were identified by machine learning. Most of the biomarkers (83%) were classified as generalist taxa, and the phylogenetically related biomarkers responded similarly to the system conditions. Many biomarkers for treatment performance perform functions that are crucial for wastewater treatment processes (e.g., carbon and nutrient removal). This study clarifies the relationships between community composition and environmental conditions in full-scale WWTPs over time.
Collapse
Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Hong Kong SAR, China
| | - 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
| |
Collapse
|
12
|
Lin H, Lao JY, Wang Q, Ruan Y, He Y, Lee PKH, Leung KMY, Lam PKS. Per- and polyfluoroalkyl substances in the atmosphere of waste management infrastructures: Uncovering secondary fluorotelomer alcohols, particle size distribution, and human inhalation exposure. Environ Int 2022; 167:107434. [PMID: 35914336 DOI: 10.1016/j.envint.2022.107434] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/22/2022] [Revised: 07/08/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) have been applied in numerous industrial and consumer products, the majority of which flow into waste management infrastructures (WMIs) at the end of their life cycles, but little is known about atmospheric releases of PFAS from these facilities. In this study, we addressed this key issue by investigating 49 PFAS, including 23 ionic and 26 neutral and precursor PFAS, in the potential sources (n = 4; within or adjacent to WMIs) and reference sites (n = 2; coastal and natural reserve sites) in urban and rural areas of Hong Kong, China. Duplicate samples of air and size-segregated particulate matter were collected for 48 h continuously using a 11-stage Micro-Orifice Uniform Deposit Impactor (MOUDI). In general, fluorotelomer alcohols (FTOHs) and perfluoroalkane sulfonamides were the predominant PFAS classes found across sampling sites. We also demonstrated the release of several less frequently observed semivolatile intermediate products (e.g., secondary FTOHs) during waste treatment. Except for perfluorooctane sulfonate, the size-segregated distributions of particulate PFAS exhibited heterogeneity across sampling sites, particularly in the WMIs, implying combined effects of sorption affinity and emission sources. A preliminary daily air emission estimation revealed that landfill was a relatively important source of PFAS relative to the wastewater treatment plant. A simplified International Commission on Radiological Protection model was used to estimate lung depositional fluxes, and the results showed that inhaled particulate PFAS were mainly deposited in the head airway while fine and ultrafine particles carried PFAS deeper into the lung alveoli. The cumulative daily inhalation dose of gaseous and particulate PFAS ranged from 81.9 to 265 pg/kg/d. In-depth research is required to understand the health effect of airborne PFAS on workers at WMIs.
Collapse
Affiliation(s)
- Huiju Lin
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China; Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Jia-Yong Lao
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China; Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Qi Wang
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China; Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Yuefei Ruan
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China; Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China.
| | - Yuhe He
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China; School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Patrick K H Lee
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China; School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Kenneth M Y Leung
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China; Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Paul K S Lam
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China; Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China; Office of the President, Hong Kong Metropolitan University, Hong Kong SAR, China.
| |
Collapse
|
13
|
Wu J, Danko D, Afshinnekoo E, Bezdan D, Bhattacharyya M, Castro-Nallar E, Chmielarczyk A, Hazrin-Chong NH, Deng Y, Dias-Neto E, Frolova A, Mason-Buck G, Iraola G, Jang S, Łabaj P, Lee PKH, Nieto-Caballero M, Osuolale OO, Ouzounis CA, Perlin MH, Prithiviraj B, Rascovan N, Różańska A, Schriml LM, Semmler T, Suzuki H, Ugalde JA, Young B, Werner J, Zambrano MM, Zhao Y, Mason C, Shi T. Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association. Environ Res 2022; 207:112183. [PMID: 34637759 DOI: 10.1016/j.envres.2021.112183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 07/16/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The co-occurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment.
Collapse
Affiliation(s)
- Jun Wu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - David Danko
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Ebrahim Afshinnekoo
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Daniela Bezdan
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, 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 Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Argentina
| | | | - Nur Hazlin Hazrin-Chong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Youping Deng
- University of Hawaii, John A. Burns School of Mecidine, USA
| | - Emmanuel Dias-Neto
- Medical Genomics Group, A.C. Camargo Cancer Center and LIM-27 Faculdade de Medicina, USP, São Paulo, Brazil
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Science of Ukraine, Ukraine
| | - Gabriella Mason-Buck
- Department of Analytical, Environmental and Forensic Sciences, King's College London, UK
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile; Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Paweł Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Poland
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marina Nieto-Caballero
- University of Colorado at Boulder, Civil, Environmental and Architectural Department, Boulder, 80303, USA
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Nigeria
| | - Christos A Ouzounis
- BCPL-CPERI, Centre for Research & Technology Hellas, Thessalonica, GR, 57001, Greece
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA
| | - Bharath Prithiviraj
- Reckitt Health, Montvale, NJ, USA; Dept. of Biology, City University of New York, Brooklyn, 11210, NY, USA
| | - Nicolás Rascovan
- Aix-Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, France
| | - Anna Różańska
- Jagiellonian University, Faculty of Medicine, Department of Microbiology, Poland
| | - Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, USA
| | | | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Germany
| | - Ben Young
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Wächterstraße 76, 72074, Tübingen, Germany
| | | | - Yongxiang Zhao
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning, 530021, China
| | - Christopher Mason
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
| |
Collapse
|
14
|
Šantl-Temkiv T, Amato P, Casamayor EO, Lee PKH, Pointing SB. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6524182. [PMID: 35137064 PMCID: PMC9249623 DOI: 10.1093/femsre/fuac009] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/31/2022] [Accepted: 02/06/2022] [Indexed: 11/30/2022] Open
Abstract
The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.
Collapse
Affiliation(s)
- Tina Šantl-Temkiv
- Department of Biology, Aarhus University, DK-8000 Aarhus, Denmark
- Stellar Astrophysics Centre, Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus, Denmark
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand, SIGMA Clermont, CNRS, Université Clermont Auvergne, 63178, Clermont-Ferrand, France
| | - Emilio O Casamayor
- Centre for Advanced Studies of Blanes, Spanish Council for Research (CSIC), 17300, Blanes, Spain
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Stephen B Pointing
- Corresponding author: Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore 138527. Tel: +65 6601 1000; E-mail:
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
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.
Collapse
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
| | | |
Collapse
|
18
|
Wang P, Zhang N, Miao T, Chan JPT, Huang H, Lee PKH, Li Y. Surface touch network structure determines bacterial contamination spread on surfaces and occupant exposure. J Hazard Mater 2021; 416:126137. [PMID: 34492926 DOI: 10.1016/j.jhazmat.2021.126137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/02/2021] [Revised: 05/08/2021] [Accepted: 05/13/2021] [Indexed: 06/13/2023]
Abstract
Fomites are known to spread infectious diseases, but their role in determining transmission risk remains unclear. The association of surface touch networks (STNs), proposed to explain this risk, with real-life surface contamination has not yet been demonstrated. To construct STNs, we collected surface touch data from 23 to 26 scholars through 2 independent experiments conducted in office spaces for 13 h each. In parallel, a tracer bacterium (Lactobacillus bulgaricus) was spread by a designated carrier in each experiment during normal activities; the subsequent extent of surface contamination was assessed using qPCR. The touch data were also analyzed using an agent-based model that predicted the observed contamination. Touching public (door handles) and hidden public (desks, chair seatbacks) surfaces that connected occupants, sparse hand-to-hand contact, and active carriers contributed significantly to contamination spread, which was also correlated with the size of the social group containing carriers. The natural and unsupervised experiments reflected realistic exposure levels of mouths (1-10 ppm of total contamination spread by one root carrier), nostrils (~1 ppm), and eyes (~0.1 ppm). We conclude that the contamination degree of known and hidden public surfaces can indicate fomite exposure risk. The social group effect could trigger superspreading events through fomite transmission.
Collapse
Affiliation(s)
- Peihua Wang
- Department of Mechanical Engineering, University of Hong Kong, Hong Kong, China
| | - Nan Zhang
- Department of Mechanical Engineering, University of Hong Kong, Hong Kong, China; Key Laboratory of Green Built Environment and Energy Efficient Technology, Beijing University of Technology, Beijing, China
| | - Te Miao
- Department of Mechanical Engineering, University of Hong Kong, Hong Kong, China
| | - Jack P T Chan
- Department of Mechanical Engineering, University of Hong Kong, Hong Kong, China
| | - Hong Huang
- Institute of Public Safety Research, Department of Engineering Physics, Tsinghua University, Beijing, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Yuguo Li
- Department of Mechanical Engineering, University of Hong Kong, Hong Kong, China; School of Public Health, University of Hong Kong, Hong Kong, China.
| |
Collapse
|
19
|
Wang L, Bian Y, Lim CK, Niu Z, Lee PKH, Chen C, Zhang L, Daoud WA, Zi Y. Tribo-charge enhanced hybrid air filter masks for efficient particulate matter capture with greatly extended service life. Nano Energy 2021; 85:106015. [PMID: 36571102 PMCID: PMC9764213 DOI: 10.1016/j.nanoen.2021.106015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 05/09/2023]
Abstract
Face masks have been an effective and indispensable personal protective measure against particulate matter pollutants and respiratory diseases, especially the novel Coronavirus disease recently. However, disposable surgical face masks suffer from low filtration efficiency for particles ranging from nano- to micro-size, and the limited service life of ~ 4 h. Here, a nano/micro fibrous hybrid air filter mask composing of electrospun nanofibrous network and poly(3,4-ethylenedioxythiophene:poly(styrenesulfonate) coated polypropylene (PP) is proposed. Furthermore, the resultant filter is supplied with tribo-charges by a freestanding sliding triboelectric nanogenerator. Through the enhanced synergistic effect of mechanical interception and electrostatic forces, the hybrid air filter demonstrates high filtration efficiency for particle size of 11.5 nm to 2.5 µm, with a 9.3-34.68% enhancement for particles of 0.3-2.5 µm compared to pristine PP, and 48-h stable filtration efficiency of 94% (0.3-0.4 µm) and 99% (1-2.5 µm) with a low pressure drop of ~110 Pa. In addition, sterilization ability of the tribo-charge enhanced air filter is demonstrated. This work provides a facile and cost-effective approach for state-of-the-art face masks toward high filtration performance of nano- to micro- particles with greatly extended service life.
Collapse
Affiliation(s)
- Lingyun Wang
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- School of Energy and Environment, City University of Hong Kong, Hong Kong, Kowloon, China
| | - Ye Bian
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- School of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Chee Kent Lim
- School of Energy and Environment, City University of Hong Kong, Hong Kong, Kowloon, China
| | - Zhuolun Niu
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, Kowloon, China
| | - Chun Chen
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Li Zhang
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Walid A Daoud
- School of Energy and Environment, City University of Hong Kong, Hong Kong, Kowloon, China
| | - Yunlong Zi
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
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.
Collapse
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.
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
Yu J, Tang SN, Lee PKH. Microbial Communities in Full-Scale Wastewater Treatment Systems Exhibit Deterministic Assembly Processes and Functional Dependency over Time. Environ Sci Technol 2021; 55:5312-5323. [PMID: 33784458 DOI: 10.1021/acs.est.0c06732] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 06/12/2023]
Abstract
Microbial communities constitute the core component of biological wastewater treatment processes. We conducted a meta-analysis based on the 16S rRNA gene of temporal samples obtained from diverse full-scale activated sludge and anaerobic digestion systems treating municipal and industrial wastewater (collected in this study and published previously) to investigate their community assembly mechanism and functional traits over time, which are not currently well understood. The influent composition was found to be the main driver of the microbial community's composition, and relatively large proportions of specialist (26.1% and 18.6%) and transient taxa (67.2% and 68.1%) were estimated in both systems. Deterministic processes, especially homogeneous selection events (accounting for >53.8% of assembly events), were consistently identified as the dominant microbial community assembly mechanisms in both systems over time. Significant and strong correlations (Pearson's r = 0.51-0.92) were detected between the dynamics of the temporal community and the functional compositions in both systems, which suggests functional dependency. In contrast, the occurrence of sludge bulking and foaming in the activated sludge system led to an increase in stochastic assembly processes (i.e., limited dispersal and undominated events), a shift toward functional redundancy and less community diversity, a decreased community niche breadth index, and a more compact co-association network. This study illustrates that the mechanism of microbial community assembly and functional traits over time can be used to diagnose system performance and provide information on potential system malfunction.
Collapse
Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Hong Kong SAR, China
| | - 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
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Nobu MK, Narihiro T, Mei R, Kamagata Y, Lee PKH, Lee PH, McInerney MJ, Liu WT. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome 2020; 8:111. [PMID: 32709258 PMCID: PMC7382037 DOI: 10.1186/s40168-020-00885-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [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: 03/27/2020] [Accepted: 06/25/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H2 transfer between organotrophs and methanogens. However, many metabolic processes are thermodynamically sensitive to H2 accumulation and can be inhibited by H2 produced from co-occurring metabolisms. Strategies for driving thermodynamically competing metabolisms in methanogenic environments remain unexplored. RESULTS To uncover how anaerobes combat this H2 conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology-methanogenic bioreactors. Through analysis of 17 anaerobic digesters, we recovered 1343 high-quality metagenome-assembled genomes and corresponding gene expression profiles for uncultured lineages spanning 66 phyla and reconstructed their metabolic capacities. We discovered that diverse uncultured populations can drive H2-sensitive metabolisms through (i) metabolic coupling with concurrent H2-tolerant catabolism, (ii) forgoing H2 generation in favor of interspecies transfer of formate and electrons (cytochrome- and pili-mediated) to avoid thermodynamic conflict, and (iii) integration of low-concentration O2 metabolism as an ancillary thermodynamics-enhancing electron sink. Archaeal populations support these processes through unique methanogenic metabolisms-highly favorable H2 oxidation driven by methyl-reducing methanogenesis and tripartite uptake of formate, electrons, and acetate. CONCLUSION Integration of omics and eco-thermodynamics revealed overlooked behavior and interactions of uncultured organisms, including coupling favorable and unfavorable metabolisms, shifting from H2 to formate transfer, respiring low-concentration O2, performing direct interspecies electron transfer, and interacting with high H2-affinity methanogenesis. These findings shed light on how microorganisms overcome a critical obstacle in methanogenic carbon cycles we had hitherto disregarded and provide foundational insight into anaerobic microbial ecology. Video Abstract.
Collapse
Affiliation(s)
- Masaru K. Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Takashi Narihiro
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, HK Hong Kong
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, Imperial College, London, UK
| | - Michael J. McInerney
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
| |
Collapse
|
27
|
Lam TYC, Mei R, Wu Z, Lee PKH, Liu WT, Lee PH. Superior resolution characterisation of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing. Water Res 2020; 178:115815. [PMID: 32380296 DOI: 10.1016/j.watres.2020.115815] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/18/2020] [Accepted: 04/08/2020] [Indexed: 05/24/2023]
Abstract
In the past decade, the characterisation of the microbial community in anaerobic digestion was primarily done by using high-throughput short-read amplicon sequencing. However, the short-read approach has inherent primer bias and low phylogenetic resolution. Our previous study using Illumina MiSeq suggested that the heterogeneity of AD microbiome was operation-driven. To advance our knowledge towards the complexity of the AD microbiome, we performed full-length 16S rRNA gene amplicon sequencing using PacBio Sequel for a more accurate phylogenetic identification. To this end, purified DNA samples from 19 global anaerobic digesters were sequenced. Sixteen methanogenic archaea were identified at the species level. Among them, Methanosarcina horonobensis and Methanosarcina flavescens had significant presence under specific operating conditions. Methanothrix concilii presented in all digesters sequenced. Unexpectedly, over 90% of the Smithella detected were closely related to alkane-degrading Smithella strains D17 and M82, not Smithella propionica. Using LEfSe and network analysis, the interspecies relationship between the fermentative and syntrophic bacteria was addressed. Comparison of the short- and long-read sequencing results were performed and discussed. From sample preparation to data analysis, this work characterised the digester microbiomes in a superior resolution.
Collapse
Affiliation(s)
- Theo Y C Lam
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Zhuoying Wu
- Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, UK.
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Lim CK, Villada JC, Chalifour A, Duran MF, Lu H, Lee PKH. Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production. Front Microbiol 2019; 10:1027. [PMID: 31143170 PMCID: PMC6520949 DOI: 10.3389/fmicb.2019.01027] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 01/31/2019] [Accepted: 04/24/2019] [Indexed: 01/05/2023] Open
Abstract
Methylorubrum extorquens (formerly Methylobacterium extorquens) AM1 is a methylotrophic bacterium with a versatile lifestyle. Various carbon sources including acetate, succinate and methanol are utilized by M. extorquens AM1 with the latter being a promising inexpensive substrate for use in the biotechnology industry. Itaconic acid (ITA) is a high-value building block widely used in various industries. Given that no wildtype methylotrophic bacteria are able to utilize methanol to produce ITA, we tested the potential of M. extorquens AM1 as an engineered host for this purpose. In this study, we successfully engineered M. extorquens AM1 to express a heterologous codon-optimized gene encoding cis-aconitic acid decarboxylase. The engineered strain produced ITA using acetate, succinate and methanol as the carbon feedstock. The highest ITA titer in batch culture with methanol as the carbon source was 31.6 ± 5.5 mg/L, while the titer and productivity were 5.4 ± 0.2 mg/L and 0.056 ± 0.002 mg/L/h, respectively, in a scaled-up fed-batch bioreactor under 60% dissolved oxygen saturation. We attempted to enhance the carbon flux toward ITA production by impeding poly-β-hydroxybutyrate accumulation, which is used as carbon and energy storage, via mutation of the regulator gene phaR. Unexpectedly, ITA production by the phaR mutant strain was not higher even though poly-β-hydroxybutyrate concentration was lower. Genome-wide transcriptomic analysis revealed that phaR mutation in the ITA-producing strain led to complex rewiring of gene transcription, which might result in a reduced carbon flux toward ITA production. Besides poly-β-hydroxybutyrate metabolism, we found evidence that PhaR might regulate the transcription of many other genes including those encoding other regulatory proteins, methanol dehydrogenases, formate dehydrogenases, malate:quinone oxidoreductase, and those synthesizing pyrroloquinoline quinone and thiamine co-factors. Overall, M. extorquens AM1 was successfully engineered to produce ITA using acetate, succinate and methanol as feedstock, further supporting this bacterium as a feasible host for use in the biotechnology industry. This study showed that PhaR could have a broader regulatory role than previously anticipated, and increased our knowledge of this regulator and its influence on the physiology of M. extorquens AM1.
Collapse
Affiliation(s)
- Chee Kent Lim
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Juan C Villada
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Annie Chalifour
- Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Maria F Duran
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Hongyuan Lu
- School of Energy and Environment, 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
| |
Collapse
|
31
|
Yeo J, Oh JI, Cheung HHL, Lee PKH, An AK. Smart Food Waste Recycling Bin (S-FRB) to turn food waste into green energy resources. J Environ Manage 2019; 234:290-296. [PMID: 30634121 DOI: 10.1016/j.jenvman.2018.12.088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 08/31/2018] [Revised: 11/28/2018] [Accepted: 12/22/2018] [Indexed: 06/09/2023]
Abstract
Effective treatment of food waste is inherently difficult due to several factors, including its heterogeneous composition, high moisture content, and low heating value. To address these issues, this study aims to convert food waste into an energy resource using naturally occurring fermentative microorganisms embedded in wooden biochips (bio-catalysis), utilizing a "Smart Food Waste Recycling Bin" (S-FRB) system. High-throughput 16S rRNA gene sequencing analysis identified the major aerobic and facultatively anaerobic bacteria with alpha-diversity in terms of the Phylogenetic Diversity index ranging from 40.8 (initial stage) to 24.5 (mature stage), which indicates the microbial communities are relatively homogeneous and effective for use in the S-FBR. Operational results indicated that the organic content of food waste traded in the system increased from 53% up to 72% in the final end-product and achieved a mass reduction rate of approximately 80%. The heating value of the end-product, which was 3300 kcal/kg waste when measured by the differential scanning calorimeter (DSC) method, confirmed its high potential as a biofuel. Overall, the S-FRB system presents a practical approach for food waste treatment that solves the putrescible waste problem and maximizes utility through resource circulation.
Collapse
Affiliation(s)
- Joonho Yeo
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Special Administrative Region
| | - Jeong-Ik Oh
- Environment Energy Division, Land & Housing Research Institute, Korea Land & Housing Corporation, 175, Jeonmin-dong, Yoseong-gu, Daejeon, South Korea
| | - Hedwig H L Cheung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Special Administrative Region
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Special Administrative Region
| | - Alicia Kyoungjin An
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Special Administrative Region.
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Cai M, Ng SK, Lim CK, Lu H, Jia Y, Lee PKH. Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification. Front Microbiol 2018. [PMID: 29535685 PMCID: PMC5835065 DOI: 10.3389/fmicb.2018.00280] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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] [Indexed: 12/31/2022] Open
Abstract
Nitrification plays a crucial role in global nitrogen cycling and treatment processes. However, the relationships between the nitrifier guilds of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) are still poorly understood, especially in freshwater habitats. This study examined the physiological interactions between the AOB and NOB present in a freshwater aquarium biofilter by culturing them, either together or separately, in a synthetic medium. Metagenomic and 16S rRNA gene sequencing revealed the presence and the draft genomes of Nitrosomonas-like AOB as well as Nitrobacter-like NOB in the cultures, including the first draft genome of Nitrobacter vulgaris. The nitrifiers exhibited different growth rates with different ammonium (NH4+) or nitrite concentrations (50-1,500 μM) and the growth rates were elevated under a high bicarbonate (HCO3-) concentration. The half-saturation constant (Ks for NH4+), the maximum growth rate (μmax), and the lag duration indicated a strong dependence on the synergistic relationships between the two guilds. Overall, the ecophysiological and metagenomic results in this study provided insights into the phylogeny of the key nitrifying players in a freshwater biofilter and showed that interactions between the two nitrifying guilds in a microbial community enhanced nitrification.
Collapse
Affiliation(s)
- Mingwei Cai
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Siu-Kin Ng
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Chee Kent Lim
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Hongyuan Lu
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Yangyang Jia
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Jia Y, Ng SK, Lu H, Cai M, Lee PKH. Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion. Biotechnol Biofuels 2018; 11:117. [PMID: 29713376 PMCID: PMC5911951 DOI: 10.1186/s13068-018-1121-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/16/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Although anaerobic digestion for biogas production is used worldwide in treatment processes to recover energy from carbon-rich waste such as cellulosic biomass, the activities and interactions among the microbial populations that perform anaerobic digestion deserve further investigations, especially at the population genome level. To understand the cellulosic biomass-degrading potentials in two full-scale digesters, this study examined five methanogenic enrichment cultures derived from the digesters that anaerobically digested cellulose or xylan for more than 2 years under 35 or 55 °C conditions. RESULTS Metagenomics and metatranscriptomics were used to capture the active microbial populations in each enrichment culture and reconstruct their meta-metabolic network and ecological roles. 107 population genomes were reconstructed from the five enrichment cultures using a differential coverage binning approach, of which only a subset was highly transcribed in the metatranscriptomes. Phylogenetic and functional convergence of communities by enrichment condition and phase of fermentation was observed for the highly transcribed populations in the metatranscriptomes. In the 35 °C cultures grown on cellulose, Clostridium cellulolyticum-related and Ruminococcus-related bacteria were identified as major hydrolyzers and primary fermenters in the early growth phase, while Clostridium leptum-related bacteria were major secondary fermenters and potential fatty acid scavengers in the late growth phase. While the meta-metabolism and trophic roles of the cultures were similar, the bacterial populations performing each function were distinct between the enrichment conditions. CONCLUSIONS Overall, a population genome-centric view of the meta-metabolism and functional roles of key active players in anaerobic digestion of cellulosic biomass was obtained. This study represents a major step forward towards understanding the microbial functions and interactions at population genome level during the microbial conversion of lignocellulosic biomass to methane. The knowledge of this study can facilitate development of potential biomarkers and rational design of the microbiome in anaerobic digesters.
Collapse
Affiliation(s)
- Yangyang Jia
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Siu-Kin Ng
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Hongyuan Lu
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Mingwei Cai
- 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
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Mei R, Nobu MK, Narihiro T, Kuroda K, Muñoz Sierra J, Wu Z, Ye L, Lee PKH, Lee PH, van Lier JB, McInerney MJ, Kamagata Y, Liu WT. Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome. Water Res 2017; 124:77-84. [PMID: 28750287 DOI: 10.1016/j.watres.2017.07.050] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 06/03/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 05/11/2023]
Abstract
Anaerobic digester (AD) microbiomes harbor complex, interacting microbial populations to achieve biomass reduction and biogas production, however how they are influenced by operating conditions and feed sludge microorganisms remain unclear. These were addressed by analyzing the microbial communities of 90 full-scale digesters at 51 municipal wastewater treatment plants from five countries. Heterogeneity detected in community structures suggested that no single AD microbiome could be defined. Instead, the AD microbiomes were classified into eight clusters driven by operating conditions (e.g., pretreatment, temperature range, and salinity), whereas geographic location of the digesters did not have significant impacts. Comparing digesters populations with those present in the corresponding feed sludge led to the identification of a hitherto overlooked feed-associated microbial group (i.e., the residue populations). They accounted for up to 21.4% of total sequences in ADs operated at low temperature, presumably due to ineffective digestion, and as low as 0.8% in ADs with pretreatment. Within each cluster, a core microbiome was defined, including methanogens, syntrophic metabolizers, fermenters, and the newly described residue populations. Our work provides insights into the key factors shaping full-scale AD microbiomes in a global scale, and draws attentions to the overlooked residue populations.
Collapse
Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Kyohei Kuroda
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Environmental Systems Engineering, Nagaoka University of Technology, Kami-tomioka, Niigata, Japan
| | - Julian Muñoz Sierra
- Section Sanitary Engineering, Department of Water Management, Delft University of Technology, Delft, The Netherlands
| | - Zhuoying Wu
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Lin Ye
- School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Jules B van Lier
- Section Sanitary Engineering, Department of Water Management, Delft University of Technology, Delft, The Netherlands
| | - Michael J McInerney
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
38
|
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.
Collapse
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
| |
Collapse
|
39
|
Lu H, Ng SK, Jia Y, Cai M, Lee PKH. Physiological and molecular characterizations of the interactions in two cellulose-to-methane cocultures. Biotechnol Biofuels 2017; 10:37. [PMID: 28191038 PMCID: PMC5297212 DOI: 10.1186/s13068-017-0719-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 01/27/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND The interspecies interactions in a biomethanation community play a vital role in substrate degradation and methane (CH4) formation. However, the physiological and molecular mechanisms of interaction among the microbial members of this community remain poorly understood due to the lack of an experimentally tractable model system. In this study, we successfully established two coculture models combining the cellulose-degrading bacterium Clostridium cellulovorans 743B with Methanosarcina barkeri Fusaro or Methanosarcina mazei Gö1 for the direct conversion of cellulose to CH4. RESULTS Physiological characterizations of these models revealed that the methanogens in both cocultures were able to efficiently utilize the products produced by C. cellulovorans during cellulose degradation. In particular, the simultaneous utilization of hydrogen, formate, and acetate for methanogenesis was observed in the C. cellulovorans-M. barkeri cocultures, whereas monocultures of M. barkeri were unable to grow with formate alone. Enhanced cellulose degradation was observed in both cocultures, and the CH4 yield of the C. cellulovorans-M. barkeri cocultures (0.87 ± 0.02 mol CH4/mol glucose equivalent) was among the highest compared to other coculture studies. A metabolic shift in the fermentation pattern of C. cellulovorans was observed in both cocultures. The expression levels of genes in key pathways that are important to the regulation and metabolism of the interactions in cocultures were examined by reverse transcription-quantitative PCR, and the expression profiles largely matched the physiological observations. CONCLUSIONS The physiological and molecular characteristics of the interactions of two CH4-producing cocultures are reported. Coculturing C. cellulovorans with M. barkeri or M. mazei not only enabled direct conversion of cellulose to CH4, but also stabilized pH for C. cellulovorans, resulting in a metabolic shift and enhanced cellulose degradation. This study deepens our understanding of interspecies interactions for CH4 production from cellulose, providing useful insights for assembling consortia as inocula for industrial biomethanation processes.
Collapse
Affiliation(s)
- Hongyuan Lu
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Siu-Kin Ng
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Yangyang Jia
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Mingwei Cai
- 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
| |
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
Leung YH, Xu X, Ma APY, Liu F, Ng AMC, Shen Z, Gethings LA, Guo MY, Djurišić AB, Lee PKH, Lee HK, Chan WK, Leung FCC. Toxicity of ZnO and TiO 2 to Escherichia coli cells. Sci Rep 2016; 6:35243. [PMID: 27731373 PMCID: PMC5378928 DOI: 10.1038/srep35243] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/27/2016] [Indexed: 12/19/2022] Open
Abstract
We performed a comprehensive investigation of the toxicity of ZnO and TiO2 nanoparticles using Escherichia coli as a model organism. Both materials are wide band gap n-type semiconductors and they can interact with lipopolysaccharide molecules present in the outer membrane of E. coli, as well as produce reactive oxygen species (ROS) under UV illumination. Despite the similarities in their properties, the response of the bacteria to the two nanomaterials was fundamentally different. When the ROS generation is observed, the toxicity of nanomaterial is commonly attributed to oxidative stress and cell membrane damage caused by lipid peroxidation. However, we found that significant toxicity does not necessarily correlate with up-regulation of ROS-related proteins. TiO2 exhibited significant antibacterial activity, but the protein expression profile of bacteria exposed to TiO2 was different compared to H2O2 and the ROS-related proteins were not strongly expressed. On the other hand, ZnO exhibited lower antibacterial activity compared to TiO2, and the bacterial response involved up-regulating ROS-related proteins similar to the bacterial response to the exposure to H2O2. Reasons for the observed differences in toxicity and bacterial response to the two metal oxides are discussed.
Collapse
Affiliation(s)
- Yu Hang Leung
- Dept. of Physics, Univ. of Hong Kong, Pokfulam Road, Hong Kong
| | - Xiaoying Xu
- School of Energy and Environment, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Angel P. Y. Ma
- School of Biological Sciences, Univ. of Hong Kong, Pokfulam Road, Hong Kong
| | - Fangzhou Liu
- Dept. of Physics, Univ. of Hong Kong, Pokfulam Road, Hong Kong
| | - Alan M. C. Ng
- Dept. of Physics, Univ. of Hong Kong, Pokfulam Road, Hong Kong
- Dept. of Physics, South University of Science and Technology of China, Shenzhen, China
| | - Zhiyong Shen
- School of Energy and Environment, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Lee A. Gethings
- Pharmaceutical and Life Sciences Division, Waters Corporation, Manchester, UK
| | - Mu Yao Guo
- Dept. of Physics, Univ. of Hong Kong, Pokfulam Road, Hong Kong
- Dept. of Physics, South University of Science and Technology of China, Shenzhen, China
| | | | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Hung Kay Lee
- Dept. of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Wai Kin Chan
- Dept. of Chemistry, Univ. of Hong Kong, Pokfulam Road, Hong Kong
| | | |
Collapse
|
42
|
Karthikeyan R, Krishnaraj N, Selvam A, Wong JWC, Lee PKH, Leung MKH, Berchmans S. Effect of composites based nickel foam anode in microbial fuel cell using Acetobacter aceti and Gluconobacter roseus as a biocatalysts. Bioresour Technol 2016; 217:113-120. [PMID: 26970695 DOI: 10.1016/j.biortech.2016.02.114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 12/24/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 06/05/2023]
Abstract
This study explores the use of materials such as chitosan (chit), polyaniline (PANI) and titanium carbide (TC) as anode materials for microbial fuel cells. Nickel foam (NF) was used as the base anode substrate. Four different types of anodes (NF, NF/PANI, NF/PANI/TC, NF/PANI/TC/Chit) are thus prepared and used in batch type microbial fuel cells operated with a mixed consortium of Acetobacter aceti and Gluconobacter roseus as the biocatalysts and bad wine as a feedstock. A maximum power density of 18.8Wm(-3) (≈2.3 times higher than NF) was obtained in the case of the anode modified with a composite of PANI/TC/Chit. The MFCs running under a constant external resistance of (50Ω) yielded 14.7% coulombic efficiency with a maximum chemical oxygen demand (COD) removal of 87-93%. The overall results suggest that the catalytic materials embedded in the chitosan matrix show the best performance and have potentials for further development.
Collapse
Affiliation(s)
- Rengasamy Karthikeyan
- Electrodics and Electrocatalysis (EEC) Division, Central Electrochemical Research Institute (CSIR-CECRI), Karaikudi 630 006, Tamil Nadu, India; Ability R&D Energy Research Center, School of Energy and Environment, City University of Hong Kong, Hong Kong, China; Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong, Hong Kong, China.
| | - Navanietha Krishnaraj
- Electrodics and Electrocatalysis (EEC) Division, Central Electrochemical Research Institute (CSIR-CECRI), Karaikudi 630 006, Tamil Nadu, India
| | - Ammaiyappan Selvam
- Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong, Hong Kong, China
| | - Jonathan Woon-Chung Wong
- Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong, Hong Kong, China
| | - Patrick K H Lee
- Ability R&D Energy Research Center, School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Michael K H Leung
- Ability R&D Energy Research Center, School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Sheela Berchmans
- Electrodics and Electrocatalysis (EEC) Division, Central Electrochemical Research Institute (CSIR-CECRI), Karaikudi 630 006, Tamil Nadu, India
| |
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
Cai M, Wilkins D, Chen J, Ng SK, Lu H, Jia Y, Lee PKH. Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems. Front Microbiol 2016; 7:778. [PMID: 27252693 PMCID: PMC4879347 DOI: 10.3389/fmicb.2016.00778] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [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: 02/29/2016] [Accepted: 05/09/2016] [Indexed: 01/06/2023] Open
Abstract
Anaerobic digestion (AD) is a microbial process widely used to treat organic wastes. While the microbes involved in digestion of municipal sludge are increasingly well characterized, the taxonomic and functional compositions of AD digesters treating industrial wastewater have been understudied. This study examined metagenomes from a biogas-producing digester treating municipal sludge in Shek Wu Hui (SWH), Hong Kong and an industrial wastewater digester in Guangzhou (GZ), China, and compared their taxonomic composition and reconstructed biochemical pathways. Genes encoding carbohydrate metabolism and protein metabolism functions were overrepresented in GZ, while genes encoding functions related to fatty acids, lipids and isoprenoids were overrepresented in SWH, reflecting the plants' feedstocks. Mapping of genera to functions in each community indicated that both digesters had a high level of functional redundancy, and a more even distribution of genera in GZ suggested that it was more functionally stable. While fermentation in both samples was dominated by Clostridia, SWH had an overrepresentation of Proteobacteria, including syntrophic acetogens, reflecting its more complex substrate. Considering the growing importance of biogas as an alternative fuel source, a detailed mechanistic understanding of AD is important and this report will be a basis for further study of industrial wastewater AD.
Collapse
Affiliation(s)
- Mingwei Cai
- School of Energy and Environment, City University of Hong Kong Hong Kong, China
| | - David Wilkins
- School of Energy and Environment, City University of Hong Kong Hong Kong, China
| | - Jiapeng Chen
- School of Energy and Environment, City University of Hong Kong Hong Kong, China
| | - Siu-Kin Ng
- School of Energy and Environment, City University of Hong Kong Hong Kong, China
| | - Hongyuan Lu
- School of Energy and Environment, City University of Hong Kong Hong Kong, China
| | - Yangyang Jia
- School of Energy and Environment, 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
| |
Collapse
|
45
|
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.
Collapse
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
| |
Collapse
|
46
|
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
|
47
|
Karthikeyan OP, Chidambarampadmavathy K, Nadarajan S, Lee PKH, Heimann K. Effect of CH4/O2 ratio on fatty acid profile and polyhydroxybutyrate content in a heterotrophic-methanotrophic consortium. Chemosphere 2015; 141:235-42. [PMID: 26247542 DOI: 10.1016/j.chemosphere.2015.07.054] [Citation(s) in RCA: 18] [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: 02/03/2015] [Revised: 06/14/2015] [Accepted: 07/19/2015] [Indexed: 05/22/2023]
Abstract
Understanding the role of heterotrophic-methanotrophic (H-Meth) communities is important for improvement of methane (CH4) oxidation capacities (MOC) particularly in conjunction with bio-product development in industrial bio-filters. Initially, a H-Meth consortium was established and enriched from marine sediments and characterized by next generation sequencing of the 16s rDNA gene. The enriched consortium was subjected to 10-50% CH4 (i.e., 0.20-1.6 CH4/O2 ratios) to study the effects on MOCs, biomass growth, fatty acid profiles and biopolymer (e.g. polyhydroxybutyrate; PHB) content. Methylocystis, Methylophaga and Pseudoxanthomonas dominated the H-Meth consortium. Culture enrichment of the H-Meth consortium resulted in 15-20-folds higher MOC compared to seed sediments. Increasing CH4 concentration (and decreased O2 levels) yielded higher MOCs, but did not improve total fatty acid contents. PHB contents varied between 2.5% and 8.5% independently of CH4/O2 ratios. The results suggest that H-Meth consortia could potentially be used in industrial bio-filters for production of biopolymer/biofuel precursors from CH4.
Collapse
Affiliation(s)
- Obulisamy P Karthikeyan
- College of Marine and Environmental Sciences, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia
| | - Karthigeyan Chidambarampadmavathy
- College of Marine and Environmental Sciences, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - Saravanan Nadarajan
- College of Marine and Environmental Sciences, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Kirsten Heimann
- College of Marine and Environmental Sciences, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Bio-discovery and Molecular Development of Therapeutics, James Cook University, Townsville 4811, Queensland, Australia.
| |
Collapse
|
48
|
Low A, Shen Z, Cheng D, Rogers MJ, Lee PKH, He J. A comparative genomics and reductive dehalogenase gene transcription study of two chloroethene-respiring bacteria, Dehalococcoides mccartyi strains MB and 11a. Sci Rep 2015; 5:15204. [PMID: 26541266 PMCID: PMC4635342 DOI: 10.1038/srep15204] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 06/29/2015] [Accepted: 09/21/2015] [Indexed: 01/02/2023] Open
Abstract
Genomes of two trichloroethene (TCE)-respiring Dehalococcoides (Dhc) mccartyi, strains MB and 11a, were sequenced to identify reductive dehalogenases (RDase) responsible for oraganohalide respiration. Transcription analyses were conducted to verify the roles of RDase subunit A genes (rdhA) in chloroethene respiration. Some interesting features of the strain MB draft genome include a large genome size, two CRISPR-cas type I systems, and 38 rdhA genes. Strain 11a has a stream-lined genome with 11 rdhA genes, of which nine are distinct. Quantitative real-time PCR transcription analysis of RDase gene transcripts showed that a single RDase gene, designated mbrA, was up-regulated upon exposure to TCE and no other RDase genes were considerably expressed in strain MB. A single RDase gene, designated vcrA, was up-regulated upon exposure to TCE and expressed at a steady level until all chloroethenes were completely dechlorinated to ethene at 147 h in strain 11a. Overall, this study reports the genomes of two distinct Dhc strains; both contain numerous uncharacterized RDase genes, but in each strain only one such gene was expressed highly during organohalide respiration.
Collapse
Affiliation(s)
- Adrian Low
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
| | - Zhiyong Shen
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Dan Cheng
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
| | - Patrick K H Lee
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
| |
Collapse
|
49
|
Wilkins D, Rao S, Lu X, Lee PKH. Effects of sludge inoculum and organic feedstock on active microbial communities and methane yield during anaerobic digestion. Front Microbiol 2015; 6:1114. [PMID: 26528262 PMCID: PMC4602121 DOI: 10.3389/fmicb.2015.01114] [Citation(s) in RCA: 30] [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: 06/25/2015] [Accepted: 09/28/2015] [Indexed: 02/01/2023] Open
Abstract
Anaerobic digestion (AD) is a widespread microbial technology used to treat organic waste and recover energy in the form of methane ("biogas"). While most AD systems have been designed to treat a single input, mixtures of digester sludge and solid organic waste are emerging as a means to improve efficiency and methane yield. We examined laboratory anaerobic cultures of AD sludge from two sources amended with food waste, xylose, and xylan at mesophilic temperatures, and with cellulose at meso- and thermophilic temperatures, to determine whether and how the inoculum and substrate affect biogas yield and community composition. All substrate and inoculum combinations yielded methane, with food waste most productive by mass. Pyrosequencing of transcribed bacterial and archaeal 16S rRNA showed that community composition varied across substrates and inocula, with differing ratios of hydrogenotrophic/acetoclastic methanogenic archaea associated with syntrophic partners. While communities did not cluster by either inoculum or substrate, additional sequencing of the bacterial 16S rRNA gene in the source sludge revealed that the bacterial communities were influenced by their inoculum. These results suggest that complete and efficient AD systems could potentially be assembled from different microbial inocula and consist of taxonomically diverse communities that nevertheless perform similar functions.
Collapse
Affiliation(s)
| | | | | | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong KongKowloon Tong, Hong Kong
| |
Collapse
|
50
|
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.
Collapse
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
| |
Collapse
|