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Gangneux JP, Sassi M, Lemire P, Le Cann P. Metagenomic Characterization of Indoor Dust Bacterial and Fungal Microbiota in Homes of Asthma and Non-asthma Patients Using Next Generation Sequencing. Front Microbiol 2020; 11:1671. [PMID: 32849345 PMCID: PMC7409152 DOI: 10.3389/fmicb.2020.01671] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022] Open
Abstract
Background The exposure of house occupants to indoor air pollutants has increased in recent decades. Among microbiological contaminants, bacterial and fungal aerosols remain poorly studied and the debate on the impact of these aerosols on respiratory health is still open. This study aimed to assess the diversity of indoor microbial communities in relationship with the health of occupants. Methods Measurements were taken from dwellings of 2 cohorts in Brittany (France), one with children without any pathology and the other with children and adults with asthma. Thirty dust samples were analyzed by next generation sequencing with a 16S and 18S targeted metagenomics approach. Analysis of sequencing data was performed using qiime 2, and univariate and multivariate statistical analysis using R software and phyloseq package. Results A total of 2,637 prokaryotic (589 at genus level) and 2,153 eukaryotic taxa were identified (856 fungal taxa (39%) and 573 metazoa (26%)). The four main bacterial phyla were identified: Proteobacteria (53%), Firmicutes (27%), Actinobacteria (11%), Bacteroidetes (8%). Among Fungi, only 136 taxa were identified at genus level. Three main fungal phyla were identified: Ascomycota (84%), Basidiomycota (12%) and Mucoromycota (3%). No bacterial nor fungal phyla were significantly associated with asthma versus control group. A significant over representation in control group versus asthma was observed for Christensenellaceae family (p-value = 0.0015, adj. p-value = 0.033). Besides, a trend for over representation in control group was observed with Dermabacteraceae family (p-value = 0.0002, adj. p-value = 0.815). Conclusions Our findings provide evidence that dust samples harbor a high diversity of human-associated bacteria and fungi. Molecular methods such as next generation sequencing are reliable tools for identifying and tracking the bacterial and fungal diversity in dust samples, a less easy strategy for the detection of eukaryotes at least using18S metagenomics approach. This study showed that the detection of some bacteria might be associated to indoor air of asthmatic patients. Regarding fungi, a higher number of samples and sequencing with more depth could allow reaching significant signatures.
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Affiliation(s)
- Jean-Pierre Gangneux
- Univ Rennes, CHU Rennes, Inserm, EHESP, Institut de Recherche en Santé, Environnement et Travail (Irset) - UMR_S 1085, Rennes, France
| | - Mohamed Sassi
- Univ Rennes, CHU Rennes, Inserm, EHESP, Institut de Recherche en Santé, Environnement et Travail (Irset) - UMR_S 1085, Rennes, France
| | - Pierre Lemire
- Univ Rennes, CHU Rennes, Inserm, EHESP, Institut de Recherche en Santé, Environnement et Travail (Irset) - UMR_S 1085, Rennes, France
| | - Pierre Le Cann
- Univ Rennes, CHU Rennes, Inserm, EHESP, Institut de Recherche en Santé, Environnement et Travail (Irset) - UMR_S 1085, Rennes, France
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Sigsgaard T, Basinas I, Doekes G, de Blay F, Folletti I, Heederik D, Lipinska-Ojrzanowska A, Nowak D, Olivieri M, Quirce S, Raulf M, Sastre J, Schlünssen V, Walusiak-Skorupa J, Siracusa A. Respiratory diseases and allergy in farmers working with livestock: a EAACI position paper. Clin Transl Allergy 2020; 10:29. [PMID: 32642058 PMCID: PMC7336421 DOI: 10.1186/s13601-020-00334-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
Farmers constitute a large professional group worldwide. In developed countries farms tend to become larger, with a concentration of farm operations. Animal farming has been associated with negative respiratory effects such as work-related asthma and rhinitis. However, being born and raised or working on a farm reduces the risk of atopic asthma and rhinitis later in life. A risk of chronic bronchitis and bronchial obstruction/COPD has been reported in confinement buildings and livestock farmers. This position paper reviews the literature linking exposure information to intensive animal farming and the risk of work-related respiratory diseases and focuses on prevention. Animal farming is associated with exposure to organic dust containing allergens and microbial matter including alive microorganisms and viruses, endotoxins and other factors like irritant gases such as ammonia and disinfectants. These exposures have been identified as specific agents/risk factors of asthma, rhinitis, chronic bronchitis, COPD and reduced FEV1. Published studies on dust and endotoxin exposure in livestock farmers do not show a downward trend in exposure over the last 30 years, suggesting that the workforce in these industries is still overexposed and at risk of developing respiratory disease. In cases of occupational asthma and rhinitis, avoidance of further exposure to causal agents is recommended, but it may not be obtainable in agriculture, mainly due to socio-economic considerations. Hence, there is an urgent need for focus on farming exposure in order to protect farmers and others at work in these and related industries from developing respiratory diseases and allergy.
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Affiliation(s)
- T Sigsgaard
- Department of Environment Occupation & Health, Dept of Public Health, Danish Ramazzini Centre, Aarhus University, Bartholins Allé 2, Build. 1260, 8000 Aarhus C, Denmark
| | - I Basinas
- Institute of Occupational Medicine, Edinburgh, UK
| | - G Doekes
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - F de Blay
- Division of Asthma and Allergy, Department of Chest Diseases, University Hospital, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
| | - I Folletti
- Occupational Medicine, Terni Hospital, University of Perugia, Perugia, Italy
| | - D Heederik
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - A Lipinska-Ojrzanowska
- Department of Occupational Diseases and Environmental Health, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - D Nowak
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, Ludwig Maximilian University, Munich, Germany.,Comprehensive Pneumology Center Munich, Member DZL, German Centre for Lung Research, Munich, Germany
| | - M Olivieri
- Unit of Occupational Medicine, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - S Quirce
- Department of Allergy, Hospital La Paz Institute for Health Research (IdiPAZ) and CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - M Raulf
- IPA Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-Universität Bochum, Bochum, Germany
| | - J Sastre
- Department of Allergy, Fundación Jiménez Díaz, CIBER de Enfermedades Respiratorias (Ciberes), Madrid, Spain
| | - V Schlünssen
- Department of Environment Occupation & Health, Dept of Public Health, Danish Ramazzini Centre, Aarhus University, Bartholins Allé 2, Build. 1260, 8000 Aarhus C, Denmark
| | - J Walusiak-Skorupa
- Department of Occupational Diseases and Environmental Health, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - A Siracusa
- Formerly Department of Clinical and Experimental Medicine, University of Perugia, Perugia, Italy
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3
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Nygaard AB, Tunsjø HS, Meisal R, Charnock C. A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes. Sci Rep 2020; 10:3209. [PMID: 32081924 PMCID: PMC7035348 DOI: 10.1038/s41598-020-59771-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/30/2020] [Indexed: 12/02/2022] Open
Abstract
There is a growing awareness of the importance of indoor microbiomes for human health. Given their complexity, these microbiomes can only be adequately surveyed using high throughput sequencing techniques. Oxford Nanopore’s MinION is the newest third generation sequencing technology on the market. With its many advantages such as portability, user friendliness, simplicity, speed of sequencing and long read length, the technology is now an actual contender to established sequencing platforms. MinION’s main disadvantage is a relatively low read accuracy compared to several other platforms, although this is constantly improving. The present study, which appears to be the first of its kind, provides the results of a preliminary analysis of the microbial communities in indoor environments based on 16S rRNA gene amplicon sequencing, using both the Oxford Nanopore Technologies (ONT) MinIOn and the Illumina MiSeq DNA sequencers. At the level of family and above, there was no significant difference between the microbial compositions as revealed by the two platforms. However, at the genus, and particularly at the species level, the ONT MinION reported greater taxonomic resolution than Illumina MiSeq.
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Affiliation(s)
- Anders B Nygaard
- Faculty of Technology, Art and Design, Department of Civil Engineering and Energy Technology, Oslo Metropolitan University (OsloMet), Oslo, Norway. .,Faculty of Health Sciences, Department of Life Sciences and Health, OsloMet, Oslo, Norway.
| | - Hege S Tunsjø
- Faculty of Health Sciences, Department of Life Sciences and Health, OsloMet, Oslo, Norway
| | | | - Colin Charnock
- Faculty of Health Sciences, Department of Life Sciences and Health, OsloMet, Oslo, Norway
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Nieto-Caballero M, Savage N, Keady P, Hernandez M. High fidelity recovery of airborne microbial genetic materials by direct condensation capture into genomic preservatives. J Microbiol Methods 2019; 157:1-3. [DOI: 10.1016/j.mimet.2018.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 11/26/2022]
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Horsley A, Thaler DS. Microwave detection and quantification of water hidden in and on building materials: implications for healthy buildings and microbiome studies. BMC Infect Dis 2019; 19:67. [PMID: 30658591 PMCID: PMC6339348 DOI: 10.1186/s12879-019-3720-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/11/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Excess water in all its forms (moisture, dampness, hidden water) in buildings negatively impacts occupant health but is hard to reliably detect and quantify. Recent advances in through-wall imaging recommend microwaves as a tool with a high potential to noninvasively detect and quantify water throughout buildings. METHODS Microwaves in both transmission and reflection (radar) modes were used to perform a simple demonstration of the detection of water both on and hidden within building materials. RESULTS We used both transmission and reflection modes to detect as little as 1 mL of water between two 7 cm thicknesses of concrete. The reflection mode was also used to detect 1 mL of water on a metal surface. We observed oscillations in transmitted and reflected microwave amplitude as a function of microwave wavelength and water layer thickness, which we attribute to thin-film interference effects. CONCLUSIONS Improving the detection of water in buildings could help design, maintenance, and remediation become more efficient and effective and perhaps increase the value of microbiome sequence data. Microwave characterization of all forms of water throughout buildings is possible; its practical development would require new collaborations among microwave physicists or engineers, architects, building engineers, remediation practitioners, epidemiologists, and microbiologists.
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Affiliation(s)
- Andrew Horsley
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056, Basel, Switzerland. .,Research School of Physics and Engineering, The Australian National University, Mills Rd., ACT 2601, Canberra, Australia.
| | - David S Thaler
- Research School of Physics and Engineering, The Australian National University, Mills Rd., ACT 2601, Canberra, Australia.,Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
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Fahimipour AK, Hartmann EM, Siemens A, Kline J, Levin DA, Wilson H, Betancourt-Román CM, Brown GZ, Fretz M, Northcutt D, Siemens KN, Huttenhower C, Green JL, Van Den Wymelenberg K. Daylight exposure modulates bacterial communities associated with household dust. MICROBIOME 2018; 6:175. [PMID: 30333051 PMCID: PMC6193304 DOI: 10.1186/s40168-018-0559-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 09/19/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Microbial communities associated with indoor dust abound in the built environment. The transmission of sunlight through windows is a key building design consideration, but the effects of light exposure on dust communities remain unclear. We report results of an experiment and computational models designed to assess the effects of light exposure and wavelengths on the structure of the dust microbiome. Specifically, we placed household dust in replicate model "rooms" with windows that transmitted visible, ultraviolet, or no light and measured taxonomic compositions, absolute abundances, and viabilities of the resulting bacterial communities. RESULTS Light exposure per se led to lower abundances of viable bacteria and communities that were compositionally distinct from dark rooms, suggesting preferential inactivation of some microbes over others under daylighting conditions. Differences between communities experiencing visible and ultraviolet light wavelengths were relatively minor, manifesting primarily in abundances of dead human-derived taxa. Daylighting was associated with the loss of a few numerically dominant groups of related microorganisms and apparent increases in the abundances of some rare groups, suggesting that a small number of microorganisms may have exhibited modest population growth under lighting conditions. Although biological processes like population growth on dust could have generated these patterns, we also present an alternate statistical explanation using sampling models from ecology; simulations indicate that artefactual, apparent increases in the abundances of very rare taxa may be a null expectation following the selective inactivation of dominant microorganisms in a community. CONCLUSIONS Our experimental and simulation-based results indicate that dust contains living bacterial taxa that can be inactivated following changes in local abiotic conditions and suggest that the bactericidal potential of ordinary window-filtered sunlight may be similar to ultraviolet wavelengths across dosages that are relevant to real buildings.
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Affiliation(s)
- Ashkaan K. Fahimipour
- Biology and the Built Environment Center, University of Oregon, 13th Ave, Eugene, OR USA
| | - Erica M. Hartmann
- Biology and the Built Environment Center, University of Oregon, 13th Ave, Eugene, OR USA
- Department of Civil and Environmental Engineering, Northwestern University, Chicago, IL USA
| | - Andrew Siemens
- Biology and the Built Environment Center, University of Oregon, 13th Ave, Eugene, OR USA
| | - Jeff Kline
- Biology and the Built Environment Center, University of Oregon, 13th Ave, Eugene, OR USA
- Energy Studies in Buildings Laboratory, University of Oregon, Eugene, OR USA
| | - David A. Levin
- Department of Mathematics, University of Oregon, Eugene, OR USA
| | - Hannah Wilson
- Biology and the Built Environment Center, University of Oregon, 13th Ave, Eugene, OR USA
| | | | - GZ Brown
- Biology and the Built Environment Center, University of Oregon, 13th Ave, Eugene, OR USA
- Energy Studies in Buildings Laboratory, University of Oregon, Eugene, OR USA
| | - Mark Fretz
- Biology and the Built Environment Center, University of Oregon, 13th Ave, Eugene, OR USA
- Energy Studies in Buildings Laboratory, University of Oregon, Eugene, OR USA
| | - Dale Northcutt
- Biology and the Built Environment Center, University of Oregon, 13th Ave, Eugene, OR USA
- Energy Studies in Buildings Laboratory, University of Oregon, Eugene, OR USA
| | - Kyla N. Siemens
- Biology and the Built Environment Center, University of Oregon, 13th Ave, Eugene, OR USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Jessica L. Green
- Biology and the Built Environment Center, University of Oregon, 13th Ave, Eugene, OR USA
- Santa Fe Institute, Santa Fe, NM USA
| | - Kevin Van Den Wymelenberg
- Biology and the Built Environment Center, University of Oregon, 13th Ave, Eugene, OR USA
- Energy Studies in Buildings Laboratory, University of Oregon, Eugene, OR USA
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Unterwurzacher V, Pogner C, Berger H, Strauss J, Strauss-Goller S, Gorfer M. Validation of a quantitative PCR based detection system for indoor mold exposure assessment in bioaerosols. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2018; 20:1454-1468. [PMID: 30225499 DOI: 10.1039/c8em00253c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Determination and assessment of airborne fungal particles is complex and results of different sampling and analytical strategies are hard to compare due to limitations of each of the techniques. Here, an indoor mold detection system based on quantitative polymerase chain reaction (qPCR) is described and validated for its reliability and stability to identify airborne fungal particles collected. Data obtained from testing the system with fungal DNA, spore suspensions and bioaerosols indicated a need for spiking and normalization of measurements due to material loss and assay specific bias. Considering the loss of material during sample processing, detection limits defined for suspensions of Tritirachium oryzae spores were roughly 18 spores per sample. Detection of fungal spore mixtures nebulized under controlled conditions in a bioaerosol chamber showed generally 2-3 times higher normalized values measured with the molecular system compared to cultivation. Data obtained from a mold infested indoor sampling site and its corresponding outdoor reference measurement showed good correlations between qPCR and high-throughput sequencing (rho = 0.83, p < 0.01), if Cladosporium species were excluded. Taking necessary data normalization into account, the described qPCR detection system shows great potential to complement commonly used culture based approaches with the aim to improve the precision of indoor mold assessments. In contrast to already available qPCR assays that detect certain molds on a species level, this system covers a broad range of relevant fungal communities, serving as a promising alternative to high-throughput sequencing to identify indoor molds.
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Affiliation(s)
- Verena Unterwurzacher
- Center for Health and Bioresources, Austrian Institute of Technology - AIT, Tulln, Austria.
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An Official American Thoracic Society Workshop Report: Presentations and Discussion of the Sixth Jack Pepys Workshop on Asthma in the Workplace. Ann Am Thorac Soc 2018; 14:1361-1372. [PMID: 28862493 DOI: 10.1513/annalsats.201706-508st] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Sixth Jack Pepys Workshop on Asthma in the Workplace focused on six key themes regarding the recognition and assessment of work-related asthma and airway diseases: (1) cleaning agents and disinfectants (including in swimming pools) as irritants and sensitizers: how to evaluate types of bronchial reactions and reduce risks; (2) population-based studies of occupational obstructive diseases: use of databanks, advantages and pitfalls, what strategies to deal with biases and confounding?; (3) damp environments, dilapidated buildings, recycling processes, and molds, an increasing problem: mechanisms, how to assess causality and diagnosis; (4) diagnosis of occupational asthma and rhinitis: how useful are recombinant allergens (component-resolved diagnosis), metabolomics, and other new tests?; (5) how does exposure to gas, dust, and fumes enhance sensitization and asthma?; and (6) how to determine probability of occupational causality in chronic obstructive pulmonary disease: epidemiological and clinical, confirmation, and compensation aspects. A summary of the presentations and discussion is provided in this proceedings document. Increased knowledge has been gained in each topic over the past few years, but there remain aspects of controversy and uncertainty requiring further research.
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9
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Li J, Riaz Rajoka MS, Shao D, Jiang C, Jin M, Huang Q, Yang H, Shi J. Strategies to increase the efficacy of using gut microbiota for the modulation of obesity. Obes Rev 2017; 18:1260-1271. [PMID: 28742949 DOI: 10.1111/obr.12590] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/03/2017] [Accepted: 06/12/2017] [Indexed: 12/16/2022]
Abstract
Obesity is one of the most serious global public health challenges of the 21st century. The adjustment of gut microbiota is often recommended as an efficient strategy to treat obesity. This modulation of gut microbiota can be performed by many methods, including dietary intervention, antibiotic application, the use of prebiotics and probiotics, bariatric surgery and faecal microbiota transplantation. In most cases, positive effects have been observed in response to treatment, but invalid and even contrary effects have also been observed in some cases due to factors that are unrelated to intervention methods, such as genetic factors, patient age or gender, environmental microbiota, climate, geography and lifestyle. These factors can cause variation of gut microbial populations and thus should also be taken into consideration when selecting modulation strategies.
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Affiliation(s)
- J Li
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - M S Riaz Rajoka
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - D Shao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - C Jiang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - M Jin
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - Q Huang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - H Yang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - J Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
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Shamarina D, Stoyantcheva I, Mason CE, Bibby K, Elhaik E. Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research. MICROBIOME 2017; 5:132. [PMID: 28978331 PMCID: PMC5628477 DOI: 10.1186/s40168-017-0349-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/20/2017] [Indexed: 05/07/2023]
Abstract
The public commonly associates microorganisms with pathogens. This suspicion of microorganisms is understandable, as historically microorganisms have killed more humans than any other agent while remaining largely unknown until the late seventeenth century with the works of van Leeuwenhoek and Kircher. Despite our improved understanding regarding microorganisms, the general public are apt to think of diseases rather than of the majority of harmless or beneficial species that inhabit our bodies and the built and natural environment. As long as microbiome research was confined to labs, the public's exposure to microbiology was limited. The recent launch of global microbiome surveys, such as the Earth Microbiome Project and MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) project, has raised ethical, financial, feasibility, and sustainability concerns as to the public's level of understanding and potential reaction to the findings, which, done improperly, risk negative implications for ongoing and future investigations, but done correctly, can facilitate a new vision of "smart cities." To facilitate improved future research, we describe here the major concerns that our discussions with ethics committees, community leaders, and government officials have raised, and we expound on how to address them. We further discuss ethical considerations of microbiome surveys and provide practical recommendations for public engagement.
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Affiliation(s)
- Daria Shamarina
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
| | - Iana Stoyantcheva
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021 USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY 10021 USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021 USA
| | - Kyle Bibby
- University of Notre Dame Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dameᅟ, IN 46556 USA
| | - Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN UK
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