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Létourneau V, Gagné MJ, Vyskocil JM, Brochu V, Robitaille K, Gauthier M, Brassard J, Duchaine C. Hunting for a viral proxy in bioaerosols of swine buildings using molecular detection and metagenomics. J Environ Sci (China) 2025; 148:69-78. [PMID: 39095200 DOI: 10.1016/j.jes.2023.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/04/2024]
Abstract
There are limited biosecurity measures directed at preventing airborne transmission of viruses in swine. The effectiveness of dust mitigation strategies such as oil sprinkling, to decrease risk of airborne virus transmission are unknown. Metagenomics and qPCR for common fecal viruses were used to hunt for a ubiquitous virus to serve as a proxy when evaluating the efficiency of mitigation strategies against airborne viral infectious agents. Air particles were collected from swine buildings using high-volume air samplers. Extracted DNA and RNA were used to perform specific RT-qPCR and qPCR and analyzed by high-throughput sequencing. Porcine astroviruses group 2 were common (from 102 to 105 genomic copies per cubic meter of air or gc/m3, 93% positivity) while no norovirus genogroup II was recovered from air samples. Porcine torque teno sus virus were detected by qPCR in low concentrations (from 101 to 102 gc/m3, 47% positivity). Among the identified viral families by metagenomics analysis, Herelleviridae, Microviridae, Myoviridae, Podoviridae, and Siphoviridae were dominant. The phage vB_AviM_AVP of Aerococcus was present in all air samples and a newly designed qPCR revealed between 101 and 105 gc/m3 among the samples taken for the present study (97% positivity) and banked samples from 5- and 15-year old studies (89% positivity). According to the present study, both the porcine astrovirus group 2 and the phage vB_AviM_AVP of Aerococcus could be proxy for airborne viruses of swine buildings.
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Affiliation(s)
- Valérie Létourneau
- Quebec Heart and Lung Institute Research Centre - Université Laval, 2725 Chemin Sainte-Foy, Quebec, G1V 4G5, Canada
| | - Marie-Josée Gagné
- Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, 3600 Casavant Boulevard West, Saint-Hyacinthe, J2S 8E3, Canada
| | - Jonathan M Vyskocil
- Department of Biochemistry, Microbiology, and Bio-informatics, Faculty of Science and Engineering, Université Laval, 1045 Avenue de la Médecine, Quebec, G1V 0A6, Canada
| | - Vincent Brochu
- Department of Biochemistry, Microbiology, and Bio-informatics, Faculty of Science and Engineering, Université Laval, 1045 Avenue de la Médecine, Quebec, G1V 0A6, Canada
| | - Kim Robitaille
- Department of Biochemistry, Microbiology, and Bio-informatics, Faculty of Science and Engineering, Université Laval, 1045 Avenue de la Médecine, Quebec, G1V 0A6, Canada
| | - Martin Gauthier
- Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, 3600 Casavant Boulevard West, Saint-Hyacinthe, J2S 8E3, Canada
| | - Julie Brassard
- Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, 3600 Casavant Boulevard West, Saint-Hyacinthe, J2S 8E3, Canada; The Swine and Poultry Infectious Diseases Research Centre, Faculty of Veterinary Medicine of Université de Montréal, 3200 Rue Sicotte, Saint-Hyacinthe, J2S 2M2, Canada
| | - Caroline Duchaine
- Quebec Heart and Lung Institute Research Centre - Université Laval, 2725 Chemin Sainte-Foy, Quebec, G1V 4G5, Canada; Department of Biochemistry, Microbiology, and Bio-informatics, Faculty of Science and Engineering, Université Laval, 1045 Avenue de la Médecine, Quebec, G1V 0A6, Canada.
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Sun Z, Hong W, Xue C, Dong N. A comprehensive review of antibiotic resistance gene contamination in agriculture: Challenges and AI-driven solutions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 953:175971. [PMID: 39236811 DOI: 10.1016/j.scitotenv.2024.175971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/24/2024] [Accepted: 08/30/2024] [Indexed: 09/07/2024]
Abstract
Since their discovery, the prolonged and widespread use of antibiotics in veterinary and agricultural production has led to numerous problems, particularly the emergence and spread of antibiotic-resistant bacteria (ARB). In addition, other anthropogenic factors accelerate the horizontal transfer of antibiotic resistance genes (ARGs) and amplify their impact. In agricultural environments, animals, manure, and wastewater are the vectors of ARGs that facilitate their spread to the environment and humans via animal products, water, and other environmental pathways. Therefore, this review comprehensively analyzed the current status, removal methods, and future directions of ARGs on farms. This article 1) investigates the origins of ARGs on farms, the pathways and mechanisms of their spread to surrounding environments, and various strategies to mitigate their spread; 2) determines the multiple factors influencing the abundance of ARGs on farms, the pathways through which ARGs spread from farms to the environment, and the effects and mechanisms of non-antibiotic factors on the spread of ARGs; 3) explores methods for controlling ARGs in farm wastes; and 4) provides a comprehensive summary and integration of research across various fields, proposing that in modern smart farms, emerging technologies can be integrated through artificial intelligence to control or even eliminate ARGs. Moreover, challenges and future research directions for controlling ARGs on farms are suggested.
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Affiliation(s)
- Zhendong Sun
- The Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Weichen Hong
- The Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Chenyu Xue
- The Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China
| | - Na Dong
- The Laboratory of Molecular Nutrition and Immunity, College of Animal Science and Technology, Northeast Agricultural University, Harbin, PR China.
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3
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Lu Y, Duan M, Li Y, Zhang S, Hu X, Liu L. Altitude-associated trends in bacterial communities in ultrahigh-altitude residences. ENVIRONMENT INTERNATIONAL 2024; 185:108503. [PMID: 38377724 DOI: 10.1016/j.envint.2024.108503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Indoor bacterial communities may change with altitude because their major contributors, outdoor bacterial communities, vary with altitude. People's health effects from bacteria inhalation exposure can also vary with altitude because human respiratory physiology changes with oxygen content in air. Accordingly, adjusting indoor bacterial communities may help to acclimate newcomers from low-altitude environments to ultrahigh-altitude environments. To lay the groundwork for further research, we aimed to first elucidate the bacterial communities in ultrahigh-altitude residences and the effects of altitude on these communities. We collected 187 environmental samples from residential communities at ultrahigh altitudes of 3811-4651 m in Ngari, China and sequenced bacterial 16S rRNA genes. RESULTS On one hand, when abundant genera in ultrahigh-altitude residences and those reported by previous studies on low-altitude residences were compared, nine genera were shared, whereas other five genera were abundant only at ultrahigh altitudes. On the other hand, when the bacterial communities of residences at different ultrahigh altitudes were further compared, the bacterial composition in indoor surface samples varied significantly with altitude. The relative abundance of five bacterial genera in indoor air samples and 10 genera and three phyla in indoor surface samples varied monotonically with altitude. CONCLUSIONS Altitude may be a long-neglected factor that shapes residential bacterial communities and thus warrants attention.
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Affiliation(s)
- Yiran Lu
- Department of Building Science, Tsinghua University, Beijing 100084, China; Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Mengjie Duan
- Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China; Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Yifan Li
- Department of Building Science, Tsinghua University, Beijing 100084, China; Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Shengyu Zhang
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaomin Hu
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Li Liu
- Department of Building Science, Tsinghua University, Beijing 100084, China; Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China.
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4
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Han J, Li M, Li X, Liu C, Li XL, Wang K, Qiao R, Yang F, Han X, Li XJ. Effects of microbes in pig farms on occupational exposed persons and the environment. AMB Express 2023; 13:136. [PMID: 38032532 PMCID: PMC10689614 DOI: 10.1186/s13568-023-01631-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
In terms of pig farming, pig gut microbes have a significant effect on farmers and the farm environment. However, it is still unclear which microbial composition is more likely to contribute to this effect. This study collected a total of 136 samples, including pigs' faeces samples, farmers' faeces samples, samples from individuals who had no contact with any type of farm animal (referred to as 'non-exposed' persons), and environmental dust samples (collected from inside and outside pig houses and the farm) from two pig farms, pig farm A and pig farm B. Whereafter, 16S rRNA sequencing and taxonomic composition analysis were performed. According to the study, compared to non-exposed persons, pig farmers had a significantly higher abundance of 7 genera. In addition, the farmers were grouped according to the duration of their occupational exposure, and it was shown that 4 genera, including Turicibacter, Terrisporobacter, and Clostridium_sensu_stricto_1, exhibited a rise in more frequent contact with pigs. As compared to outside the pig house, the environmental dust has a greater concentration of the 3 bacteria mentioned before. Therefore, these 3 microbes can be considered as co-occurring microbes that may exist both in humans and the environment. Also, the 3 co-occurring microbes are involved in the fermentation and production of short-chain fatty acids and their effectiveness decreased as distance from the farm increased. This study shows that the 3 microbes where pig farmers co-occur with the environment come from pig farms, which provides fresh ideas for preventing the spread of microbial aerosols in pig farms and reducing pollution.
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Affiliation(s)
- Jinyi Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Mengyu Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xin Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chuang Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiu-Ling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Xin-Jian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
- Sanya Institute, Hainan Academy of Agricultural Science, Sanya, China.
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5
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Rittscher AE, Vlasblom AA, Duim B, Scherpenisse P, van Schothorst IJ, Wouters IM, Van Gompel L, Smit LAM. A comparison of passive and active dust sampling methods for measuring airborne methicillin-resistant Staphylococcus aureus in pig farms. Ann Work Expo Health 2023; 67:1004-1010. [PMID: 37300560 PMCID: PMC10516621 DOI: 10.1093/annweh/wxad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Methicillin-resistant strains of Staphylococcus aureus (MRSA) are resistant to most β-lactam antibiotics. Pigs are an important reservoir of livestock-associated MRSA (LA-MRSA), which is genetically distinct from both hospital and community-acquired MRSA. Occupational exposure to pigs on farms can lead to LA-MRSA carriage by workers. There is a growing body of research on MRSA found in the farm environment, the airborne route of transmission, and its implication on human health. This study aims to directly compare two sampling methods used to measure airborne MRSA in the farm environment; passive dust sampling with electrostatic dust fall collectors (EDCs), and active inhalable dust sampling using stationary air pumps with Gesamtstaubprobenahme (GSP) sampling heads containing Teflon filters. Paired dust samples using EDCs and GSP samplers, totaling 87 samples, were taken from 7 Dutch pig farms, in multiple compartments housing pigs of varying ages. Total nucleic acids of both types of dust samples were extracted and targets indicating MRSA (femA, nuc, mecA) and total bacterial count (16S rRNA) were quantified using quantitative real-time PCRs. MRSA could be measured from all GSP samples and in 94% of the EDCs, additionally MRSA was present on every farm sampled. There was a strong positive relationship between the paired MRSA levels found in EDCs and those measured on filters (Normalized by 16S rRNA; Pearson's correlation coefficient r = 0.94, Not Normalized; Pearson's correlation coefficient r = 0.84). This study suggests that EDCs can be used as an affordable and easily standardized method for quantifying airborne MRSA levels in the pig farm setting.
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Affiliation(s)
- Anne E Rittscher
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Abel A Vlasblom
- Department of Infectious Diseases and Immunology (I&I), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology (I&I), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
| | - Peter Scherpenisse
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Isabella J van Schothorst
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Inge M Wouters
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
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6
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Alhamwe BA, Gao Z, Alhamdan F, Harb H, Pichene M, Garnier A, Andari JE, Kaufmann A, Graumann PL, Kesper D, Daviaud C, Garn H, Tost J, Potaczek DP, Blaser MJ, Renz H. Intranasal administration of Acinetobacter lwoffii in a murine model of asthma induces IL-6-mediated protection associated with cecal microbiota changes. Allergy 2023; 78:1245-1257. [PMID: 36458896 PMCID: PMC10160012 DOI: 10.1111/all.15606] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 09/30/2022] [Accepted: 10/13/2022] [Indexed: 12/05/2022]
Abstract
BACKGROUND Early-life exposure to certain environmental bacteria including Acinetobacter lwoffii (AL) has been implicated in protection from chronic inflammatory diseases including asthma later in life. However, the underlying mechanisms at the immune-microbe interface remain largely unknown. METHODS The effects of repeated intranasal AL exposure on local and systemic innate immune responses were investigated in wild-type and Il6-/- , Il10-/- , and Il17-/- mice exposed to ovalbumin-induced allergic airway inflammation. Those investigations were expanded by microbiome analyses. To assess for AL-associated changes in gene expression, the picture arising from animal data was supplemented by in vitro experiments of macrophage and T-cell responses, yielding expression and epigenetic data. RESULTS The asthma preventive effect of AL was confirmed in the lung. Repeated intranasal AL administration triggered a proinflammatory immune response particularly characterized by elevated levels of IL-6, and consequently, IL-6 induced IL-10 production in CD4+ T-cells. Both IL-6 and IL-10, but not IL-17, were required for asthma protection. AL had a profound impact on the gene regulatory landscape of CD4+ T-cells which could be largely recapitulated by recombinant IL-6. AL administration also induced marked changes in the gastrointestinal microbiome but not in the lung microbiome. By comparing the effects on the microbiota according to mouse genotype and AL-treatment status, we have identified microbial taxa that were associated with either disease protection or activity. CONCLUSION These experiments provide a novel mechanism of Acinetobacter lwoffii-induced asthma protection operating through IL-6-mediated epigenetic activation of IL-10 production and with associated effects on the intestinal microbiome.
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Affiliation(s)
- Bilal Alashkar Alhamwe
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
- Institute for Tumor Immunology, Clinic for Hematology, Oncology and Immunology, Center for Tumor Biology, and Immunology (ZTI), Philipps University Marburg, Marburg, Germany
- College of Pharmacy, International University for Science and Technology (IUST), Daraa 15, Syria
| | - Zhan Gao
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ
| | - Fahd Alhamdan
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
- Department of Medicine, Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
| | - Hani Harb
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
- Institute for Medical Microbiology and Virology, Technical University Dresden, Dresden, Germany
- Psychoneuroimmunology Laboratory, Department of Psychosomatic Medicine and Psychotherapy, Justus-Liebig University Giessen, Giessen, Germany
| | - Matthieu Pichene
- The Laboratory for Epigenetics and Environment, Centre National de Recherche en Genomique Humaine, CEA–Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, France
| | - Abel Garnier
- The Laboratory for Epigenetics and Environment, Centre National de Recherche en Genomique Humaine, CEA–Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, France
| | - Jihad El Andari
- SYNMIKRO, LOEWE Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Andreas Kaufmann
- Institute for Immunology, Philipps-University Marburg, Marburg, Germany
| | - Peter L. Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Dörthe Kesper
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
| | - Christian Daviaud
- The Laboratory for Epigenetics and Environment, Centre National de Recherche en Genomique Humaine, CEA–Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, France
| | - Holger Garn
- Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
| | - Jörg Tost
- The Laboratory for Epigenetics and Environment, Centre National de Recherche en Genomique Humaine, CEA–Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, France
| | - Daniel P. Potaczek
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
- Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
- Bioscientia MVZ Labor Mittelhessen GmbH, Gießen, Germany
| | - Martin J. Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ
| | - Harald Renz
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
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7
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Amin H, Marshall IPG, Bertelsen RJ, Wouters IM, Schlünssen V, Sigsgaard T, Šantl-Temkiv T. Optimization of bacterial DNA and endotoxin extraction from settled airborne dust. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159455. [PMID: 36252657 DOI: 10.1016/j.scitotenv.2022.159455] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Collecting and obtaining sufficient amount of airborne particles for multiple microbial component assessments can be challenging. A passive dust sampling device, the electrostatic dust fall collector (EDC) has been established for assessing airborne exposures including endotoxin and glucans. Recently, with advances in next-generation sequencing techniques, EDCs were used to collect microbial cells for DNA sequencing analysis to promote the study of airborne bacterial and fungal communities. However, low DNA yields have been problematic when employing passive sampling with EDC. To address this challenge, we attempted to increase the efficiency of extraction. We compared DNA extraction efficiency of bacterial components from EDCs captured on filters through filtration using five extraction techniques. By measuring the abundance, diversity and structure of bacterial communities using qPCR and amplicon sequencing targeting 16S rRNA genes, we found that two techniques outperformed the rest. Furthermore, we developed protocols to simultaneously extract both DNA and endotoxin from a single EDC cloth. Our technique promotes a high quality to price ratio and may be employed in large epidemiological studies addressing airborne bacterial exposure where a large number of samples is needed.
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Affiliation(s)
- Hesham Amin
- Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Ian P G Marshall
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Randi J Bertelsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Inge M Wouters
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Vivi Schlünssen
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Torben Sigsgaard
- Department of Public Health, Environment, Work and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Tina Šantl-Temkiv
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
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8
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Amin H, Šantl-Temkiv T, Cramer C, Vestergaard DV, Holst GJ, Elholm G, Finster K, Bertelsen RJ, Schlünssen V, Sigsgaard T, Marshall IPG. Cow Farmers’ Homes Host More Diverse Airborne Bacterial Communities Than Pig Farmers’ Homes and Suburban Homes. Front Microbiol 2022; 13:883991. [PMID: 35847077 PMCID: PMC9278274 DOI: 10.3389/fmicb.2022.883991] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/05/2022] [Indexed: 01/04/2023] Open
Abstract
Living on a farm has been linked to a lower risk of immunoregulatory disorders, such as asthma, allergy, and inflammatory bowel disease. It is hypothesized that a decrease in the diversity and composition of indoor microbial communities is a sensible explanation for the upsurge in immunoregulatory diseases, with airborne bacteria contributing to this protective effect. However, the composition of this potentially beneficial microbial community in various farm and suburban indoor environments is still to be characterized. We collected settled airborne dust from stables and the associated farmers’ homes and from suburban homes using electrostatic dust collectors (EDCs) over a period of 14 days. Then, quantitative PCR (qPCR) was used to assess bacterial abundance. The V3–V4 region of the bacterial 16S rRNA gene was amplified and sequenced using Ilumina MiSeq in order to assess microbial diversity. The Divisive Amplicon Denoising Algorithm (DADA2) algorithm was used for the inference of amplicon sequence variants from amplicon data. Airborne bacteria were significantly more abundant in farmers’ indoor environments than in suburban homes (p < 0.001). Cow farmers’ homes had significantly higher bacterial diversity than pig farmers’ and suburban homes (p < 0.001). Bacterial taxa, such as Firmicutes, Prevotellaceae, Lachnospiraceae, and Lactobacillus were significantly more abundant in farmers’ homes than suburban homes, and the same was true for beneficial intestinal bacterial species, such as Lactobacillus amylovorus, Eubacterium hallii, and Faecalibacterium prausnitzii. Furthermore, we found a higher similarity between bacterial communities in individual farmers’ homes and their associated cow stables than for pig stables. Our findings contribute with important knowledge on bacterial composition, abundance, and diversity in different environments, which is highly valuable in the discussion on how microbial exposure may contribute to the development of immune-mediated diseases in both children and adults.
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Affiliation(s)
- Hesham Amin
- Department of Clinical Science, University of Bergen, Bergen, Norway
- *Correspondence: Hesham Amin,
| | - Tina Šantl-Temkiv
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Christine Cramer
- Department of Public Health, Environment, Work, and Health, Danish Ramazzini Center, Aarhus University, Aarhus, Denmark
- Department of Occupational Medicine, Danish Ramazzini Center, Aarhus University Hospital, Aarhus, Denmark
| | - Ditte V. Vestergaard
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
- Department of Public Health, Environment, Work, and Health, Danish Ramazzini Center, Aarhus University, Aarhus, Denmark
| | - Gitte J. Holst
- Department of Public Health, Environment, Work, and Health, Danish Ramazzini Center, Aarhus University, Aarhus, Denmark
| | - Grethe Elholm
- Department of Public Health, Environment, Work, and Health, Danish Ramazzini Center, Aarhus University, Aarhus, Denmark
| | - Kai Finster
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Vivi Schlünssen
- Department of Public Health, Environment, Work, and Health, Danish Ramazzini Center, Aarhus University, Aarhus, Denmark
- The National Research Center for the Working Environment, Copenhagen, Denmark
| | - Torben Sigsgaard
- Department of Public Health, Environment, Work, and Health, Danish Ramazzini Center, Aarhus University, Aarhus, Denmark
| | - Ian P. G. Marshall
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
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Gregorič M, Kutnjak D, Bačnik K, Gostinčar C, Pecman A, Ravnikar M, Kuntner M. Spider webs as eDNA samplers: biodiversity assessment across the tree of life. Mol Ecol Resour 2022; 22:2534-2545. [PMID: 35510791 DOI: 10.1111/1755-0998.13629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/03/2022] [Accepted: 04/11/2022] [Indexed: 11/25/2022]
Abstract
The concept of environmental DNA (eDNA) utilizes nucleic acids of organisms directly from the environment. Recent breakthrough studies have successfully detected a wide spectrum of prokaryotic and eukaryotic eDNA from a variety of environments, ranging from ancient to modern, and from terrestrial to aquatic. With their diversity and ubiquity in nature, spider webs might act as powerful biofilters and could thus represent a promising new source of eDNA, but their utility under natural field conditions is severely understudied. Here, we bridge this knowledge gap to establish spider webs as a source of eDNA with far reaching implications. First, we conducted a field study to track specific arthropod targets from different spider webs. We then employed high-throughput amplicon sequencing of taxonomic barcodes to investigate the utility of spider web eDNA for biodiversity monitoring of animals, fungi, and bacteria. Our results show that genetic remains on spider webs allow the detection of even the smallest target organisms. We also demonstrate that eDNA from spider webs is useful in research of community compositions across the different domains of life, with potentially highly detailed temporal and spatial information.
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Affiliation(s)
- Matjaž Gregorič
- Jovan Hadži Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Novi trg 2, 1000, Ljubljana, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Katarina Bačnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva ulica 101, 1000, Ljubljana, Slovenia
| | - Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.,Wine Research Centre, University of Nova Gorica, Vipavska 13, 5000, Nova Gorica, Slovenia
| | - Matjaž Kuntner
- Jovan Hadži Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Novi trg 2, 1000, Ljubljana, Slovenia.,Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution, NW, Washington DC, 20560-0105, USA.,Centre for Behavioural Ecology and Evolution, College of Life Sciences, Hubei University, 368 Youyi Road, Wuhan, Hubei, 430062, China
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10
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Applying the exposome concept to working life health. Environ Epidemiol 2022; 6:e185. [PMID: 35434456 PMCID: PMC9005258 DOI: 10.1097/ee9.0000000000000185] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/14/2021] [Indexed: 12/14/2022] Open
Abstract
Exposures at work have a major impact on noncommunicable diseases (NCDs). Current risk reduction policies and strategies are informed by existing scientific evidence, which is limited due to the challenges of studying the complex relationship between exposure at work and outside work and health. We define the working life exposome as all occupational and related nonoccupational exposures. The latter includes nonoccupational exposures that may be directly or indirectly influenced by or interact with the working life of the individual in their relation to health. The Exposome Project for Health and Occupational Research aims to advance knowledge on the complex working life exposures in relation to disease beyond the single high exposure–single health outcome paradigm, mapping and relating interrelated exposures to inherent biological pathways, key body functions, and health. This will be achieved by combining (1) large-scale harmonization and pooling of existing European cohorts systematically looking at multiple exposures and diseases, with (2) the collection of new high-resolution external and internal exposure data. Methods and tools to characterize the working life exposome will be developed and applied, including sensors, wearables, a harmonized job exposure matrix (EuroJEM), noninvasive biomonitoring, omics, data mining, and (bio)statistics. The toolbox of developed methods and knowledge will be made available to policy makers, occupational health practitioners, and scientists. Advanced knowledge on working life exposures in relation to NCDs will serve as a basis for evidence-based and cost-effective preventive policies and actions. The toolbox will also enable future scientists to further expand the working life exposome knowledge base.
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11
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Abstract
Particulate matter (PM) represents an air quality management challenge for confined swine production systems. Due to the limited space and ventilation rate, PM can reach relatively high concentrations in swine barns. PM in swine barns possesses different physical, chemical, and biological characteristics than that in the atmosphere and other indoor environments. As a result, it exerts different environmental and health effects and creates some unique challenges regarding PM measurement and mitigation. Numerous research efforts have been made, generating massive data and information. However, relevant review reports are sporadic. This study aims to provide an updated comprehensive review of swine barn PM, focusing on publications since 1990. It covers various topics including PM characteristics, sources, measurement methods, and in-barn mitigation technologies. As PM in swine barns is primarily of biological origins, bioaerosols are reviewed in great detail. Relevant topics include bacterial/fungal counts, viruses, microbial community composition, antibiotic-resistant bacteria, antibiotic resistance genes, endotoxins, and (1→3)-β-D-glucans. For each topic, existing knowledge is summarized and discussed and knowledge gaps are identified. Overall, PM in swine barns is complicated in chemical and biological composition and highly variable in mass concentrations, size, and microbial abundance. Feed, feces, and skins constitute the major PM sources. Regarding in-barn PM mitigation, four technologies (oil/water sprinkling, ionization, alternation of feed and feeders, and recirculating air filtration) are dominant. However, none of them have been widely used in commercial barns. A collective discussion of major knowledge gaps and future research needs is offered at the end of the report.
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12
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Bai H, He LY, Wu DL, Gao FZ, Zhang M, Zou HY, Yao MS, Ying GG. Spread of airborne antibiotic resistance from animal farms to the environment: Dispersal pattern and exposure risk. ENVIRONMENT INTERNATIONAL 2022; 158:106927. [PMID: 34673316 DOI: 10.1016/j.envint.2021.106927] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/16/2021] [Accepted: 10/06/2021] [Indexed: 05/05/2023]
Abstract
Animal farms have been considered as the critical reservoir of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). Spread of antibiotic resistance from animal farms to the surrounding environments via aerosols has become a growing concern. Here we investigated the dispersal pattern and exposure risk of airborne ARGs (especially in zoonotic pathogens) in the environment of chicken and dairy farms. Aerosol, dust and animal feces samples were collected from the livestock houses and surrounding environments (upwind and downwind areas) for assessing ARG profiles. Antibiotic resistance phenotype and genotype of airborne Staphylococcus spp. was especially analyzed to reveal the exposure risk of airborne ARGs. Results showed that airborne ARGs were detected from upwind (50 m/100 m) and downwind (50 m/100 m/150 m) air environment, wherein at least 30% of bacterial taxa dispersed from the animal houses. Moreover, atmospheric dispersion modeling showed that airborne ARGs can disperse from the animal houses to a distance of 10 km along the wind direction. Clinically important pathogens were identified in airborne culturable bacteria. Genus of Staphylococcus, Sphingomonas and Acinetobacter were potential bacterial host of airborne ARGs. Airborne Staphylococcus spp. were isolated from the environment of chicken farm (n = 148) and dairy farm (n = 87). It is notable that all isolates from chicken-related environment were multidrug-resistance (>3 clinical-relevant antibiotics), with more than 80% of them carrying methicillin resistance gene (mecA) and associated ARGs and MGEs. Presence of numerous ARGs and diverse pathogens in dust from animal houses and the downwind residential areas indicated the accumulation of animal feces origin ARGs in bioaerosols. Employees and local residents in the chick farming environment are exposed to chicken originated ARGs and multidrug resistant Staphylococcus spp. via inhalation. This study highlights the potential exposure risks of airborne ARGs and antibiotic resistant pathogens to human health.
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Affiliation(s)
- Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
| | - Dai-Ling Wu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China; Aquatic Ecology and Water Quality Management Group, Wageningen University, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Min Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Hai-Yan Zou
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Mao-Sheng Yao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
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13
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Kuthyar S, Reese AT. Variation in Microbial Exposure at the Human-Animal Interface and the Implications for Microbiome-Mediated Health Outcome. mSystems 2021; 6:e0056721. [PMID: 34342530 PMCID: PMC8407385 DOI: 10.1128/msystems.00567-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The human gut microbiome varies between populations, largely reflecting ecological differences. One ecological variable that is rarely considered but may contribute substantially to microbiome variation is the multifaceted nature of human-animal interfaces. We present the hypothesis that different interactions with animals contribute to shaping the human microbiome globally. We utilize a One Health framework to explore how changes in microbial exposure from human-animal interfaces shape the microbiome and, in turn, contribute to differential human health across populations, focusing on commensal and pathogen exposure, changes in colonization resistance and immune system training, and the potential for other functional shifts. Although human-animal interfaces are known to underlie human health and particularly infectious disease disparities, since their impact on the human microbiome remains woefully understudied, we propose foci for future research. We believe it will be crucial to understand this critical aspect of biology and its impacts on human health around the globe.
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Affiliation(s)
- Sahana Kuthyar
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Aspen T. Reese
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
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14
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Wang Z, Lai Z, Zhang X, Huang P, Xie J, Jiang Q, Zhang Q, Chung KF. Altered gut microbiome compositions are associated with the severity of asthma. J Thorac Dis 2021; 13:4322-4338. [PMID: 34422359 PMCID: PMC8339736 DOI: 10.21037/jtd-20-2189] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 05/31/2021] [Indexed: 12/31/2022]
Abstract
Background Despite substantial evidence on the contribution of the diversity of the gut microbiome to the pathogenesis of asthma and allergic diseases, little is known about their relationship with asthma severity and/or clinical phenotypes. We analyzed the difference in composition of the gut microbiome between subjects with asthma and healthy subjects and explored its role in the development of asthma. Methods Fecal samples from 15 subjects with severe asthma (SA), 14 with non-severe asthma (NSA), and 15 healthy subjects were assessed by 16S ribosomal RNA gene sequencing methods to identify the gut bacterial composition. Results Compared with those in the NSA group, patients in the SA group had a higher dose of inhaled corticosteroids, and there were more atopic subjects (60% vs. 35.7%, respectively). No significant differences were found at the phylum level either in operational taxonomic unit numbers or in diversity scores among the SA, NSA, and healthy groups. However, at the family level, the relative abundance of Acidaminococcaceae in the SA group was remarkedly lower than that in the group with healthy subjects (P<0.05). Furthermore, Veillonellaceae and Prevotellaceae were significantly more common in samples from the SA group than in those from the NSA group (P<0.05). In the SA group, positive correlations were observed between the relative abundance of Veillonellaceae and mid-expiratory flow 25% (MEF25%) predicted (r=0.538, P=0.047), as well as between the relative abundance of Acidaminococcaceae and body mass index (r=0642, P=0.010). Principal component analysis suggested that the relative abundances of Acidaminococcaceae and Prevotellaceae were associated with severe asthma. Moreover, we found that class Betaproteobacteria, order Burkholderiales, and family Alcaligenaceae were significantly different among the groups defined by serum immunoglobulin E (IgE) levels. Conclusions Our findings suggest that altered gut microbiome compositions are involved in the severity of asthma and that there are specific bacteria related to different asthma phenotypes in terms of serum IgE levels.
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Affiliation(s)
- Zhiqiang Wang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Hexian Memorial Hospital of PanYu District, Guangzhou, China
| | - Zhengdao Lai
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Dongguan Institute of Respiratory and Critical Care Medicine, Afliated Dongguan People's Hospital, Southern Medicial University, Dongguan, China
| | - Xiaoxian Zhang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Peikai Huang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Respiration Medicine, Huizhou Municipal Central Hospital, Huizhou, China
| | - Jiaxing Xie
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qian Jiang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qingling Zhang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Kian Fan Chung
- National Heart & Lung Institute, Imperial College London & Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, UK
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15
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Mahdavinia M, Greenfield LR, Moore D, Botha M, Engen P, Gray C, Lunjani N, Hlela C, Basera W, Hobane L, Watkins A, Mankahla A, Gaunt B, Facey-Thomas H, Landay A, Keshavarzian A, Levin ME. House dust microbiota and atopic dermatitis; effect of urbanization. Pediatr Allergy Immunol 2021; 32:1006-1012. [PMID: 33570236 DOI: 10.1111/pai.13471] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 01/09/2023]
Abstract
BACKGROUND Previous studies have shown that a child's risk of developing atopic disease is impacted by both genetic and environmental factors. Because small children spend the majority of their time in their homes, exposure to microbial factors in their home environment may be protective or risk factors for development of atopic diseases, such as atopic dermatitis. METHODS Dust samples from the homes of 86 Black South African children 12 to 36 months old were collected for analysis of the bacterial microbiome. This case-control study design included children with and without atopic dermatitis from rural and urban environments. RESULTS Significant differences in bacterial composition and diversity were found when comparing children with and without atopic dermatitis. Furthermore, house dust microbiota was significantly different in rural and urban areas. Differences were best accounted for by higher relative abundance of Ruminococcaceae, Lachnospiraceae, and Bacteroidaceae families in rural compared with urban houses. Levels of Ruminococcaceae were also found to be significantly depleted in the house dust of rural children with atopic dermatitis as compared to control children. CONCLUSIONS House dust composition may be an important risk factor for the development of atopic disease, and this association may be driven in part by the gut microbiome. Low levels of the Ruminococcaceae family from Clostridia class in particular may explain the association between urban living and atopy. However, further research is needed to elucidate these links.
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Affiliation(s)
- Mahboobeh Mahdavinia
- Department of Internal Medicine, Allergy and Immunology Division, Rush University Medical Center, Chicago, IL, USA.,InVivo Planetary Health Network, Chicago, IL, USA
| | - Leah R Greenfield
- Department of Internal Medicine, Allergy and Immunology Division, Rush University Medical Center, Chicago, IL, USA.,Rush Medical College, Chicago, IL, USA
| | - Donyea Moore
- Department of Internal Medicine, Allergy and Immunology Division, Rush University Medical Center, Chicago, IL, USA
| | - Maresa Botha
- InVivo Planetary Health Network, Chicago, IL, USA.,Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | | | - Claudia Gray
- Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.,Department of Dermatology, University of Cape Town, Cape Town, South Africa
| | - Nonhlanhla Lunjani
- Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Carol Hlela
- Department of Dermatology, University of Cape Town, Cape Town, South Africa
| | - Wisdom Basera
- Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Lelani Hobane
- Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Alexandra Watkins
- Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Avumile Mankahla
- Eastern Cape Department of Health, Zithulele Hospital, Mqanduli, South Africa
| | - Ben Gaunt
- Division of Dermatology, Department of Medicine and Pharmacology, Walter Sisulu University, Mthatha, South Africa
| | - Heidi Facey-Thomas
- Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Alan Landay
- Geriatrics Division, Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Ali Keshavarzian
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL, USA
| | - Michael E Levin
- InVivo Planetary Health Network, Chicago, IL, USA.,Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
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16
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Hong SW, Park J, Jeong H, Kim M. Evaluation of the microbiome composition in particulate matter inside and outside of pig houses. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2021; 63:640-650. [PMID: 34189511 PMCID: PMC8203996 DOI: 10.5187/jast.2021.e52] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/24/2021] [Accepted: 02/28/2021] [Indexed: 12/12/2022]
Abstract
Particulate matter (PM) produced in pig houses may contain microbes which can
spread by airborne transmission, and PM and microbes in PM adversely affect
human and animal health. To investigate the microbiome in PM from pig houses,
nine PM samples were collected in summer 2020 inside and outside of pig houses
located in Jangseong-gun, Jeollanam-do Province, Korea, comprising three PM
samples from within a nursery pig house (I-NPH), three samples from within a
finishing pig house (I-FPH), and three samples from outside of the pig houses
(O-PH). Microbiomes were analyzed using 16S rRNA gene amplicon sequencing.
Firmicutes was the most dominant phylum and accounted for 64.8%–97.5% of
total sequences in all the samples, followed by Proteobacteria
(1.4%–21.8%) and Bacteroidetes (0.3%–13.7%). In total, 31 genera
were represented by > 0.3% of all sequences, and only
Lactobacillus, Turicibacter, and
Aerococcus differed significantly among the three PM sample
types. All three genera were more abundant in the I-FPH samples than in the O-PH
samples. Alpha diversity indices did not differ significantly among the three PM
types, and a principal coordinate analysis suggested that overall microbial
communities were similar across PM types. The concentration of PM did not
significantly differ among the three PM types, and no significant correlation of
PM concentration with the abundance of any potential pathogen was observed. The
present study demonstrates that microbial composition in PM inside and outside
of pig houses is similar, indicating that most microbe-containing PM inside pig
houses leaks to the outside from where it, along with microbe-containing PM on
the outside, may re-enter the pig houses. Our results may provide useful
insights regarding strategies to mitigate potential risk associated with pig
farming PM and pathogens in PM.
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Affiliation(s)
- Se-Woon Hong
- Department of Rural and Biosystems Engineering, Chonnam National University, Gwangju 61186, Korea.,Education and Research Unit for Climate-Smart Reclaimed-Tideland Agriculture, Chonnam National University, Gwangju 61186, Korea.,AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju 61186, Korea
| | - Jinseon Park
- AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju 61186, Korea
| | - Hanna Jeong
- Department of Rural and Biosystems Engineering, Chonnam National University, Gwangju 61186, Korea.,Education and Research Unit for Climate-Smart Reclaimed-Tideland Agriculture, Chonnam National University, Gwangju 61186, Korea
| | - Minseok Kim
- AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju 61186, Korea.,Department of Animal Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
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17
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Crawford MS, Nordgren TM, McCole DF. Every breath you take: Impacts of environmental dust exposure on intestinal barrier function-from the gut-lung axis to COVID-19. Am J Physiol Gastrointest Liver Physiol 2021; 320:G586-G600. [PMID: 33501887 PMCID: PMC8054554 DOI: 10.1152/ajpgi.00423.2020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 01/31/2023]
Abstract
As countries continue to industrialize, major cities experience diminished air quality, whereas rural populations also experience poor air quality from sources such as agricultural operations. These exposures to environmental pollution from both rural and populated/industrialized sources have adverse effects on human health. Although respiratory diseases (e.g., asthma and chronic obstructive pulmonary disease) are the most commonly reported following long-term exposure to particulate matter and hazardous chemicals, gastrointestinal complications have also been associated with the increased risk of lung disease from inhalation of polluted air. The interconnectedness of these organ systems has offered valuable insights into the roles of the immune system and the micro/mycobiota as mediators of communication between the lung and the gut during disease states. A topical example of this relationship is provided by reports of multiple gastrointestinal symptoms in patients with coronavirus disease 2019 (COVID-19), whereas the rapid transmission and increased risk of COVID-19 has been linked to poor air quality and high levels of particulate matter. In this review, we focus on the mechanistic effects of environmental pollution on disease progression with special emphasis on the gut-lung axis.
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Affiliation(s)
- Meli'sa S Crawford
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California
| | - Tara M Nordgren
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California
| | - Declan F McCole
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California
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18
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Mikkelsen S, Dinh KM, Boldsen JK, Pedersen OB, Holst GJ, Petersen MS, Kaspersen KA, Møller BK, Nielsen KR, Paarup HM, Rostgaard K, Hjalgrim H, Sørensen E, Handgaard LJ, Hansen TF, Banasik K, Burgdorf KS, Ullum H, Sigsgaard T, Erikstrup C. Combinations of self-reported rhinitis, conjunctivitis, and asthma predicts IgE sensitization in more than 25,000 Danes. Clin Transl Allergy 2021; 11:e12013. [PMID: 33900050 PMCID: PMC8099331 DOI: 10.1002/clt2.12013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 12/01/2022] Open
Abstract
Background Allergic rhinitis (AR), allergic conjunctivitis (AC), and asthma composing multiple phenotypes and improved understanding of these phenotypes and their respective risk factors are needed. Objectives The objective of this study was to define the prevalence of AR, AC, and asthma and their association with allergen‐specific immunoglobulin E (sIgE) sensitization in a large cohort of blood donors and identify risk factors. Methods From the nationwide population‐based Danish Blood Donor Study, 52,976 participants completed an electronic questionnaire including AR, AC, asthma, allergic predisposition, and childhood residence. Of these, 25,257 were additionally tested for sIgE to inhalation allergens (Phadiatop). Results The prevalence of sIgE sensitization, AR, AC, and asthma was 30%, 19%, 15%, and 9%, respectively. The youngest birth cohorts had the highest prevalence of sIgE sensitization and symptoms of asthma, AR, and AC, and for asthma, they apparently experienced symptoms at an earlier age. The sIgE sensitization was positively associated with male sex. The sIgE seroprevalence was higher in participants with both AR and AC (ARC) than in participants with either AR or AC. Allergic predisposition and sIgE sensitization increased the risk of the diseases, while farm upbringing was associated with reduced prevalence of ARC, however, only in sIgE sensitized participants. Conclusion Birth year, childhood residence, sIgE sensitization, and allergic predisposition were associated with asthma, AR, and AC prevalence. Individuals with self‐reported ARC represent a primarily sIgE‐positive phenotype, while those with either AR or AC represent more diverse phenotypes.
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Affiliation(s)
- Susan Mikkelsen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Khoa Manh Dinh
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Kjaergaard Boldsen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark.,Danish Big Data Centre for Environment and Health (BERTHA), Aarhus University, Roskilde, Denmark
| | - Ole Birger Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Gitte Juel Holst
- The Danish Clinical Quality Program-National Clinical Registries (RKKP), Central Denmark Region, Aarhus, Denmark
| | | | - Kathrine Agergård Kaspersen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark.,Danish Big Data Centre for Environment and Health (BERTHA), Aarhus University, Roskilde, Denmark
| | - Bjarne Kuno Møller
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Kaspar Rene Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Klaus Rostgaard
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Linda Jenny Handgaard
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas Folkmann Hansen
- Department of Neurology, Danish Headache Center, Copenhagen University Hospital, Glostrup, Denmark.,Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Karina Banasik
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Henrik Ullum
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark.,Statens Serum Institut, Copenhagen, Denmark
| | - Torben Sigsgaard
- Danish Big Data Centre for Environment and Health (BERTHA), Aarhus University, Roskilde, Denmark.,Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark.,Danish Big Data Centre for Environment and Health (BERTHA), Aarhus University, Roskilde, Denmark
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19
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Zhang Y, Zheng Y, Zhu Z, Chen Y, Dong H. Dispersion of Antibiotic Resistance Genes (ARGs) from stored swine manure biogas digestate to the atmosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:144108. [PMID: 33360136 DOI: 10.1016/j.scitotenv.2020.144108] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/17/2020] [Accepted: 11/21/2020] [Indexed: 05/23/2023]
Abstract
Biogas digestate is a reservoir of antibiotic resistance genes (ARGs) and could pose a high health risk to both human and animals if the host microorganisms of ARGs become aerosolized. The purpose of this study was to investigate the diversity and relative abundance characteristics of aerosol-loaded ARGs from biogas digestate during storage, and to explore whether the change of ARGs in biogas digestate directly affect the dispersion of aerosol-loaded ARGs. This study reported for the first time that 28 of 42 ARG subtypes detected in the biogas digestate could be dispersed to the atmosphere via aerosol dispersion in a lab-scale dynamic emission vessels experiment. The relative abundance or diversity of ARGs in aerosols were different from that in biogas digestate, and no significant correlation were observed between the relative abundance of ARGs in biogas digestate and aerosols. The dominant ARGs were tetracycline resistance genes in biogas digestate and β-lactam resistance genes in aerosols. The process of biogas digestate storage reduced the total relative abundance of targeted ARGs in biogas digestate, decreased by 0.35 copies/16S rRNA after 30 days of storage, but increased the abundance of some ARG subtypes, including tetM, tetX, tetQ, tetS, ermF and sul2. High-concerned ARGs, including NDM-1, mcr-1 and vancomycin resistance genes (including vanA, vanB, vanRA and vanSA), were found in biogas digestate, and NDM-1 and vanB were also detected in aerosols. These results indicated a potential risk of ARGs dispersion during biogas digestate storage. Further research on the dispersion of ARGs from biogas digestate is required to elucidate the emission mechanism and develop mitigation measures.
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Affiliation(s)
- Yu Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Energy Conservation and Waste utilization in Agriculture, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Yunhao Zheng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Energy Conservation and Waste utilization in Agriculture, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Zhiping Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Energy Conservation and Waste utilization in Agriculture, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Yongxing Chen
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Energy Conservation and Waste utilization in Agriculture, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Hongmin Dong
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Energy Conservation and Waste utilization in Agriculture, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
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20
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Flies EJ, Jones P, Buettel JC, Brook BW. Compromised Ecosystem Services From Urban Aerial Microbiomes: A Review of Impacts on Human Immune Function. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.568902] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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21
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Flies EJ, Clarke LJ, Brook BW, Jones P. Urbanisation reduces the abundance and diversity of airborne microbes - but what does that mean for our health? A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:140337. [PMID: 32806360 DOI: 10.1016/j.scitotenv.2020.140337] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 05/21/2023]
Abstract
Over half of people live in cities and while urban environments offer myriad social, cultural and economic benefits, they alter the microbial communities to which people are exposed: with potentially important but underexplored health impacts. In particular, higher rates of asthma and allergies in urban areas have been linked to urban-altered microbial communities - including aerial microbial communities. To date, however, there has been no synthesis of the disparate literature on the impacts of urbanisation on aerial microbial communities, making it difficult to ascertain potential health impacts. We fill this knowledge gap by systematically examining studies that compare the characteristics (e.g. microbial abundance/diversity) and/or health effects of airborne fungal and bacterial communities (hereafter referred to as 'aerobiomes') across urban and rural locations. We included 19 studies, with 31 distinct urban-rural comparisons, in our analysis. We found that rural aerobiomes more often have a greater abundance of microbes (57% of studies). Aerobiome diversity was under-reported but when comparisons were made, rural aerobiome diversity was often higher (67%). Only two studies experimentally examined the impact of urban and rural aerobiomes on human health outcomes; both found rural aerobiomes shifted immune function away from allergic (Th2-type) responses. Overall, we conclude that significant gaps remain in our understanding of how urbanisation impacts aerobiomes and the health implications of those changes. We highlight the need to standardise methods and make aerobiome data open access to facilitate cross-study comparisons. Further mechanistic studies are urgently needed to examine the impact of aerobiome composition on immune function to demonstrate how urban-driven changes to the aerobiome impact human health - ultimately facilitating the development of healthier cities.
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Affiliation(s)
- Emily J Flies
- School of Natural Sciences, University of Tasmania, Australia.
| | - Laurence J Clarke
- Antarctic Climate & Ecosystems Cooperative Research Centre, University of Tasmania, Australia; Institute for Marine and Antarctic Studies, University of Tasmania, Australia
| | - Barry W Brook
- School of Natural Sciences, University of Tasmania, Australia; ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), Australia
| | - Penelope Jones
- Menzies Institute for Medical Research, University of Tasmania, Australia
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22
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Luiken REC, Van Gompel L, Bossers A, Munk P, Joosten P, Hansen RB, Knudsen BE, García-Cobos S, Dewulf J, Aarestrup FM, Wagenaar JA, Smit LAM, Mevius DJ, Heederik DJJ, Schmitt H. Farm dust resistomes and bacterial microbiomes in European poultry and pig farms. ENVIRONMENT INTERNATIONAL 2020; 143:105971. [PMID: 32738764 DOI: 10.1016/j.envint.2020.105971] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents. Although dust is a potential route of transmission, little is known about the resistome and bacterial microbiome of farm dust. OBJECTIVES We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers' stool resistomes was explored. METHODS In the EFFORT-study, resistomes and bacterial microbiomes of indoor farm dust collected on Electrostatic Dust fall Collectors (EDCs), and animal feces of 35 conventional broiler and 44 farrow-to-finish pig farms from nine European countries were determined by shotgun metagenomic analysis. The analysis also included 79 stool samples from farmers working or living at 12 broiler and 19 pig farms and 46 human controls. Relative abundance of and variation in resistome and bacterial composition of farm dust was described and compared to animal feces and farmers' stool. RESULTS The farm dust resistome contained a large variety of antimicrobial resistance genes (ARGs); more than the animal fecal resistome. For both poultry and pigs, composition of dust resistomes finds (partly) its origin in animal feces as dust resistomes correlated significantly with fecal resistomes. The dust bacterial microbiome also correlated significantly with the dust resistome composition. A positive association between AMU in animals on the farm and the total abundance of the dust resistome was found. Occupational exposure to pig farm dust or animal feces may contribute to farmers' resistomes, however no major shifts in farmers resistome towards feces or dust resistomes were found in this study. CONCLUSION Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome.
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Affiliation(s)
- Roosmarijn E C Luiken
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands.
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands; Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands
| | - Patrick Munk
- Section for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Philip Joosten
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
| | | | - Berith E Knudsen
- Section for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Silvia García-Cobos
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, PO Box 30.001, 9700 RB Groningen, the Netherlands
| | - Jeroen Dewulf
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
| | - Frank M Aarestrup
- Section for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Jaap A Wagenaar
- Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands; Dept. Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Dik J Mevius
- Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands; Dept. Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Heike Schmitt
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721MA Bilthoven, the Netherlands
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23
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Tan SC, Chong CW, Yap IKS, Thong KL, Teh CSJ. Comparative assessment of faecal microbial composition and metabonome of swine, farmers and human control. Sci Rep 2020; 10:8997. [PMID: 32488118 PMCID: PMC7265441 DOI: 10.1038/s41598-020-65891-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal tract of humans and swine consist of a wide range of bacteria which interact with hosts metabolism. Due to the differences in co-evolution and co-adaptation, a large fraction of the gut microbiome is host-specific. In this study, we evaluated the effect of close human-animal interaction to the faecal metagenome and metabonome of swine, farmer and human control. Three distinct clusters were observed based on T-RFLP-derived faecal microbial composition. However, 16S-inferred faecal microbiota and metabolic profiles showed that only human control was significantly different from the swine (P < 0.05). The metabonome of farmers and human controls were highly similar. Notably, higher trimethylamine N-oxide (TMAO) and butyrate were detected in human control and swine, respectively. The relative abundance of TMAO was positively correlated with Prevotella copri. Overall, we compared and established the relationship between the metabolites and microbiota composition of swine, farmers and human control. Based on the data obtained, we deduced that long term occupational exposure to swine and farm environment had affected the gut bacterial composition of farmers. Nonetheless, the effect was less prominent in the metabolite profiles, suggesting the gut bacteria expressed high functional plasticity and are therefore resilience to the level of community shift detected.
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Affiliation(s)
- Shiang Chiet Tan
- Institute of Biological Science, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Chun Wie Chong
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Malaysia
- Centre for Translational Research, Institute for Research, Development and Innovation (IRDI), International Medical University, 57000, Kuala Lumpur, Malaysia
| | - Ivan Kok Seng Yap
- Sarawak Research and Development Council, 11th Floor LCDA Tower, The Isthmus, Off Jalan Bako, 93050, Kuching, Sarawak, Malaysia
| | - Kwai Lin Thong
- NANOCAT Research Centre, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Cindy Shuan Ju Teh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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24
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Tang Q, Huang K, Liu J, Shen D, Dai P, Li Y, Li C. Seasonal variations of microbial assemblage in fine particulate matter from a nursery pig house. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 708:134921. [PMID: 31771854 DOI: 10.1016/j.scitotenv.2019.134921] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
The microorganisms contained in PM2.5 from livestock houses can spread over long distances through airborne transmission. As such, the potential bacterial pathogens and fungal allergens within can pose a formidable threat to nearby residents' health and the overall environment. However, little is known about the microbial assemblage contained in PM2.5 from pig houses. In this study, 16S and 18S rRNA gene sequencing was employed to analyze the bacterial and fungal assemblage contained in PM2.5 from a nursery pig house across four seasons, respectively. The results showed that alpha diversity was higher in summer and autumn compared to the spring and winter. The bacterial and fungal assemblage varied according to season. At the phylum level, the dominant bacteria and fungi were Firmicutes and Basidiomycota, respectively, across the four seasons. At the genus level, a total of five potential bacterial pathogen and 20 potential fungal allergen genera were identified across the samples. The most abundant bacterial pathogen and fungal allergen genera were observed in summer and autumn, respectively, but neither had a significant correlation with PM2.5 concentration. Moreover, microbial diversity and the relative abundance of fungal allergen genera were positively correlated with temperature and relative humidity. It can be concluded that microbial diversity and assemblage varied significantly among the seasons in a nursery pig house, and this can be useful in exploring the potential risks of PM2.5 from pig houses across all four seasons.
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Affiliation(s)
- Qian Tang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Huang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Junze Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Dan Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengyuan Dai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yansen Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunmei Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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25
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Horve PF, Lloyd S, Mhuireach GA, Dietz L, Fretz M, MacCrone G, Van Den Wymelenberg K, Ishaq SL. Building upon current knowledge and techniques of indoor microbiology to construct the next era of theory into microorganisms, health, and the built environment. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2020; 30:219-235. [PMID: 31308484 PMCID: PMC7100162 DOI: 10.1038/s41370-019-0157-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/23/2019] [Accepted: 06/30/2019] [Indexed: 05/06/2023]
Abstract
In the constructed habitat in which we spend up to 90% of our time, architectural design influences occupants' behavioral patterns, interactions with objects, surfaces, rituals, the outside environment, and each other. Within this built environment, human behavior and building design contribute to the accrual and dispersal of microorganisms; it is a collection of fomites that transfer microorganisms; reservoirs that collect biomass; structures that induce human or air movement patterns; and space types that encourage proximity or isolation between humans whose personal microbial clouds disperse cells into buildings. There have been recent calls to incorporate building microbiology into occupant health and exposure research and standards, yet the built environment is largely viewed as a repository for microorganisms which are to be eliminated, instead of a habitat which is inexorably linked to the microbial influences of building inhabitants. Health sectors have re-evaluated the role of microorganisms in health, incorporating microorganisms into prevention and treatment protocols, yet no paradigm shift has occurred with respect to microbiology of the built environment, despite calls to do so. Technological and logistical constraints often preclude our ability to link health outcomes to indoor microbiology, yet sufficient study exists to inform the theory and implementation of the next era of research and intervention in the built environment. This review presents built environment characteristics in relation to human health and disease, explores some of the current experimental strategies and interventions which explore health in the built environment, and discusses an emerging model for fostering indoor microbiology rather than fearing it.
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Affiliation(s)
- Patrick F Horve
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Savanna Lloyd
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Gwynne A Mhuireach
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Leslie Dietz
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Mark Fretz
- Institute for Health and the Built Environment, University of Oregon, Portland, OR, 97209, USA
| | - Georgia MacCrone
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Kevin Van Den Wymelenberg
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
- Institute for Health and the Built Environment, University of Oregon, Portland, OR, 97209, USA
| | - Suzanne L Ishaq
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA.
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26
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Karlsson E, Johansson AM, Ahlinder J, Lundkvist MJ, Singh NJ, Brodin T, Forsman M, Stenberg P. Airborne microbial biodiversity and seasonality in Northern and Southern Sweden. PeerJ 2020; 8:e8424. [PMID: 32025374 PMCID: PMC6991134 DOI: 10.7717/peerj.8424] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/17/2019] [Indexed: 01/04/2023] Open
Abstract
Microorganisms are essential constituents of ecosystems. To improve our understanding of how various factors shape microbial diversity and composition in nature it is important to study how microorganisms vary in space and time. Factors shaping microbial communities in ground level air have been surveyed in a limited number of studies, indicating that geographic location, season and local climate influence the microbial communities. However, few have surveyed more than one location, at high latitude or continuously over more than a year. We surveyed the airborne microbial communities over two full consecutive years in Kiruna, in the Arctic boreal zone, and Ljungbyhed, in the Southern nemoral zone of Sweden, by using a unique collection of archived air filters. We mapped both geographic and seasonal differences in bacterial and fungal communities and evaluated environmental factors that may contribute to these differences and found that location, season and weather influence the airborne communities. Location had stronger influence on the bacterial community composition compared to season, while location and season had equal influence on the fungal community composition. However, the airborne bacterial and fungal diversity showed overall the same trend over the seasons, regardless of location, with a peak during the warmer parts of the year, except for the fungal seasonal trend in Ljungbyhed, which fluctuated more within season. Interestingly, the diversity and evenness of the airborne communities were generally lower in Ljungbyhed. In addition, both bacterial and fungal communities varied significantly within and between locations, where orders like Rhizobiales, Rhodospirillales and Agaricales dominated in Kiruna, whereas Bacillales, Clostridiales and Sordariales dominated in Ljungbyhed. These differences are a likely reflection of the landscape surrounding the sampling sites where the landscape in Ljungbyhed is more homogenous and predominantly characterized by artificial and agricultural surroundings. Our results further indicate that local landscape, as well as seasonal variation, shapes microbial communities in air.
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Affiliation(s)
- Edvin Karlsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden
| | | | - Jon Ahlinder
- Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden
| | - Moa J Lundkvist
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Navinder J Singh
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Tomas Brodin
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Mats Forsman
- Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden
| | - Per Stenberg
- Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden.,Department of Ecology and Environmental Sciences, Umeå University, Umeå, Sweden
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27
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Porras AM, Brito IL. The internationalization of human microbiome research. Curr Opin Microbiol 2019; 50:50-55. [PMID: 31683111 PMCID: PMC6907006 DOI: 10.1016/j.mib.2019.09.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/27/2022]
Abstract
The human microbiome has now been linked with myriad diseases, yet most of this research has been conducted on American and European populations that make up only 1/6th of the world's population. With growing recognition that human microbiomes differ tremendously across global populations, it is especially important to understand how these compositional differences impact health outcomes. Recent advances in infectious disease and malnutrition research have demonstrated the potential for microbiome-based strategies to address the biggest challenges in global health. This review highlights major advances toward understanding microbiome diversity across the world and its contributions to disease, and outlines key questions, challenges, and opportunities to broaden the scope of and promote inclusivity within microbiome research.
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Affiliation(s)
- Ana Maria Porras
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14850, United States
| | - Ilana Lauren Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14850, United States.
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28
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White JK, Nielsen JL, Madsen AM. Microbial species and biodiversity in settling dust within and between pig farms. ENVIRONMENTAL RESEARCH 2019; 171:558-567. [PMID: 30771719 DOI: 10.1016/j.envres.2019.01.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/30/2018] [Accepted: 01/04/2019] [Indexed: 05/14/2023]
Abstract
The airborne fungal and bacterial species present in pig farm dust have not been well characterised even though these bioaerosols are known to cause inflammation and other airway maladies. In this study, the microbial species and composition in airborne dust within and between pig farms were investigated. Passively sedimenting dust from six pig farms were collected using electrostatic dust collectors. The bacterial and fungal species were identified using matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and next generation sequencing (NGS). Dust samples taken within the same stable section revealed high resemblance and stability. Constrained statistical analysis of the microbial community compositions indicated that the types of stable did not appear to have a great effect on the bacterial and fungal β-diversity. In contrast to this, the farm from which samples were taken appeared to have the greatest effect on the bacterial β-diversity, but this trend was not observed for the fungal β-diversity. The most common bacteria and fungi according to NGS data were anaerobes typically associated with the pig intestinal tract and yeasts respectively. Bacterial sedimentation varied at a rate between 103 and 109 CFU/m2/day, with the most common species after aerobic incubation being Aerococcus viridans and Staphylococcus equorum, while Clostridium perfringens and Staphylococcus simulans were the most common species after anaerobic incubation. A total of 28 different species of bacteria and fungi were classifiable as pathogens. In conclusion, the biodiversity in pig farm dust shows a high diversity of bacterial species. However, samples from the same stable section resembled each other, but also different sections within the same farm also resembled each other, thus indicating a high degree of community stability in the dust source. In regards to fungal identification, the biodiversity was observed to be similar between samples from different stable sections and farms, indicating a higher degree of similarities in the mycobiomes found across pig farms studied.
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Affiliation(s)
- John Kerr White
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7 H, 9220 Aalborg Ø, Denmark; The National Research Centre for the Working Environment, Lersø Parkallé 105, 2100 Copenhagen Ø, Denmark.
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7 H, 9220 Aalborg Ø, Denmark.
| | - Anne Mette Madsen
- The National Research Centre for the Working Environment, Lersø Parkallé 105, 2100 Copenhagen Ø, Denmark.
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29
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Trinh P, Zaneveld JR, Safranek S, Rabinowitz PM. One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review. Front Public Health 2018; 6:235. [PMID: 30214898 PMCID: PMC6125393 DOI: 10.3389/fpubh.2018.00235] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/08/2018] [Indexed: 12/17/2022] Open
Abstract
The One Health concept stresses the ecological relationships between human, animal, and environmental health. Much of the One Health literature to date has examined the transfer of pathogens from animals (e.g., emerging zoonoses) and the environment to humans. The recent rapid development of technology to perform high throughput DNA sequencing has expanded this view to include the study of entire microbial communities. Applying the One Health approach to the microbiome allows for consideration of both pathogenic and non-pathogenic microbial transfer between humans, animals, and the environment. We review recent research studies of such transmission, the molecular and statistical methods being used, and the implications of such microbiome relationships for human health. Our review identified evidence that the environmental microbiome as well as the microbiome of animals in close contact can affect both the human microbiome and human health outcomes. Such microbiome transfer can take place in the household as well as the workplace setting. Urbanization of built environments leads to changes in the environmental microbiome which could be a factor in human health. While affected by environmental exposures, the human microbiome also can modulate the response to environmental factors through effects on metabolic and immune function. Better understanding of these microbiome interactions between humans, animals, and the shared environment will require continued development of improved statistical and ecological modeling approaches. Such enhanced understanding could lead to innovative interventions to prevent and manage a variety of human health and disease states.
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Affiliation(s)
- Pauline Trinh
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Jesse R Zaneveld
- Division of Biological Sciences, School of Science, Technology, Education, and Mathematics, University of Washington, Bothell, WA, United States
| | - Sarah Safranek
- Health Sciences Library, University of Washington, Seattle, WA, United States
| | - Peter M Rabinowitz
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
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