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Obregon-Gutierrez P, Bonillo-Lopez L, Correa-Fiz F, Sibila M, Segalés J, Kochanowski K, Aragon V. Gut-associated microbes are present and active in the pig nasal cavity. Sci Rep 2024; 14:8470. [PMID: 38605046 PMCID: PMC11009223 DOI: 10.1038/s41598-024-58681-9] [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: 06/21/2023] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
The nasal microbiota is a key contributor to animal health, and characterizing the nasal microbiota composition is an important step towards elucidating the role of its different members. Efforts to characterize the nasal microbiota composition of domestic pigs and other farm animals frequently report the presence of bacteria that are typically found in the gut, including many anaerobes from the Bacteroidales and Clostridiales orders. However, the in vivo role of these gut-microbiota associated taxa is currently unclear. Here, we tackled this issue by examining the prevalence, origin, and activity of these taxa in the nasal microbiota of piglets. First, analysis of the nasal microbiota of farm piglets sampled in this study, as well as various publicly available data sets, revealed that gut-microbiota associated taxa indeed constitute a substantial fraction of the pig nasal microbiota that is highly variable across individual animals. Second, comparison of herd-matched nasal and rectal samples at amplicon sequencing variant (ASV) level showed that these taxa are largely shared in the nasal and rectal microbiota, suggesting a common origin driven presumably by the transfer of fecal matter. Third, surgical sampling of the inner nasal tract showed that gut-microbiota associated taxa are found throughout the nasal cavity, indicating that these taxa do not stem from contaminations introduced during sampling with conventional nasal swabs. Finally, analysis of cDNA from the 16S rRNA gene in these nasal samples indicated that gut-microbiota associated taxa are indeed active in the pig nasal cavity. This study shows that gut-microbiota associated taxa are not only present, but also active, in the nasal cavity of domestic pigs, and paves the way for future efforts to elucidate the function of these taxa within the nasal microbiota.
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Affiliation(s)
- Pau Obregon-Gutierrez
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
| | - Laura Bonillo-Lopez
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
| | - Florencia Correa-Fiz
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
| | - Marina Sibila
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
| | - Joaquim Segalés
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
| | - Karl Kochanowski
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain.
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain.
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain.
| | - Virginia Aragon
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain.
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain.
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain.
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2
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Mahmud B, Vargas RC, Sukhum KV, Patel S, Liao J, Hall LR, Kesaraju A, Le T, Kitchner T, Kronholm E, Koshalek K, Bendixsen CG, VanWormer JJ, Shukla SK, Dantas G. Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes. Nat Microbiol 2024; 9:1007-1020. [PMID: 38570675 DOI: 10.1038/s41564-024-01639-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
Globally, half a billion people are employed in animal agriculture and are directly exposed to the associated microorganisms. However, the extent to which such exposures affect resident human microbiomes is unclear. Here we conducted a longitudinal profiling of the nasal and faecal microbiomes of 66 dairy farmers and 166 dairy cows over a year-long period. We compare farmer microbiomes to those of 60 age-, sex- and ZIP code-matched people with no occupational exposures to farm animals (non-farmers). We show that farming is associated with microbiomes containing livestock-associated microbes; this is most apparent in the nasal bacterial community, with farmers harbouring a richer and more diverse nasal community than non-farmers. Similarly, in the gut microbial communities, we identify more shared microbial lineages between cows and farmers from the same farms. Additionally, we find that shared microbes are associated with antibiotic resistance genes. Overall, our study demonstrates the interconnectedness of human and animal microbiomes.
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Affiliation(s)
- Bejan Mahmud
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Rhiannon C Vargas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Kimberley V Sukhum
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Sanket Patel
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - James Liao
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Lindsey R Hall
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Akhil Kesaraju
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Thao Le
- Integrated Research Development Laboratory, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Terrie Kitchner
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Erik Kronholm
- Center for Clinical Epidemiology & Population Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Kyle Koshalek
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Casper G Bendixsen
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Jeffrey J VanWormer
- Center for Clinical Epidemiology & Population Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA.
- Computational Informatics in Biology and Medicine program, University of Wisconsin-Madison, Madison, WI, USA.
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
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3
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Robinson JM, Breed AC, Camargo A, Redvers N, Breed MF. Biodiversity and human health: A scoping review and examples of underrepresented linkages. ENVIRONMENTAL RESEARCH 2024; 246:118115. [PMID: 38199470 DOI: 10.1016/j.envres.2024.118115] [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: 11/20/2023] [Revised: 12/09/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
Mounting evidence supports the connections between exposure to environmental typologies(such as green and blue spaces)and human health. However, the mechanistic links that connect biodiversity (the variety of life) and human health, and the extent of supporting evidence remain less clear. Here, we undertook a scoping review to map the links between biodiversity and human health and summarise the levels of associated evidence using an established weight of evidence framework. Distinct from other reviews, we provide additional context regarding the environment-microbiome-health axis, evaluate the environmental buffering pathway (e.g., biodiversity impacts on air pollution), and provide examples of three under- or minimally-represented linkages. The examples are (1) biodiversity and Indigenous Peoples' health, (2) biodiversity and urban social equity, and (3) biodiversity and COVID-19. We observed a moderate level of evidence to support the environmental microbiota-human health pathway and a moderate-high level of evidence to support broader nature pathways (e.g., greenspace) to various health outcomes, from stress reduction to enhanced wellbeing and improved social cohesion. However, studies of broader nature pathways did not typically include specific biodiversity metrics, indicating clear research gaps. Further research is required to understand the connections and causative pathways between biodiversity (e.g., using metrics such as taxonomy, diversity/richness, structure, and function) and health outcomes. There are well-established frameworks to assess the effects of broad classifications of nature on human health. These can assist future research in linking biodiversity metrics to human health outcomes. Our examples of underrepresented linkages highlight the roles of biodiversity and its loss on urban lived experiences, infectious diseases, and Indigenous Peoples' sovereignty and livelihoods. More research and awareness of these socioecological interconnections are needed.
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Affiliation(s)
- Jake M Robinson
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia.
| | - Andrew C Breed
- Epidemiology and One Health Section, Department of Agriculture, Water, and the Environment, Canberra, ACT, Australia; School of Veterinary Science, University of Queensland, Gatton, Qld, Australia
| | | | - Nicole Redvers
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
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Lu C, Xiao Z, Li H, Han R, Sun A, Xiang Q, Zhu Z, Li G, Yang X, Zhu YG, Chen QL. Aboveground plants determine the exchange of pathogens within air-phyllosphere-soil continuum in urban greenspaces. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133149. [PMID: 38056267 DOI: 10.1016/j.jhazmat.2023.133149] [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: 10/28/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
The microbiome in the air-phyllosphere-soil continuum of urban greenspaces plays a crucial role in re-connecting urban populations with biodiverse environmental microbiomes. However, little is known about whether plant type affects the airborne microbiomes, as well as the extent to which soil and phyllosphere microbiomes contribute to airborne microbiomes. Here we collected soil, phyllosphere and airborne microbes with different plant types (broadleaf tree, conifer tree, and grass) in urban parks. Despite the significant impacts of plant type on soil and phyllosphere microbiomes, plant type had no obvious effects on the diversity of airborne microbes but shaped airborne bacterial composition in urban greenspaces. Soil and phyllosphere microbiomes had a higher contribution to airborne bacteria in broadleaf trees (37.56%) compared to conifer trees (9.51%) and grasses (14.29%). Grass areas in urban greenspaces exhibited a greater proportion of potential pathogens compared to the tree areas. The abundance of bacterial pathogens in phyllosphere was significantly higher in grasses compared to broadleaf and conifer trees. Together, our study provides novel insights into the microbiome patterns in air-phyllosphere-soil continuum, highlighting the potential significance of reducing the proportion of extensively human-intervened grass areas in future urban environment designs to enhance the provision of ecosystem services in urban greenspaces.
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Affiliation(s)
- Changyi Lu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Zufei Xiao
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruixia Han
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Qian Xiang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Zhe Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham, Ningbo 315100, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Cuny C, Layer-Nicolaou F, Werner G, Witte W. A look at staphylococci from the one health perspective. Int J Med Microbiol 2024; 314:151604. [PMID: 38367509 DOI: 10.1016/j.ijmm.2024.151604] [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: 11/08/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 02/19/2024] Open
Abstract
Staphylococcus aureus and other staphylococcal species are resident and transient multihost colonizers as well as conditional pathogens. Especially S. aureus represents an excellent model bacterium for the "One Health" concept because of its dynamics at the human-animal interface and versatility with respect to host adaptation. The development of antimicrobial resistance plays another integral part. This overview will focus on studies at the human-animal interface with respect to livestock farming and to companion animals, as well as on staphylococci in wildlife. In this context transmissions of staphylococci and of antimicrobial resistance genes between animals and humans are of particular significance.
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Affiliation(s)
- Christiane Cuny
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany.
| | - Franziska Layer-Nicolaou
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany
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Ngo C, Suwimonteerabutr J, Apiwatsiri P, Saenkankam I, Prapasarakul N, Morrell JM, Tummaruk P. Boar Seminal Microbiota in Relation to Sperm Quality under Tropical Environments. Animals (Basel) 2023; 13:3837. [PMID: 38136874 PMCID: PMC10740666 DOI: 10.3390/ani13243837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The present study was carried out to determine the seminal microbiota of boars and their correlation with sperm quality. A total of 17 ejaculates were collected from 17 Duroc boars and were classified according to sperm quality into two groups: low-quality (n = 8) and high-quality (n = 9). Each ejaculate was subjected to (i) semen evaluation, (ii) bacterial culture and MALDI-TOF identification, and (iii) 16S rRNA gene sequencing and bioinformatic analyses. No difference in the total bacterial count, alpha diversity, and beta diversity between the high-quality group and the low-quality group was detected (p > 0.05). While Globicatella sanguinis was negatively correlated with sperm quality (p < 0.05), Delftia acidovorans was positively correlated with sperm quality (p < 0.05). Lactobacillales (25.2%; LB) and Enterobacterales (10.3%; EB) were the most dominant bacteria and negatively correlated: EB = 507.3 - 0.5 × LB, R2 = 0.24, p < 0.001. Moreover, the abundance of Escherichia-shigella was negatively correlated with LB (r = -0.754, p < 0.001) and positively correlated with Proteus (r = 0.533, p < 0.05). Alysiella was positively correlated with Lactobacillus (r = 0.485, p < 0.05), Prevotella (r = 0.622, p < 0.01), and Staphylococcus (r = 0.489, p < 0.05). In conclusion, seminal microbiota is significantly associated with boar semen qualities. The distributions of the most dominant bacterial genera, the differences in the abundance of small subset microbes, and their correlation appear to have far more impact than the overall seminal bacterial content (e.g., total bacterial count, alpha diversity, and beta diversity) on sperm quality.
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Affiliation(s)
- CongBang Ngo
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (C.N.); (J.S.)
| | - Junpen Suwimonteerabutr
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (C.N.); (J.S.)
- Center of Excellent in Swine Reproduction, Chulalongkorn University, Bangkok 10330, Thailand
| | - Prasert Apiwatsiri
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (P.A.); (I.S.); (N.P.)
| | - Imporn Saenkankam
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (P.A.); (I.S.); (N.P.)
| | - Nuvee Prapasarakul
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (P.A.); (I.S.); (N.P.)
- Center of Excellence in Diagnosis and Monitoring for Animal Pathogens, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jane M. Morrell
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden;
| | - Padet Tummaruk
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (C.N.); (J.S.)
- Center of Excellent in Swine Reproduction, Chulalongkorn University, Bangkok 10330, Thailand
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7
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Meyer S, Hüttig N, Zenk M, Jäckel U, Pöther D. Bioaerosols in swine confinement buildings: A metaproteomic view. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:684-697. [PMID: 37919246 PMCID: PMC10667663 DOI: 10.1111/1758-2229.13208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023]
Abstract
Swine confinement buildings represent workplaces with high biological air pollution. It is suspected that individual components of inhalable air are causatives of chronic respiratory disease that are regularly detected among workers. In order to understand the relationship between exposure and stress, it is necessary to study the components of bioaerosols in more detail. For this purpose, bioaerosols from pig barns were collected on quartz filters and analysed via a combinatorial approach of 16S rRNA amplicon sequencing and metaproteomics. The study reveals the presence of peptides from pigs, their feed and microorganisms. The proportion of fungal peptides detected is considered to be underrepresented compared to bacterial peptides. In addition, the metaproteomic workflow enabled functional predictions about the discovered peptides. Housekeeping proteins were found in particular, but also evidence for the presence of bacterial virulence factors (e.g., serralysin-like metalloprotease) as well as plant (e.g., chitinase) and fungal allergens (e.g., alt a10). Metaproteomic analyses can thus be used to identify factors that may be relevant to the health of pig farmers. Accordingly, such studies could be used in the future to assess the adverse health potential of an occupationally relevant bioaerosol and help consider defined protective strategies for workers.
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Affiliation(s)
- Susann Meyer
- Federal Institute for Occupational Safety and HealthBerlinGermany
| | - Nicole Hüttig
- Federal Institute for Occupational Safety and HealthBerlinGermany
| | - Marianne Zenk
- Research Institute for Farm Animal Biology (FBN)DummerstorfGermany
| | - Udo Jäckel
- Federal Institute for Occupational Safety and HealthBerlinGermany
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8
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Liu T, Li G, Liu Z, Xi L, Ma W, Gao X. Characteristics of aerosols from swine farms: A review of the past two-decade progress. ENVIRONMENT INTERNATIONAL 2023; 178:108074. [PMID: 37441818 DOI: 10.1016/j.envint.2023.108074] [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: 02/26/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023]
Abstract
With the rapid development of large-scale and intensive swine production, the emission of aerosols from swine farms has become a growing concern, attracting extensive attention. While aerosols are found in various environments, those from swine farms are distinguished from human habitats, such as residential, suburban, and urban areas. In order to gain a comprehensive understanding of aerosols from swine farms, this paper reviewed relevant studies conducted between 2000 and 2022. The main components, concentrations, and size distribution of the aerosols were systematically reviewed. The differences between aerosols from swine farms and human living and working environments were compared. Finally, the sources, influencing factors, and reduction technologies for aerosols from swine farms were thoroughly elucidated. The results demonstrated that the concentrations of aerosols inside swine farms varied considerably, and most exceeded safety thresholds. However, further exploration is needed to fully understand the difference in airborne microorganism community structure and particles with small sizes (<1 μm) between swine farms and human living and working environments. More airborne bacterial and viruses were adhered to large particles in swine houses, while the proportion of airborne fungi in the respirable fraction was similar to that of human living and working environments. In addition, swine farms have a higher abundance and diversity of potential pathogens, airborne resistant microorganisms and resistant genes compared to the human living and working environments. The aerosols of swine farms mainly originated from sources such as manure, feed, swine hair and skin, secondary production, and waste treatment. According to the source analysis and factors influencing aerosols in swine farms, various technologies could be employed to mitigate aerosol emissions, and some end-of-pipe technologies need to be further improved before they are widely applied. Swine farms are advised not to increase aerosol concentration in human living and working environments, in order to decrease the impact of aerosols from swine farms on human health and restrain the spread of airborne potential pathogens. This review provides critical insights into aerosols of swine farms, offering guidance for taking appropriate measures to enhance air quality inside and surrounding swine farms.
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Affiliation(s)
- Tongshuai Liu
- College of Animal Science & Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan 450046, China; Henan Engineering Research Center on Animal Healthy Environment and Intelligent Equipment, Zhengzhou, Henan 450046, China
| | - Guoming Li
- Department of Poultry Science, The University of Georgia, Athens, GA 30602, USA; Institute for Artificial Intelligence, The University of Georgia, Athens, GA 30602, USA.
| | - Zhilong Liu
- Henan University of Animal Husbandry and Economy Library, Zhengzhou, Henan 450046, China
| | - Lei Xi
- College of Animal Science & Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan 450046, China; Henan Engineering Research Center on Animal Healthy Environment and Intelligent Equipment, Zhengzhou, Henan 450046, China
| | - Wei Ma
- College of Animal Science & Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan 450046, China; Henan Engineering Research Center on Animal Healthy Environment and Intelligent Equipment, Zhengzhou, Henan 450046, China
| | - Xuan Gao
- College of Animal Science & Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan 450046, China
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Abdugheni R, Li L, Yang ZN, Huang Y, Fang BZ, Shurigin V, Mohamad OAA, Liu YH, Li WJ. Microbial Risks Caused by Livestock Excrement: Current Research Status and Prospects. Microorganisms 2023; 11:1897. [PMID: 37630456 PMCID: PMC10456746 DOI: 10.3390/microorganisms11081897] [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: 06/05/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Livestock excrement is a major pollutant yielded from husbandry and it has been constantly imported into various related environments. Livestock excrement comprises a variety of microorganisms including certain units with health risks and these microorganisms are transferred synchronically during the management and utilization processes of livestock excrement. The livestock excrement microbiome is extensively affecting the microbiome of humans and the relevant environments and it could be altered by related environmental factors as well. The zoonotic microorganisms, extremely zoonotic pathogens, and antibiotic-resistant microorganisms are posing threats to human health and environmental safety. In this review, we highlight the main feature of the microbiome of livestock excrement and elucidate the composition and structure of the repertoire of microbes, how these microbes transfer from different spots, and they then affect the microbiomes of related habitants as a whole. Overall, the environmental problems caused by the microbiome of livestock excrement and the potential risks it may cause are summarized from the microbial perspective and the strategies for prediction, prevention, and management are discussed so as to provide a reference for further studies regarding potential microbial risks of livestock excrement microbes.
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Affiliation(s)
- Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Ni Yang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yin Huang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
| | - Vyacheslav Shurigin
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
| | - Osama Abdalla Abdelshafy Mohamad
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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10
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Wang X, Chen D, Du J, Cheng K, Fang C, Liao X, Liu Y, Sun J, Lian X, Ren H. Occupational exposure in swine farm defines human skin and nasal microbiota. Front Microbiol 2023; 14:1117866. [PMID: 37065142 PMCID: PMC10090692 DOI: 10.3389/fmicb.2023.1117866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/07/2023] [Indexed: 03/31/2023] Open
Abstract
Anthropogenic environments take an active part in shaping the human microbiome. Herein, we studied skin and nasal microbiota dynamics in response to the exposure in confined and controlled swine farms to decipher the impact of occupational exposure on microbiome formation. The microbiota of volunteers was longitudinally profiled in a 9-months survey, in which the volunteers underwent occupational exposure during 3-month internships in swine farms. By high-throughput sequencing, we showed that occupational exposure compositionally and functionally reshaped the volunteers’ skin and nasal microbiota. The exposure in farm A reduced the microbial diversity of skin and nasal microbiota, whereas the microbiota of skin and nose increased after exposure in farm B. The exposure in different farms resulted in compositionally different microbial patterns, as the abundance of Actinobacteria sharply increased at expense of Firmicutes after exposure in farm A, yet Proteobacteria became the most predominant in the volunteers in farm B. The remodeled microbiota composition due to exposure in farm A appeared to stall and persist, whereas the microbiota of volunteers in farm B showed better resilience to revert to the pre-exposure state within 9 months after the exposure. Several metabolic pathways, for example, the styrene, aminobenzoate, and N-glycan biosynthesis, were significantly altered through our PICRUSt analysis, and notably, the function of beta-lactam resistance was predicted to enrich after exposure in farm A yet decrease in farm B. We proposed that the differently modified microbiota patterns might be coordinated by microbial and non-microbial factors in different swine farms, which were always environment-specific. This study highlights the active role of occupational exposure in defining the skin and nasal microbiota and sheds light on the dynamics of microbial patterns in response to environmental conversion.
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Affiliation(s)
- Xiran Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Dongrui Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Juan Du
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ke Cheng
- Guangxi State Farms Yongxin Jinguang Animal Husbandry Group Co., Ltd, Nanning, China
| | - Chang Fang
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xiaoping Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yahong Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jian Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
- *Correspondence: Jian Sun,
| | - Xinlei Lian
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Xinlei Lian,
| | - Hao Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Hao Ren,
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11
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Exel CE, Geus YD, Spaninks M, Koop G, Benedictus L. Colonization of Extramammary Sites with Mastitis-Associated S. aureus Strains in Dairy Goats. Pathogens 2023; 12:pathogens12040515. [PMID: 37111401 PMCID: PMC10140999 DOI: 10.3390/pathogens12040515] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Staphylococcus aureus (S. aureus), a major mastitis pathogen in dairy goats, is classified as a contagious pathogen. Although previous research has shown that extramammary body sites can be colonized with S. aureus, it is unknown whether these sites are reservoirs for intramammary infections. The aim of this research was to determine whether extramammary sites can be colonized with mastitis-associated S. aureus strains in dairy goats. Milk samples were collected from 207 primiparous goats and from 120 of these goats, extramammary site samples (hock, groin, nares, vulva and udder) were collected from a large commercial dairy goat herd in the Netherlands during four sampling visits. Extramammary site swabs and milk samples were (selectively) cultured and S. aureus isolates were spa genotyped. The prevalence of colonization of the extramammary sites at goat level was 51.7% and the prevalence of S. aureus intramammary infections was 7.2%. The nares were colonized most frequently (45%), while the groin area was colonized the least (2.5%). Six spa genotypes were identified in this herd and there was no significant difference in the distribution of spa genotypes between the milk or the extramammary sites (p = 0.141). Both in the extramammary sites and in the milk, spa genotypes t544 (82.3% and 53.3%) and t1236 (22.6% and 33.3%) were the dominant genotypes. These results show that in goats, extramammary sites, particularly the nares, are frequently colonized with mastitis-associated S. aureus strains. Extramammary sites may, thus, be a source of S. aureus intramammary infections that are not targeted by the intervention measures aimed at preventing transmission from infected udder glands.
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12
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Bacterial topography of the upper and lower respiratory tract in pigs. Anim Microbiome 2023; 5:5. [PMID: 36647171 PMCID: PMC9843957 DOI: 10.1186/s42523-023-00226-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/24/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Understanding the complex structures and interactions of the bacterial communities inhabiting the upper (URT) and lower (LRT) respiratory tract of pigs is at an early stage. The objective of this study was to characterize the bacterial topography of three URT (nostrils, choana, and tonsils) and LRT (proximal trachea, left caudal lobe and secondary bronchi) sites in pigs. Thirty-six post-mortem samples from six pigs were analysed by 16S rRNA gene quantification and sequencing, and the microbiota in nostrils and trachea was additionally profiled by shotgun sequencing. RESULTS The bacterial composition obtained by the two methods was congruent, although metagenomics recovered only a fraction of the diversity (32 metagenome-assembled genomes) due to the high proportion (85-98%) of host DNA. The highest abundance of 16S rRNA copies was observed in nostrils, followed by tonsils, trachea, bronchi, choana and lung. Bacterial richness and diversity were lower in the LRT compared to the URT. Overall, Firmicutes and Proteobacteria were identified as predominant taxa in all sample types. Glasserella (15.7%), Streptococcus (14.6%) and Clostridium (10.1%) were the most abundant genera but differences in microbiota composition were observed between the two tracts as well as between sampling sites within the same tract. Clear-cut differences were observed between nasal and tonsillar microbiomes (R-values 0.85-0.93), whereas bacterial communities inhabiting trachea and lung were similar (R-values 0.10-0.17). Moraxella and Streptococcus were more common in bronchial mucosal scraping than in lavage, probably because of mucosal adherence. The bacterial microbiota of the choana was less diverse than that of the nostrils and similar to the tracheal microbiota (R-value 0.24), suggesting that the posterior nasal cavity serves as the primary source of bacteria for the LRT. CONCLUSION We provide new knowledge on microbiota composition and species abundance in distinct ecological niches of the pig respiratory tract. Our results shed light on the distribution of opportunistic bacterial pathogens across the respiratory tract and support the hypothesis that bacteria present in the lungs originate from the posterior nasal cavity. Due to the high abundance of host DNA, high-resolution profiling of the pig respiratory microbiota by shotgun sequencing requires methods for host DNA depletion.
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13
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Shang P, Dong S, Han Y, Bo S, Ye Y, Duan M, Chamba Y. Environmental exposure to swine farms reshapes human gut microbiota. CHEMOSPHERE 2022; 307:135558. [PMID: 35780983 DOI: 10.1016/j.chemosphere.2022.135558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The gut microbiota can change to varying degrees because of changes in the environment. In the present study, we performed microbial amplicon sequencing on the feces of people who had long-term exposure to swine farms (F) and that of people living in normal environments (S) to investigate the impact of the environment on the human gut microbiota. A total of 1,283,503 high-quality ordered sequences were obtained, which provided different levels of microbial classification and statistics. We found that different environments did not alter the richness and diversity of the microbial communities in participants, but caused significant changes in the proportion of some bacteria. The main bacterial phyla found in group F participants were Firmicutes (69.44-89.03%), Actinobacteria (1.7-18.95%), and Bacteroidetes (1.17-22.35%); those found in group S participants were Firmicutes (49.93-95.04%), Bacteroidetes (0.62-39.59%), and Proteobacteria (0.98-11.95%). Additionally, because of changes in phylum proportions, the Bugbase phenotypic classification predicted an increase in the proportion of Gram-positive bacteria in group F and an increase in the proportion of Gram-negative bacteria in group S. In conclusion, our findings suggest that human exposure to swine farms can reshape the gut microbiota, resulting in changes in the microbial abundances. This change can potentially reduce the odds of developing bowel disease and contribute to the prevention of intestinal diseases, providing a theoretical basis for improving human health.
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Affiliation(s)
- Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Shixiong Dong
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Yuqing Han
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Suxue Bo
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Yourong Ye
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Mengqi Duan
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People's Republic of China; The Provincial and Ministerial Co-founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, People's Republic of China.
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14
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Influence of occupational exposure to pigs or chickens on human gut microbiota composition in Thailand. One Health 2022; 15:100463. [DOI: 10.1016/j.onehlt.2022.100463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
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15
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Cyprowski M, Ławniczek-Wałczyk A, Stobnicka-Kupiec A, Gołofit-Szymczak M, Górny RL. Across-Shift Changes in Viable Nasal Bacteria among Waste-Incineration Plant Workers-A Pilot Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19158984. [PMID: 35897354 PMCID: PMC9331216 DOI: 10.3390/ijerph19158984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022]
Abstract
The aim of this pilot study was to assess the time-related changes in viable nasal bacteria concentrations among waste-incineration plant (WIP) workers compared to a group of office building (OB) workers outside the plant. In total, 20 volunteers participated in the study, including 14 WIP and 6 OB workers. WIP workers were divided into two sub-groups: supervisory staff (SVS) and maintenance and repair workers (MRW). Nasal swabs were collected before and after the morning work shift. Airborne bacteria were sampled with a six-stage impactor to assess the bioaerosol size distribution. The analysis showed that a significant, almost three-fold increase in nasal bacterial concentration was found only among WIP workers, and this referred mainly to anaerobic species. The load of anaerobic bacteria at the beginning of work was 12,988 CFU/mL, and after work shift 36,979 CFU/mL (p < 0.01). Significant increases in microbial concentrations was found only in the MRW subgroup, among non-smoking workers only. The results showed increased bacterial concentration in WIP nasal samples for as many as 12 bacterial species, including, e.g., Streptococcus constellatus, Peptostreptococcus spp., E. coli, and P. mirabilis. These preliminary data confirmed that the nasal swab method was helpful for assessment of the workers’ real-time exposure to airborne bacteria.
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16
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Gao M, Zhang X, Yue Y, Qiu T, Wang J, Wang X. Air path of antimicrobial resistance related genes from layer farms: Emission inventory, atmospheric transport, and human exposure. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128417. [PMID: 35183825 DOI: 10.1016/j.jhazmat.2022.128417] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/26/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Animal husbandry is a significant contributor to increased environmental antimicrobial resistance (AMR), but little is known regarding the dissemination of AMR from animal farms via airborne transmission. Here, we connected the air path of AMR related genes tailored to layer poultry farms from source of escape to end of sedimentation. The emission inventories of 8 AMR related genes from all 163-layer poultry farms around Beijing city were quantified. We developed the atmospheric transport model with a gene degradation module to estimate the spatiotemporal distribution of airborne AMR, and also assessed their corresponding regional exposure and sedimentation. Total emissions of 16 S rDNA and AMR related genes from layer houses ranged from 1015 to 1016 copies year-1. Those layer-sourced genes contributed 1-14.6% of antimicrobial resistant genes, 4.9% of Staphylococcus spp. and 2.2% of CintI1 to the corresponding annual genetic burden of Beijing's urban air. The average exposure of the Beijing residents to layer-sourced airborne 16 S rDNA was 1.39 × 104 copies year-1 person-1, approximately 87% of them would be deposited in the upper respiratory tract. The findings highlight that air medium represents an important dissemination pathway of animal-sourced genes to AMR burden in humans and environment.
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Affiliation(s)
- Min Gao
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaole Zhang
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland
| | - Yang Yue
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland
| | - Tianlei Qiu
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jing Wang
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland.
| | - Xuming Wang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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17
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Particulate Matter in Swine Barns: A Comprehensive Review. ATMOSPHERE 2022. [DOI: 10.3390/atmos13030490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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WORKbiota: A Systematic Review about the Effects of Occupational Exposure on Microbiota and Workers' Health. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031043. [PMID: 35162072 PMCID: PMC8834335 DOI: 10.3390/ijerph19031043] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/14/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022]
Abstract
The characterization of human microbiota and the impact of its modifications on the health of individuals represent a current topic of great interest for the world scientific community. Scientific evidence is emerging regarding the role that microbiota has in the onset of important chronic illnesses. Since individuals spend most of their life at work, occupational exposures may have an impact on the organism’s microbiota. The purpose of this review is to explore the influence that different occupational exposures have on human microbiota in order to set a new basis for workers’ health protection and disease prevention. The literature search was performed in PubMed, Cochrane, and Scopus. A total of 5818 references emerged from the online search, and 31 articles were included in the systematic review (26 original articles and 5 reviews). Exposure to biological agents (in particular direct contact with animals) was the most occupational risk factor studied, and it was found involved in modifications of the microbiota of workers. Changes in microbiota were also found in workers exposed to chemical agents or subjected to work-related stress and altered dietary habits caused by specific microclimate characteristics or long trips. Two studies evaluated the role of microbiota changes on the development of occupational lung diseases. Occupational factors can interface with the biological rhythms of the bacteria of the microbiota and can contribute to its modifications and to the possible development of diseases. Future studies are needed to better understand the role of the microbiota and its connection with occupational exposure to promote projects for the prevention and protection of global health.
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Wallenborn JT, Vonaesch P. OUP accepted manuscript. Gastroenterol Rep (Oxf) 2022; 10:goac010. [PMID: 35419206 PMCID: PMC8996373 DOI: 10.1093/gastro/goac010] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/10/2021] [Accepted: 02/16/2022] [Indexed: 11/15/2022] Open
Abstract
The intestinal microbiota plays a crucial role in health and changes in its composition are linked with major global human diseases. Fully understanding what shapes the human intestinal microbiota composition and knowing ways of modulating the composition are critical for promotion of life-course health, combating diseases, and reducing global health disparities. We aim to provide a foundation for understanding what shapes the human intestinal microbiota on an individual and global scale, and how interventions could utilize this information to promote life-course health and reduce global health disparities. We briefly review experiences within the first 1,000 days of life and how long-term exposures to environmental elements or geographic specific cultures have lasting impacts on the intestinal microbiota. We also discuss major public health threats linked to the intestinal microbiota, including antimicrobial resistance and disappearing microbial diversity due to globalization. In order to promote global health, we argue that the interplay of the larger ecosystem with intestinal microbiota research should be utilized for future research and urge for global efforts to conserve microbial diversity.
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Affiliation(s)
- Jordyn T Wallenborn
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore Campus UNIL-Sorge, Lausanne, Switzerland
- Corresponding author. Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland. Tel: +41-21-692-5600;
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Moor J, Wüthrich T, Aebi S, Mostacci N, Overesch G, Oppliger A, Hilty M. Influence of pig farming on human Gut Microbiota: role of airborne microbial communities. Gut Microbes 2021; 13:1-13. [PMID: 34060426 PMCID: PMC8172160 DOI: 10.1080/19490976.2021.1927634] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
It has been hypothesized that both genetics and diet influence the composition of the human cecal microbiota. However, it remains unclear whether and how occupational exposure to microbes impacts the microbial communities in human guts. Using a One Health approach, we visited pig farms (n = 26) and collected stool specimens from pig workers (n = 59), pig barn air samples (n = 19), and rectal swabs from pigs at three different growth stages (n = 144). Stool samples from cattle workers were included as a control group (n = 22). Each sample's microbiota was characterized using 16S rRNA gene sequencing and the DADA2 pipeline.We obtained a significantly different clustering of the microbial compositions of pig and cattle workers by permutational multivariate analysis of variance (PERMANOVA; P < .001). Workers primarily exposed to pigs had higher relative abundances of Prevotellaceae and less Bacteroidaceae than workers exposed to cattle. We also found that the microbial compositions of pig workers' stool samples shared extensive fractions with the samples from their pigs. We also identified amplicon sequencing variants (ASVs) in the airborne microbiota which were likely involved in zoonotic transmission events.We hypothesize that ASVs originating from pig feces are aerosolized and, through breathing, get trapped in the pig farm workers' upper respiratory tract from where they can get swallowed. Consequently, some of the animal associated ASVs are transferred into the gastrointestinal tracts (GITs) which leads to changes in the composition of the human gut microbiota. The importance of this finding for human health must be investigated further.
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Affiliation(s)
- Julia Moor
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Tsering Wüthrich
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Nadezda Mostacci
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Gudrun Overesch
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Anne Oppliger
- Unisante, Department of Occupational and Environmental Health, University of Lausanne, Lausanne, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland,Markus Hilty Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001Bern, Switzerland, Phone +41 31 632 49 83
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Dietary supplementation of fructooligosaccharides alleviates enterotoxigenic E. coli-induced disruption of intestinal epithelium in a weaned piglet model. Br J Nutr 2021; 128:1526-1534. [PMID: 34763738 DOI: 10.1017/s0007114521004451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Diarrhea caused by pathogens such as enterotoxigenic E. coli (ETEC) is a serious threat to the health of young animals and human infants. Here, we investigated the protective effect of fructooligosaccharides (FOS) on the intestinal epithelium with ETEC-challenge in a weaned piglet model. Twenty-four weaned piglets were randomly divided into three groups: (1) non-ETEC-challenged control (CON), (2) ETEC-challenged control (ECON), and (3) ETEC challenge + 2.5 g/kg FOS (EFOS). On day 19, the CON pigs were orally infused with sterile culture, while the ECON and EFOS pigs were orally infused with active ETEC (2.5 × 109 colony-forming units). On day 21, pigs were slaughtered to collect venous blood and small intestine. Result showed that the pre-treatment of FOS improved the antioxidant capacity and the integrity of intestinal barrier in the ETEC-challenged pigs without affecting their growth performance. Specifically, comparing with ECON pigs, the level of GSH-Px (glutathione peroxidase) and CAT (catalase) in the plasma and intestinal mucosa of EFOS pigs was increased (P<0.05), and the intestinal barrier marked by ZO-1 and plasmatic DAO was also improved in EFOS pigs. A lower level (P<0.05) of inflammatory cytokines in the intestinal mucosa of EFOS pigs might be involved in the inhibition of TLR4/MYD88/NF-κB pathway. The apoptosis of jejunal cells in EFOS pigs was also lower than that in ECON pigs (P<0.05). Our findings provide convincing evidence of possible prebiotic and protective effect of FOS on the maintenance of intestinal epithelial function under the attack of pathogens.
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Dynamics of the Human Nasal Microbiota and Staphylococcus aureus CC398 Carriage in Pig Truck Drivers across One Workweek. Appl Environ Microbiol 2021; 87:e0122521. [PMID: 34191530 PMCID: PMC8388827 DOI: 10.1128/aem.01225-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Drivers of pig trucks constitute a potential route of human transmission of livestock-associated methicillin-resistant Staphylococcus aureus clonal complex 398 (LA-MRSA CC398). In this study, we determined MRSA prevalence in pig truck drivers (n = 47) and monitored the nasal microbiota of 9 drivers 3 times daily throughout 1 workweek (n = 113 samples) and compared it to that of their spouses (n = 25 samples from 6 spouses) and 89 nonexposed subjects. S. aureus isolates (n = 232) derived from a subset of nasal and truck samples were whole-genome sequenced. The nasal alpha diversity of drivers in the beginning of the workday was lower than that of nonexposed subjects. During the workday, it increased significantly. Similarly, the drivers’ nasal composition shifted during the workday, becoming increasingly different from that of their spouses and nonexposed individuals. Clustering into community state types (CSTs) revealed frequent switches from either S. aureus- or Corynebacterium-dominated CSTs in the mornings to a Psychrobacter-dominated CST during the workday. Six intermittent MRSA carriers were mostly MRSA negative in the mornings, and their nasal microbiota resembled that of nonexposed subjects. When acquiring MRSA during the workday, they switched to the Psychrobacter-dominated CST. In contrast, the nasal microbiota of two persistent MRSA carriers was dominated by staphylococci. In conclusion, we show that the nasal microbiota of pig truck drivers is very dynamic, undergoes drastic changes during workdays, and differs from that of nonexposed subjects even before pig contact. MRSA-carrying drivers may eventually introduce MRSA into the community and health care facilities. Carriage dynamics, however, showed that for most drivers, CC398 MRSA is rapidly lost and only rarely causes transmission to spouses. IMPORTANCE In Denmark, the number of human methicillin-resistant Staphylococcus aureus (MRSA) cases has increased dramatically since the early 2000s, starting from imported cases and spreading in the community. However, today, approximately one-third of all new cases are attributed to livestock-associated MRSA clonal complex 398 (LA-MRSA CC398). This mirrors the increase in pig farms, of which 95% are now positive for LA-MRSA, and this has been caused mainly by three dominant lineages enriched for a number of key antimicrobial resistance genes. Although most human LA-MRSA CC398 infections in Denmark are linked to livestock contact, still up to one-third are not. Pig truck drivers constitute a previously understudied occupation group which may transmit LA-MRSA CC398 to household members, the community, and hospitals. In this study, we demonstrate dramatic work-related changes in the nasal microbiota of pig truck drivers, as well as in their carriage of LA-MRSA CC398. However, they likely do not constitute an important reservoir for LA-MRSA CC398 dissemination.
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Kraemer JG, Aebi S, Hilty M, Oppliger A. Nasal microbiota composition dynamics after occupational change in animal farmers suggest major shifts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 782:146842. [PMID: 33838360 DOI: 10.1016/j.scitotenv.2021.146842] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 03/08/2021] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Previous studies have suggested a significantly higher diversity in the nasal microbiota of pig farmers compared to people having no contact with farm animals. However, the fate of this nasal microbiota specificity after farmers stop being in contact with the pig farm environment is unknown. The aim of this study was to investigate the change in the nasal microbiota of pig-farmers after the change of occupation. METHODS: Anterior and posterior nasal swabs were collected from seven people during employment on pig farms, and again after a period of at least 50 days after leaving the pig farm. Illumina MiSeq sequencing of 16S rRNA was conducted to characterize the dynamics of the nasal microbiota. The microbiota of actively working pig farmers was compared to microbiota after they had stopped working (ex-pig-farmers) and to control groups (cow farmers and non-exposed individuals). RESULTS: Following a prolonged period without exposure to pigs, α-diversity of both anterior and posterior cavities dropped significantly. The composition of the microbiota of pig-farmers had a low inter-similarity with the non-exposed group while ex-pig-farmers were more similar to cow-farmers and the non-exposed group than to their own microbiota during pig farming.
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Affiliation(s)
- Julia G Kraemer
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Unisanté, the Center for Primary Care and Public Health, Department of Occupational and Environmental Health (DSTE), University of Lausanne, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
| | - Anne Oppliger
- Unisanté, the Center for Primary Care and Public Health, Department of Occupational and Environmental Health (DSTE), University of Lausanne, Switzerland.
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Martikainen MV, Tossavainen T, Täubel M, Wolczkiewicz K, Lähde A, Roponen M. Toxicological and microbiological characterization of cow stable dust. Toxicol In Vitro 2021; 75:105202. [PMID: 34166725 DOI: 10.1016/j.tiv.2021.105202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/27/2021] [Accepted: 06/17/2021] [Indexed: 10/21/2022]
Abstract
Exposure to farm environment has been shown to both protect from allergic diseases and increase the risk of respiratory syndromes. Mechanisms have been previously investigated by using farm dust extracts or specific components of dust. The use of authentic farm dust would better reflect the natural exposure. The aim of our study was to highlight the importance of proper assessment of the cow stable dust characteristics before conducting further investigations. For this purpose, we characterized microbiome and size distribution of unprocessed cow stable dust and its toxicological properties, as they have been often overlooked in search of protective factors. Stable dust samples from four Finnish dairy farms were collected by utilizing two different collection methods. Toxicological potential was analysed by stimulating co-cultures of lung epithelial and macrophage-like cells with dust. Size and mass distributions of airborne particles in the stables and bacterial and fungal microbiota of the dust were analysed. Stimulation with dust did not affect viability, but heightened oxidative stress responses and cytokine secretion, and slightly reduced the metabolic activity. There were a few differences in responses between farms, however, the differences were mainly in the intensity and not in the direction of the response. Cellular responses induced by dusts collected by different sampling methods did not differ substantially. Unprocessed stable dust samples showed relatively low direct toxicity but were able to trigger immune responses in studied cell model. This suggest that these dust collection methods could be utilized when investigating e.g. asthma-protective mechanisms.
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Affiliation(s)
- Maria-Viola Martikainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland.
| | - Tarleena Tossavainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Martin Täubel
- Environmental Health Unit, Department of Health Security, National Institute for Health and Welfare, Kuopio, Finland
| | - Kirsi Wolczkiewicz
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Anna Lähde
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Marjut Roponen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
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Moor J, Aebi S, Rickli S, Mostacci N, Overesch G, Oppliger A, Hilty M. Dynamics of extended-spectrum cephalosporin-resistant Escherichia coli in pig farms: A longitudinal study. Int J Antimicrob Agents 2021; 58:106382. [PMID: 34157404 DOI: 10.1016/j.ijantimicag.2021.106382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 05/31/2021] [Accepted: 06/12/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Point prevalence estimates of extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R-Ec) are important surveillance measures but may not uncover the ESC-R-Ec dynamics within pig farms. A longitudinal study was therefore performed by sampling individual pigs, pig farmers and the environment. METHODS On average, 30 (range 10-46) piglets of 31 Swiss farms were sampled during the suckling, weaning and fattening stages (n= 2437 samples). In addition, stool from pig farmers and environmental samples were obtained and metadata collected by questionnaires. ESC-R-Ec was identified by routine culture, and clonal relationships and resistance genes were derived from whole genome sequencing data. RESULTS Working on pig farms was not associated with an increased prevalence of ESC-R-Ec in humans. ESC-R-Ec prevalence significantly decreased from 6.2% to 3.9% and 1.8% for the suckling, weaned and fattening pigs, respectively (P < 0.001). Within the 57 ESC-R-positive suckling piglets, persisting carriage was detected in 25 animals at two consecutive time points and one animal at three consecutive time points. Clonal spread (n=7 farms, 22.6%) and horizontal gene transfer (n=1 farm, 3%) within pigs but not between humans and animals was detected. Liquid manure (n=10 samples, 16.7%) was identified as the major environmental reservoir of ESC-R-Ec in the pig farm environment. CONCLUSIONS Pig farming practices like all-in-all-out systems, but not antimicrobial usage, were associated with reduced risk of ESC-R-Ec at the farm level. As carriage duration is normally short within the individual pigs, the risk of recolonisation and clonal spread of ESC-R-Ec might be reduced by applying appropriate decontamination strategies.
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Affiliation(s)
- Julia Moor
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Susanne Rickli
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Nadezda Mostacci
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Gudrun Overesch
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Anne Oppliger
- Unisante, Department of Occupational and Environmental Health, University of Lausanne, Lausanne, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
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Abstract
The nasopharyngeal microbiome is a dynamic microbial interface of the aerodigestive tract, and a diagnostic window in the fight against respiratory infections and antimicrobial resistance. As its constituent bacteria, viruses and mycobacteria become better understood and sampling accuracy improves, diagnostics of the nasopharynx could guide more personalized care of infections of surrounding areas including the lungs, ears and sinuses. This review will summarize the current literature from a clinical perspective and highlight its growing importance in diagnostics and infectious disease management.
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Affiliation(s)
- Matthew Flynn
- School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
- Otolaryngology Department, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - James Dooley
- School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
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Satora M, Rząsa A, Rypuła K, Płoneczka-Janeczko K. Model research of the pig’s microbiome based on
“One Health” concept in the light of the shared human
and animal health. POSTEP HIG MED DOSW 2021. [DOI: 10.5604/01.3001.0014.8758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The human microbiome in terms of the number of bacteria exceeds the number of cells in the
human body. It is defined as an additional “forgotten organ” and plays a key role in maintaining
a high health status, which is conditioned by the maintenance of certain proportions and
natural relations between bacteria and cells of the host organism. New diagnostic methods
can enable profiling not only the human microbiome, but also livestock. An innovative analytical
method, which is next generation sequencing (NGS), is increasingly used in the study
of the microbiome. Many bacteria are referred to as “uncultivated” or “non-culturable” and metagenomics has played an important role in detecting these bacteria and has contributed
to the development of new media for their cultivation. The main application of NGS in microbiology
is to replace the conventional characterization of pathogens based on the assessment
of morphology, staining properties and metabolic traits with their genome related characteristics.
There are several platforms, i.e. “diagnostic tools”, that use a variety of DNA sequencing
technologies, among others Ion Torrent Personal Genome Machine (PGM), Pacific
Biosciences (PacBio) and Illumina MiSeq. In the case of swine microbiome, studies of the microbiome
with the use of modern sequencing technologies seem to be particularly interesting
in the aspect of the upcoming, inevitable changes in preventive and therapeutic procedures
in animals. Analyses of this type integrate with the concept of the shared human and animal
health and enable an in-depth assessment of the impact of specific factors on the population
of intestinal microbes and learning how to “form” the composition of the microbiome
in order to improve the quality of husbandry and to maintain the pig’s proper health status.
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Affiliation(s)
- Marta Satora
- Zakład Chorób Zakaźnych i Administracji Weterynaryjnej, Katedra Epizootiologii z Kliniką Ptaków i Zwierząt Egzotycznych, Wydział Medycyny Weterynaryjnej, Uniwersytet Przyrodniczy we Wrocławiu
| | - Anna Rząsa
- Zakład Immunologii i Prewencji Weterynaryjnej, Katedra Immunologii, Patofizjologii i Prewencji Weterynaryjnej, Wydział Medycyny Weterynaryjnej, Uniwersytet Przyrodniczy we Wrocławiu
| | - Krzysztof Rypuła
- Zakład Chorób Zakaźnych i Administracji Weterynaryjnej, Katedra Epizootiologii z Kliniką Ptaków i Zwierząt Egzotycznych, Wydział Medycyny Weterynaryjnej, Uniwersytet Przyrodniczy we Wrocławiu
| | - Katarzyna Płoneczka-Janeczko
- Zakład Chorób Zakaźnych i Administracji Weterynaryjnej, Katedra Epizootiologii z Kliniką Ptaków i Zwierząt Egzotycznych, Wydział Medycyny Weterynaryjnej, Uniwersytet Przyrodniczy we Wrocławiu
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Kaiser-Thom S, Hilty M, Axiak S, Gerber V. The skin microbiota in equine pastern dermatitis: a case-control study of horses in Switzerland. Vet Dermatol 2021; 32:646-e172. [PMID: 33830562 PMCID: PMC9290916 DOI: 10.1111/vde.12955] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/28/2020] [Accepted: 11/16/2020] [Indexed: 01/04/2023]
Abstract
Background Equine pastern dermatitis (EPD), a multifactorial syndrome, manifests as skin lesions of variable severity in the pastern area. Despite the widespread use of antibacterial therapy for treating this condition, little is known about the contributing bacteria. Hypothesis/Objectives To investigate the bacterial skin microbiota in EPD‐affected and unaffected (control) pasterns. Animals Case‐control study with 80 client‐owned horses; each with at least one EPD‐affected and one control pastern. Methods and materials Horses were grouped by the form of EPD (mild, exudative or proliferative), the assigned severity grade and type of pretreatment (disinfectant, topical antibacterial or no antibacterial pretreatment). Skin swabs were obtained, and the microbiota composition was compared between the groups. Results Bacterial alpha diversity was reduced in affected pasterns (P < 0.001) and this reduction was significantly associated with the EPD forms (P < 0.001), and not with the type of pretreatment (P > 0.14). Analyses of beta‐diversity confirmed a disordering of the skin microbiota (P = 0.004) in affected versus control pasterns, that was particularly profound in more severe lesions. The type of pretreatment was not significantly associated with this disordering. Four differentially abundant families were detected, of which Staphylococcaceae was the most distinct. The relative abundance of staphylococci was significantly increased in affected pasterns (P = 0.011), particularly in those that had received antibacterial treatment previously. Conclusions and clinical relevance Changes in the microbiota are associated with the EPD form or severity of lesions. The role of bacteria in the pathogenesis of EPD as well as the propriety and consequences of antibacterial treatment should therefore be further investigated.
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Affiliation(s)
- Sarah Kaiser-Thom
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3012, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
| | - Shannon Axiak
- Clinical Anaesthesiology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Länggassstrasse 124, 3012, Bern, Switzerland
| | - Vinzenz Gerber
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3012, Bern, Switzerland
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Kaiser-Thom S, Hilty M, Gerber V. Effects of hypersensitivity disorders and environmental factors on the equine intestinal microbiota. Vet Q 2021; 40:97-107. [PMID: 32189583 PMCID: PMC7170319 DOI: 10.1080/01652176.2020.1745317] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Recent evidence suggests that an altered intestinal microbiota, specifically a reduction of bacterial diversity or a shift in microbial composition, is associated with the development of hypersensitivity disorders in humans, but this is unknown for horses. Objectives In this study we hypothesized that horses affected by either Culicoides hypersensitivity or severe equine asthma or both show a decreased diversity of their intestinal microbiota. We also investigated environmental effects. Methods Rectal swab samples of a total of 140 horses were collected and the owners completed a detailed questionnaire about their horse. For each allergic horse, a healthy peer from the same stable was equally sampled as an environmentally matched control. Microbiota in the swabs was determined by assessing the V4 region of the bacterial 16S rRNA gene. Structures of bacterial communities were investigated by means of alpha and beta diversity indices. Results Group wise comparisons between healthy and allergic horses showed no significant differences regarding alpha (p = 0.9) and beta diversity (p = 0.5). However, the microbial structure was associated with environmental factors such as the type of stable (p = 0.001), access to pasture (p = 0.001) or the type of feeding (p = 0.003). There was also a strong location effect meaning that the microbiota was more similar within the same as compared between farms within this study. Conclusion Our observations suggest that hypersensitivity disorders in adult horses are not associated with an alteration of the intestinal microbiota, but environmental and/or location factors strongly influence these bacteria.
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Affiliation(s)
- S Kaiser-Thom
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
| | - M Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - V Gerber
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
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Skowron K, Bauza-Kaszewska J, Kraszewska Z, Wiktorczyk-Kapischke N, Grudlewska-Buda K, Kwiecińska-Piróg J, Wałecka-Zacharska E, Radtke L, Gospodarek-Komkowska E. Human Skin Microbiome: Impact of Intrinsic and Extrinsic Factors on Skin Microbiota. Microorganisms 2021; 9:543. [PMID: 33808031 PMCID: PMC7998121 DOI: 10.3390/microorganisms9030543] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
The skin is the largest organ of the human body and it protects the body from the external environment. It has become the topic of interest of researchers from various scientific fields. Microorganisms ensure the proper functioning of the skin. Of great importance, are the mutual relations between such microorganisms and their responses to environmental impacts, as dysbiosis may contribute to serious skin diseases. Molecular methods, used for microorganism identification, allow us to gain a better understanding of the skin microbiome. The presented article contains the latest reports on the skin microbiota in health and disease. The review discusses the relationship between a properly functioning microbiome and the body's immune system, as well as the impact of internal and external factors on the human skin microbiome.
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Affiliation(s)
- Krzysztof Skowron
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (Z.K.); (N.W.-K.); (K.G.-B.); (J.K.-P.); (E.G.-K.)
| | - Justyna Bauza-Kaszewska
- Department of Microbiology and Food Technology, UTP University of Science and Technology, 85-029 Bydgoszcz, Poland;
| | - Zuzanna Kraszewska
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (Z.K.); (N.W.-K.); (K.G.-B.); (J.K.-P.); (E.G.-K.)
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (Z.K.); (N.W.-K.); (K.G.-B.); (J.K.-P.); (E.G.-K.)
| | - Katarzyna Grudlewska-Buda
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (Z.K.); (N.W.-K.); (K.G.-B.); (J.K.-P.); (E.G.-K.)
| | - Joanna Kwiecińska-Piróg
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (Z.K.); (N.W.-K.); (K.G.-B.); (J.K.-P.); (E.G.-K.)
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, 31 C.K. Norwida St., 50-375 Wrocław, Poland;
| | - Laura Radtke
- Faculty of Civil and Environmental Engineering and Architecture, UTP University of Science and Technology in Bydgoszcz, Al. prof. S. Kaliskiego 7, 85-796 Bydgoszcz, Poland;
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (Z.K.); (N.W.-K.); (K.G.-B.); (J.K.-P.); (E.G.-K.)
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Relationships among Fecal, Air, Oral, and Tracheal Microbial Communities in Pigs in a Respiratory Infection Disease Model. Microorganisms 2021; 9:microorganisms9020252. [PMID: 33513772 PMCID: PMC7912642 DOI: 10.3390/microorganisms9020252] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
The association of the lower respiratory tract microbiome in pigs with that of other tissues and environment is still unclear. This study aimed to describe the microbiome of tracheal and oral fluids, air, and feces in the late stage of Mycoplasma hyopneumoniae infection in pigs, and assess the association between the tracheal microbiome and those from air, feces, and oral fluids. Tracheal fluids (n = 73), feces (n = 71), oropharyngeal fluids (n = 8), and air (n = 12) were collected in seeder pigs (inoculated with M. hyopneumoniae) and contact pigs (113 days post exposure to seeder pigs). After DNA extraction, the V4 region from 16S rRNA gene was sequenced and reads were processed using Divisive Amplicon Denoising Algorithm (DADA2). Clostridium and Streptococcus were among the top five genera identified in all sample types. Mycoplasma hyopneumoniae in tracheal fluids was associated with a reduction of diversity and increment of M. hyorhinis, Glaesserella parasuis, and Pasteurella multocida in tracheal fluids, as well as a reduction of Ruminiclostridium, Barnesiella, and Lactobacillus in feces. Air contributed in a greater proportion to bacteria in the trachea compared with feces and oral fluids. In conclusion, evidence suggests the existence of complex interactions between bacterial communities from distant and distinct niches.
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Sangiorgio DB, Hilty M, Kaiser-Thom S, Epper PG, Ramseyer AA, Overesch G, Gerber VM. The influence of clinical severity and topical antimicrobial treatment on bacteriological culture and the microbiota of equine pastern dermatitis. Vet Dermatol 2021; 32:173-e41. [PMID: 33417744 PMCID: PMC8048527 DOI: 10.1111/vde.12912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 07/30/2020] [Accepted: 08/17/2020] [Indexed: 01/11/2023]
Abstract
Background Equine pastern dermatitis (EPD) is a common dermatological problem in horses, yet its aetiology and pathogenesis are poorly understood. Objectives This study aimed to investigate the effects of lesion severity and topical antimicrobial treatment on bacterial flora of EPD‐affected skin. Animals Sixteen horses with EPD were investigated. Methods and materials An observational study was conducted by assigning a clinical severity score ranging from 0 (macroscopically nonlesional) to 21 (severe), and sampling the most and least severely affected limbs of 16 horses (32 limbs) for bacteriological culture and 16S rRNA sequencing. Topical antimicrobial treatment in the month before sampling was recorded. The limbs were allocated to a nonlesional or mildly affected group (Group A, score 0–3) and a moderate to severely affected group (Group B, score 4–21). Results The most commonly cultured bacterial species was Staphylococcus aureus (one of 15 Group A versus nine of 17 Group B). Within Group B, S. aureus was found in three of six limbs treated with topical antimicrobials and in six of 11 untreated limbs. β‐haemolytic streptococci (three of 32) and Trueperella pyogenes (two of 32) also were cultured exclusively in the untreated limbs of Group B. Staphylococci and streptococci were found more often by 16S rRNA sequencing than in culture. Limbs with higher lesion severity and topical antimicrobial treatment appeared to have a lower alpha diversity and different beta diversity compared to milder and untreated lesions. Conclusions and clinical importance Observed differences in microbiota of equine skin are likely to be linked to the presence and severity of EPD and topical antimicrobial treatment. Further research is needed to establish causal bacteria.
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Affiliation(s)
- Daphne B Sangiorgio
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, Bern, 3012, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Friedbühlstrasse 51, Bern, 3010, Switzerland
| | - Sarah Kaiser-Thom
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, Bern, 3012, Switzerland
| | - Pascale G Epper
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, Bern, 3012, Switzerland
| | - Alessandra A Ramseyer
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, Bern, 3012, Switzerland
| | - Gudrun Overesch
- Institute for Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, Bern, 3012, Switzerland
| | - Vinzenz M Gerber
- Swiss Institute of Equine Medicine (ISME), Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, Bern, 3012, Switzerland
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Madsen AM, White JK, Markouch A, Kadhim S, de Jonge N, Thilsing T, Hansen VM, Bælum J, Nielsen JL, Vogel U, Tendal K. A cohort study of cucumber greenhouse workers' exposure to microorganisms as measured using NGS and MALDI-TOF MS and biomarkers of systemic inflammation. ENVIRONMENTAL RESEARCH 2021; 192:110325. [PMID: 33068575 DOI: 10.1016/j.envres.2020.110325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 10/07/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Work in greenhouses entails exposure to airborne fungi and bacteria. The aims of this study are to obtain knowledge about whether exposure to fungal and bacterial genera and species during work in a cucumber greenhouse is affected by work tasks, and whether a cohort of greenhouse workers' serum levels of serum amyloid A (SAA) and C-reactive protein (CRP), biomarkers of systemic inflammation, are associated with this. Data on personal exposure to airborne fungal and bacterial species measured over 4 years as well as serum levels of SAA and CRP sampled over two years were analyzed. For data analysis, the main work tasks were grouped into three different groups, called 'grouped work task'. Microorganisms were identified using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF MS) and next-generation sequencing (NGS). The 'daily exposure' of greenhouse workers' were as follows: 4.8 × 104 CFU bacteria/m3, 1.4 × 106 CFU fungi/m3, and 392 EU/m3 of endotoxin. Workers were exposed to many different microbial species including several species within the genera Acinetobacter, Bacillus, Microbacterium, Pseudomonas, Staphylococcus, and Streptomyces. The genera Ralstonia and Cladosporium were found in most samples. The exposure levels as well as the microbial composition were associated significantly with grouped work task and season with high exposures during tasks in close contact with mature and old plants and in the autumn. CRP and SAA levels were also associated with exposure level and grouped work tasks. The Shannon-Wiener indices were not different in the 3 'grouped work tasks'. Several specific species including e.g. Halomonas elongata, Stenotrophomonas maltophilia, Podosphaera fusca, and Wallemia spp. were found frequently or in high concentrations in the exposures associated with the highest levels of CRP and SAA. The microorganisms S. maltophilia, P. fusca, and Wallemia spp. were also found on the cucumber plant leaves. In conclusion, both exposure level and the species composition seem to have an effect on the serum levels of CRP and SAA of exposed workers. The greenhouse workers were exposed to only a few species characterized as human pathogens.
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Affiliation(s)
- Anne Mette Madsen
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen, Denmark.
| | - John Kerr White
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen, Denmark; Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg Ø, Denmark.
| | - Amal Markouch
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen, Denmark.
| | - Sarah Kadhim
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen, Denmark.
| | - Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg Ø, Denmark.
| | - Trine Thilsing
- Research Unit for General Practice, Institute of Public Health, University of Southern Denmark, J. B. Winsløws Vej 9, DK-5000, Odense C, Denmark.
| | - Vinni M Hansen
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen, Denmark.
| | - Jesper Bælum
- Research Unit for General Practice, Institute of Public Health, University of Southern Denmark, J. B. Winsløws Vej 9, DK-5000, Odense C, Denmark.
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg Ø, Denmark.
| | - Ulla Vogel
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen, Denmark.
| | - Kira Tendal
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen, Denmark.
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Hilty M, Wüthrich TM, Godel A, Adelfio R, Aebi S, Burgener SS, Illgen-Wilcke B, Benarafa C. Chronic cigarette smoke exposure and pneumococcal infection induce oropharyngeal microbiota dysbiosis and contribute to long-lasting lung damage in mice. Microb Genom 2020; 6:mgen000485. [PMID: 33295863 PMCID: PMC8116676 DOI: 10.1099/mgen.0.000485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/10/2020] [Indexed: 12/17/2022] Open
Abstract
Environmental factors, such as cigarette smoking or lung infections, may influence chronic obstructive pulmonary disease (COPD) progression by modifying the respiratory tract microbiome. However, whether the disease itself induces or maintains dysbiosis remains undefined. In this longitudinal study, we investigated the oropharyngeal microbiota composition and disease progression of mice (in cages of 5-10 mice per cage) before, during and up to 3 months after chronic cigarette smoke exposure or exposure to room air for 6 months. Cigarette smoke exposure induced pulmonary emphysema measurable at the end of exposure for 6 months, as well as 3 months following smoke exposure cessation. Using both classical culture methods and 16S rRNA sequencing, we observed that cigarette smoke exposure altered the relative composition of the oropharyngeal microbiota and reduced its diversity (P <0.001). More than 60 taxa were substantially reduced after 6 months of smoke exposure (P <0.001) However, oropharyngeal microbiota disordering was reversed 3 months after smoke exposure cessation and no significant difference was observed compared to age-matched control mice. The effects of lung infection with Streptococcus pneumoniae on established smoke-induced emphysema and on the oropharyngeal microbiota were also evaluated. Inoculation with S. pneumoniae induced lung damage and altered the microbiota composition for a longer time compared to control groups infected but not previously exposed to smoke (P=0.01). Our data demonstrate effects of cigarette smoke and pneumococcus infection leading to altered microbiota and emphysema development. The reversal of the disordering of the microbiota composition, but not lung damage, following smoke exposure cessation and after clearance of infection suggest that changes in lung structure are not sufficient to sustain a disordered microbiota in mice. Whether changes in the airway microbiota contribute to inducing emphysema requires further investigation.
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Affiliation(s)
- Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Tsering M. Wüthrich
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Freiestrasse 1, 3012 Bern, Switzerland
| | - Aurélie Godel
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland
| | - Roberto Adelfio
- Department of Infectious Diseases and Pathobiology (DIP), Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Susanne Aebi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Sabrina S. Burgener
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology (DIP), Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | | | - Charaf Benarafa
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology (DIP), Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
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Robinson JM, Cando-Dumancela C, Liddicoat C, Weinstein P, Cameron R, Breed MF. Vertical Stratification in Urban Green Space Aerobiomes. ENVIRONMENTAL HEALTH PERSPECTIVES 2020; 128:117008. [PMID: 33236934 PMCID: PMC7687659 DOI: 10.1289/ehp7807] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/27/2020] [Accepted: 11/06/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Exposure to a diverse environmental microbiome is thought to play an important role in "educating" the immune system and facilitating competitive exclusion of pathogens to maintain human health. Vegetation and soil are key sources of airborne microbiota--the aerobiome. A limited number of studies have attempted to characterize the dynamics of near surface green space aerobiomes, and no studies to date have investigated these dynamics from a vertical perspective. Vertical stratification in the aerobiome could have important implications for public health and for the design, engineering, and management of urban green spaces. OBJECTIVES The primary objectives of this study were to: a) assess whether significant vertical stratification in bacterial species richness and evenness (alpha diversity) of the aerobiome occurred in a parkland habitat in Adelaide, South Australia; b) assess whether significant compositional differences (beta diversity) between sampling heights occurred; and c) to preliminarily assess whether there were significant altitudinal differences in potentially pathogenic and beneficial bacterial taxa. METHODS We combined an innovative columnar sampling method at soil level, 0.0, 0.5, 1.0, and 2.0 m , using passive petri dish sampling to collect airborne bacteria. We used a geographic information system (GIS) to select study sites, and we used high-throughput sequencing of the bacterial 16S rRNA gene to assess whether significant vertical stratification of the aerobiome occurred. RESULTS Our results provide evidence of vertical stratification in both alpha and beta (compositional) diversity of airborne bacterial communities, with diversity decreasing roughly with height. We also found significant vertical stratification in potentially pathogenic and beneficial bacterial taxa. DISCUSSION Although additional research is needed, our preliminary findings point to potentially different exposure attributes that may be contingent on human height and activity type. Our results lay the foundations for further research into the vertical characteristics of urban green space aerobiomes and their implications for public health and urban planning. https://doi.org/10.1289/EHP7807.
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Affiliation(s)
- Jake M Robinson
- Department of Landscape, The University of Sheffield, Sheffield, UK
- inVIVO Planetary Health of the Worldwide Universities Network (WUN), West New York, New Jersey, USA
- College of Science and Engineering, Flinders University, Bedford Park, Australia
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
| | - Christian Cando-Dumancela
- College of Science and Engineering, Flinders University, Bedford Park, Australia
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
| | - Craig Liddicoat
- College of Science and Engineering, Flinders University, Bedford Park, Australia
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
- School of Public Health and the Environment Institute, University of Adelaide, Adelaide, Australia
| | - Philip Weinstein
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
- School of Public Health and the Environment Institute, University of Adelaide, Adelaide, Australia
| | - Ross Cameron
- Department of Landscape, The University of Sheffield, Sheffield, UK
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, Australia
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
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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: 52] [Impact Index Per Article: 13.0] [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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Wu JY, Zhu YS, Guo C, Xia Y, Guo ZM, Li QL, Lu JH. A Comparative Study of Associated Microbiota Between Pig Farm and Pig Slaughterhouse in Guangdong, China. Curr Microbiol 2020; 77:3310-3320. [PMID: 32915289 PMCID: PMC7485193 DOI: 10.1007/s00284-020-02187-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 08/26/2020] [Indexed: 12/11/2022]
Abstract
The goal of this study was to compare the microbiota in different pig-present settings in China. Bioaerosol samples from pig farms and slaughterhouses and nasal samples from pig farmers and slaughterhouse workers were collected in Guangdong, southern China. The bacterial genomic DNA was isolated and subjected to 16S sequencing. The data were analyzed using QIIME2 with the DADA2 pipeline. A total of 14,923,551 clean reads and 2785 operational taxonomic units (OTUs) were obtained, which were mostly grouped into 4 phyla (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) and 220 families. The microbiota richness of nasal samples in pig-present workers was higher than that of bioaerosols collected in the vicinity of the pig enclosures. There were 31.7% (620/1954) shared OTUs between pig farm bioaerosols and pig farmers which was higher than that between pig slaughterhouses and slaughterhouse workers (23.4%, 364/1553) (p < 0.001). Acinetobacter and Pseudomonas were the most abundant in pig-present bioaerosols, and Staphylococcus, Pseudomonas, and Corynebacterium were dominant bacterial genus in pig farmers. The bacterial patterns are also specific to the location of sample collected. The results suggest that bioaerosol microbiota interact with human nasal microbes in the vicinity of the pig farm enclosures, providing the basis for further analysis of microbial transmission across hosts in pig-present settings.
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Affiliation(s)
- Jian-Yong Wu
- School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yan-Shan Zhu
- School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, 10032, USA
| | - Yao Xia
- School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Zhong-Min Guo
- Laboratory Animal Center, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Qian-Lin Li
- School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jia-Hai Lu
- School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China.
- Key Laboratory for Tropical Disease Control of Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou, 510080, China.
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Zhang J, Liu H, Yang Q, Li P, Wen Y, Han X, Li B, Jiang H, Li X. Genomic Sequencing Reveals the Diversity of Seminal Bacteria and Relationships to Reproductive Potential in Boar Sperm. Front Microbiol 2020; 11:1873. [PMID: 32903829 PMCID: PMC7438901 DOI: 10.3389/fmicb.2020.01873] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 07/16/2020] [Indexed: 02/01/2023] Open
Abstract
A number of emerging studies suggest that pathogenic microorganisms in semen may cause a decline in the reproductive potential of spermatozoa, and the bacterial diversity and profile of ejaculated boar semen in different seasons are currently unknown. To explore the bacterial composition and changes in ejaculated boar semen from winter and summer, and the underlying mechanism of decline in sperm quality and fertility capacity in summer, 120 ejaculated semen samples were examined for bacterial communities using genomic sequencing technology, and the associations between microbial composition and sperm reproductive potential were investigated. The results showed that Proteobacteria (57.53%), Firmicutes (31.17%), Bacteroidetes (4.24%), and Actinobacteria (3.41%) are the dominant phyla in the ejaculated semen, and the dominant genera were Pseudomonas (34.41%) and Lactobacillus (19.93%), which belong to the phyla of Proteobacteria and Firmicutes, respectively. Interestingly, the higher diversity of bacteria in ejaculated semen of winter differs from that of summer semen, potentially due to seasonal changes related to changes in semen quality and sperm fertilizing capacity. Furthermore, the highly abundant Lactobacillus in winter samples were positively associated with sperm quality and reproductive performance obtained from sows inseminated with such semen samples, while in contrast, the highly abundant Pseudomonas in summer samples was negatively associated with sperm quality and reproductive potential. Additionally, our results strongly indicated that Lactobacillus is not only a potential probiotic for semen quality and fertility potential but also beneficial for restraining the negative influence of Pseudomonas. Overall, our findings significantly contribute to the current understanding of the phenotypes and etiology of male "summer infertility," and may represent a frontier in male reproductive disorders and possible early prevention against pathogenic bacteria.
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Affiliation(s)
- Jing Zhang
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Huan Liu
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qiangzhen Yang
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Peifei Li
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Wen
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuejun Han
- Shanghai Engineering Research Center of Breeding Pig, Shanghai, China
| | - Bushe Li
- Shanghai Engineering Research Center of Breeding Pig, Shanghai, China
| | - Hongju Jiang
- Shanghai Engineering Research Center of Breeding Pig, Shanghai, China
| | - Xinhong Li
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Developmental Origins of Health and Disease: Impact of environmental dust exposure in modulating microbiome and its association with non-communicable diseases. J Dev Orig Health Dis 2020; 11:545-556. [PMID: 32536356 DOI: 10.1017/s2040174420000549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Non-communicable diseases (NCDs) including obesity, diabetes, and allergy are chronic, multi-factorial conditions that are affected by both genetic and environmental factors. Over the last decade, the microbiome has emerged as a possible contributor to the pathogenesis of NCDs. Microbiome profiles were altered in patients with NCDs, and shift in microbial communities was associated with improvement in these health conditions. Since the genetic component of these diseases cannot be altered, the ability to manipulate the microbiome holds great promise for design of novel therapies in the prevention and treatment of NCDs. Together, the Developmental Origins of Health and Disease concept and the microbial hypothesis propose that early life exposure to environmental stimuli will alter the development and composition of the human microbiome, resulting in health consequences. Recent studies indicated that the environment we are exposed to in early life is instrumental in shaping robust immune development, possibly through modulation of the human microbiome (skin, airway, and gut). Despite much research into human microbiome, the origin of their constituent microbiota remains unclear. Dust (also known as particulate matter) is a key determinant of poor air quality in the modern urban environment. It is ubiquitous and serves as a major source and reservoir of microbial communities that modulates the human microbiome, contributing to health and disease. There are evidence that reported significant associations between environmental dust and NCDs. In this review, we will focus on the impact of dust exposure in shaping the human microbiome and its possible contribution to the development of NCDs.
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Islam MZ, Johannesen TB, Lilje B, Urth TR, Larsen AR, Angen Ø, Larsen J. Investigation of the human nasal microbiome in persons with long- and short-term exposure to methicillin-resistant Staphylococcus aureus and other bacteria from the pig farm environment. PLoS One 2020; 15:e0232456. [PMID: 32353071 PMCID: PMC7192431 DOI: 10.1371/journal.pone.0232456] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 04/15/2020] [Indexed: 12/15/2022] Open
Abstract
Since its emergence in the early 2000s, livestock-associated methicillin-resistant Staphylococcus aureus clonal complex 398 (LA-MRSA CC398) has led to an increasing number of human infections in Denmark and other European countries with industrial pig production. LA-MRSA CC398 is primarily associated with skin infections among pig farm workers but is also increasingly recognized as a cause of life-threatening disease among elderly and immunocompromised people. Pig farm workers may serve as vehicles for the spread of LA-MRSA CC398 and other farm-origin bacteria between farms and into the general population. Yet, little is known about the bacterial community dynamics in pig farm workers and other persons with long- and short-term exposure to the pig farm environment. To gain insight into this, we investigated the nasal microbiomes in pig farm workers during a workweek on four LA-MRSA CC398-positive pig farms, as well as in short-term visitors two hours before, immediately after, and 48 hours after a 1-hour visit to another LA-MRSA CC398-positive pig farm. S. aureus and LA-MRSA CC398 carriage was quantified by means of culture, and the composition of the bacterial communities was investigated through sequencing of the 16S rRNA gene. Pig farm workers often carried LA-MRSA CC398 and other bacteria from the pig farm environment, both at work and at home, although at lower levels at home. In contrast, short-term visitors were subject to a less dramatic and rapidly reversible change in the nasal bacterial community composition. These results suggest that pig farm workers may be an important source of LA-MRSA CC398 and perhaps other pathogens of human and veterinary relevance.
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Affiliation(s)
- Md Zohorul Islam
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Berit Lilje
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Tinna Ravnholt Urth
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Øystein Angen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jesper Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
- * E-mail:
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Abstract
PURPOSE OF REVIEW Recent evidence suggests that environmental exposures change the adult human microbiome. Here, we review recent evidence on the impact of the work microbiome and work-related chemical, metal and particulate exposures on the human microbiome. RECENT FINDINGS Prior literature on occupational microbial exposures has focused mainly on the respiratory effects of endotoxin, but a recent study suggests that not all endotoxin is the same; endotoxin from some species is proinflammatory, whereas endotoxin from other species is anti-inflammatory. Work with animals can change the adult human microbiome, likely through colonization. Early studies in military personnel and animal models of gulf war illness show that military exposures change the gut microbiome and increase gut permeability. Heavy metal and particulate matter exposure, which are often elevated in occupational settings, also change the gut microbiome. SUMMARY An emerging body of literature shows that work-related exposures can change the human microbiome. The health effects of these changes are currently not well studied. If work exposures lead to disease through alterations in the human microbiome, exposure cessation without addressing changes to the human microbiome may be ineffective for disease prevention and treatment.
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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: 17] [Impact Index Per Article: 4.3] [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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Huang Z, Zeng S, Xiong J, Hou D, Zhou R, Xing C, Wei D, Deng X, Yu L, Wang H, Deng Z, Weng S, Kriengkrai S, Ning D, Zhou J, He J. Microecological Koch's postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome. MICROBIOME 2020; 8:32. [PMID: 32156316 PMCID: PMC7065354 DOI: 10.1186/s40168-020-00802-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 02/10/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Recently, increasing evidence supports that some complex diseases are not attributed to a given pathogen, but dysbiosis in the host intestinal microbiota (IM). The full intestinal ecosystem alterations, rather than a single pathogen, are associated with white feces syndrome (WFS), a globally severe non-infectious shrimp disease, while no experimental evidence to explore the causality. Herein, we conducted comprehensive metagenomic and metabolomic analysis, and intestinal microbiota transplantation (IMT) to investigate the causal relationship between IM dysbiosis and WFS. RESULTS Compared to the Control shrimp, we found dramatically decreased microbial richness and diversity in WFS shrimp. Ten genera, such as Vibrio, Candidatus Bacilloplasma, Photobacterium, and Aeromonas, were overrepresented in WFS, whereas 11 genera, including Shewanella, Chitinibacter, and Rhodobacter were enriched in control. The divergent changes in these populations might contribute the observation that a decline of pathways conferring lipoic acid metabolism and mineral absorption in WFS. Meanwhile, some sorts of metabolites, especially lipids and organic acids, were found to be related to the IM alteration in WFS. Integrated with multiomics and IMT, we demonstrated that significant alterations in the community composition, functional potentials, and metabolites of IM were closely linked to shrimp WFS. The distinguished metabolites which were attributed to the IM dysbiosis were validated by feed-supplementary challenge. Both homogenous selection and heterogeneous selection process were less pronounced in WFS microbial community assembly. Notably, IMT shrimp from WFS donors eventually developed WFS clinical signs, while the dysbiotic IM can be recharacterized in recipient shrimp. CONCLUSIONS Collectively, our findings offer solid evidence of the causality between IM dysbiosis and shrimp WFS, which exemplify the 'microecological Koch's postulates' (an intestinal microbiota dysbiosis, a disease) in disease etiology, and inspire our cogitation on etiology from an ecological perspective. Video abstract.
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Affiliation(s)
- Zhijian Huang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
- Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
| | - Shenzheng Zeng
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, People’s Republic of China
| | - Dongwei Hou
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
| | - Renjun Zhou
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
| | - Chengguang Xing
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
| | - Dongdong Wei
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
| | - Xisha Deng
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
| | - Lingfei Yu
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
| | - Hao Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
| | - Zhixuan Deng
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
- Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
| | | | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK USA
| | - Jianguo He
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
- Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong People’s Republic of China
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Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China. mSystems 2019; 4:4/6/e00206-19. [PMID: 31848308 PMCID: PMC6918024 DOI: 10.1128/msystems.00206-19] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to exacerbate the antibiotic resistance in humans due to the abuse of antibiotics in pig production in various parts of the world. This study delineates an intricate picture of swine gut microbiome and antibiotic resistome in industrialized feedlots and may provide insight for the pig producing industry. To characterize the diversity and richness and explore the function and structure of swine gut microbiome and resistome in common pig-farming feedlots, we sampled and metagenomic sequenced the feces of pigs from four different industrialized feedlots located in four distant provinces across China. Surprisingly, more than half of the nonredundant genes (1,937,648, 54.3%) in the current catalogue were newly found compared with the previously published reference gene catalogue (RGC) of the pig gut microbiome. Additionally, 16 high-completeness draft genomes were obtained by analyzing the dominant species on each feedlot. Notably, seven of these species often appeared in the human body sites. Despite a smaller number of nonredundant genes, our study identified more antibiotic resistance genes than those available in the RGC. Tetracycline, aminoglycoside, and multidrug resistance genes accounted for nearly 70% of the relative abundance in the current catalogue. Slightly higher sharing ratios were shown between the industrialized feedlot pig gut microbiomes and human gut microbiomes than that between the RGC and human counterpart (14.7% versus 12.6% in genes and 94.1% versus 87.7% in functional groups, respectively). Furthermore, a remarkably high number of the antibiotic resistance proteins (n =141) were identified to be shared by the pig, human, and mouse resistome, indicating the potential for horizontal transfer of resistance genes. Of the antibiotic resistance proteins shared by pigs and humans, 50 proteins were related to tetracycline resistance, and 49 were related to aminoglycoside resistance. IMPORTANCE The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to exacerbate the antibiotic resistance in humans due to the abuse of antibiotics in pig production in various parts of the world. This study delineates an intricate picture of swine gut microbiome and antibiotic resistome in industrialized feedlots and may provide insight for the pig producing industry.
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Park J, Kim EB. Differences in microbiome and virome between cattle and horses in the same farm. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:1042-1055. [PMID: 32054207 PMCID: PMC7206377 DOI: 10.5713/ajas.19.0267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/28/2019] [Indexed: 02/06/2023]
Abstract
Objective The ecosystem of an animal farm is composed of various elements, such as animals, farmers, plants, feed, soil, and microorganisms. A domesticated animal’s health is largely connected with the reservoir of bacteria and viruses in animal farms. Although a few studies have focused on exploring the gut microbiome of animals, communities of microbiota and viruses in feedlots have not been thoroughly investigated. Methods Here, we collected feces and dust samples (4 groups: cattle feces, C_F; horse feces, H_F; cattle dust, C_D; and horse dust, H_D) from cattle and horse farms sharing the same housing and investigated their microbiome/virome communities by Illumina sequencing. Results Dust groups (C_D and H_D) showed higher microbial diversity than feces groups (C_F and H_F) regardless of animal species. From the microbial community analysis, all the samples from the four groups have major phyla such as Proteobacteria (min 37.1% to max 42.8%), Firmicutes (19.1% to 24.9%), Bacteroidetes (10.6% to 22.1%), and Actinobacteria (6.1% to 20.5%). The abundance of Streptococcus, which commonly recognized as equine pathogens, was significantly higher in the horse group (H_D and H_F). Over 99% among the classified virome reads were classified as Caudovirales, a group of tailed bacteriophages, in all four groups. Foot-and-mouth disease virus and equine adenovirus, which cause deadly diseases in cattle and horse, respectively, were not detected. Conclusion Our results will provide baseline information to understand different gut and environmental microbial ecology between two livestock species.
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Affiliation(s)
- Jongbin Park
- Department of Animal Life Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Korea
| | - Eun Bae Kim
- Department of Animal Life Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Korea.,Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Korea
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Shen F, Zheng Y, Niu M, Zhou F, Wu Y, Wang J, Zhu T, Wu Y, Wu Z, Hu M, Zhu T. Characteristics of biological particulate matters at urban and rural sites in the North China Plain. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 253:569-577. [PMID: 31330349 DOI: 10.1016/j.envpol.2019.07.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/05/2019] [Accepted: 07/06/2019] [Indexed: 06/10/2023]
Abstract
Depending on their concentrations, sizes, and types, particulate matters of biological origins (bioPM) significantly affect human health. However, for different air environments, they are not well characterized and can vary considerably. As an example, we investigated the bioPM differences at an urban (Beijing) site and a rural (Wangdu) site in the North China Plain (NCP) using an online monitoring instrument, an ultraviolet aerodynamic particle sizer (UV-APS), the limulus amebocyte lysate (LAL) assay, and a high-throughput sequencing method. Generally, lower concentrations of viable bioPM (hourly mean: 1.3 × 103 ± 1.6 × 103 m-3) and endotoxin (0.66 ± 0.16 EU/m3) in Beijing were observed compared to viable bioPM (0.79 × 105 ± 1.4 × 105 m-3) and endotoxin (15.1 ± 23.96 EU/m3) at the Wangdu site. The percentage of viable bioPM number concentration in the total PM was 3.1% in Beijing and 6.4% in Wangdu. Approximately 80% of viable bioPM was found to be in the range from 1 to 2.5 μm. Nevertheless, the size distribution patterns for viable bioPM at the Beijing and Wangdu sites differed and were affected by PM pollution, leading to distinct lung deposition profiles. Moreover, the distinct diurnal variations in viable bioPM on clean days were dimmed by the PM pollution at both sites. Distinct bacterial community structures were found in the air from the Beijing and Wangdu sites. The bacterial community in urban Beijing was dominated by genus Lactococcus (49.5%) and Pseudomonas (15.1%), while the rural Wangdu site was dominated by Enterococcus (65%) and Paenibacillus (10%). Human-derived genera, including Myroides, Streptococcus, Propionibacterium, Dietzia, Helcococcus, and Facklamia, were higher in Beijing, suggesting bacterial emission from humans in the urban air environment. Our results show that different air harbors different biological species, and people residing in different environments thus could have very different biological particle exposure.
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Affiliation(s)
- Fangxia Shen
- School of Space and Environment, Beihang University, Beijing, 102206, China.
| | - Yunhao Zheng
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mutong Niu
- School of Space and Environment, Beihang University, Beijing, 102206, China
| | - Feng Zhou
- School of Space and Environment, Beihang University, Beijing, 102206, China
| | - Yan Wu
- School of Environmental Science and Engineering, Shandong University, Qingdao, 250100, China
| | - Junxia Wang
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Tong Zhu
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Yusheng Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Zhijun Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Min Hu
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Tianle Zhu
- School of Space and Environment, Beihang University, Beijing, 102206, China
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Mbareche H, Morawska L, Duchaine C. On the interpretation of bioaerosol exposure measurements and impacts on health. JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION (1995) 2019; 69:789-804. [PMID: 30821643 DOI: 10.1080/10962247.2019.1587552] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Bioaerosols are recognized as one of the main transmission routes for infectious diseases and are responsible for other various types of health effects through inhalation and potential ingestion. Associating exposure with bioaerosol and health problems is challenging, and adequate exposure monitoring is a top priority for aerosol scientists. The multiple factors affecting bioaerosol content, the variability in the focus of each bioaerosol exposure study, and the variations in experimental design and the standardization of methods make bioaerosol exposure studies very difficult. Therefore, the health impacts of bioaerosol exposure are still poorly understood. This paper presents a brief description of a state-of-the-art development in bioaerosol exposure studies supported by studies on several related subjects. The main objective of this paper is to propose new considerations for bioaerosol exposure guidelines and the development of tools and study designs to better interpret bioaerosol data. The principal observations and findings are the discrepancy of the applicable methods in bioaerosol studies that makes result comparison impossible. Furthermore, the silo mentality helps in creating a bigger gap in the knowledge accumulated about bioaerosol exposure. Innovative and original ideas are presented for aerosol scientists and health scientists to consider and discuss. Although many examples cited herein are from occupational exposure, the discussion has relevance to any human environment. This work gives concrete suggestions for how to design a full bioaerosol study that includes all of the key elements necessary to help understand the real impacts of bioaerosol exposure in the short term. The creation of the proposed bioaerosol public database could give crucial information to control the public health. Implications: How can we move toward a bioaerosol exposure guidelines? The creation of the bioaerosol public database will help accumulate information for long-term association studies and help determine specific exposure biomarkers to bioaerosols. The implementation of such work will lead to a deeper understanding and more efficient utilization of bioaerosol studies to prevent public health hazards.
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Affiliation(s)
- Hamza Mbareche
- a Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec , Quebec City , Quebec , Canada
- b Département de biochimie, de microbiologie et de bio-informatique , Faculté des sciences et de génie, Université Laval , Quebec City , Quebec , Canada
| | - Lidia Morawska
- c School of Chemistry, Physics, and Mechanical Engineering, Department of Environmental Technologies , Queensland University of Technology , Brisbane , Queensland , Australia
| | - Caroline Duchaine
- a Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec , Quebec City , Quebec , Canada
- b Département de biochimie, de microbiologie et de bio-informatique , Faculté des sciences et de génie, Université Laval , Quebec City , Quebec , Canada
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Sommerstein R, Merz TM, Berger S, Kraemer JG, Marschall J, Hilty M. Patterns in the longitudinal oropharyngeal microbiome evolution related to ventilator-associated pneumonia. Antimicrob Resist Infect Control 2019; 8:81. [PMID: 31139364 PMCID: PMC6530040 DOI: 10.1186/s13756-019-0530-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/28/2019] [Indexed: 01/15/2023] Open
Abstract
Background The aim of the study was to evaluate the composition and the temporal evolution of the oropharyngeal microbiome in antibiotic-naïve patients requiring mechanical ventilation and to gain new insights into the pathogenesis of ventilator-associated pneumonia (VAP). Methods Prospective, observational single-center nested case-control study. Patients with acute critical illness and anticipated duration of mechanical ventilation > 4 days were eligible. We took oropharyngeal swabs (and if available, tracheal secretions) daily, starting at the day of intubation. The microbiota was characterized by 16S rRNA high-throughput sequencing and compared between patients developing VAP versus controls. Results Five patients developed VAP. In three patient the causative pathogens were Enterobacteriaceae and in two Haemophilus influenzae. Locally weighted polynomial regression suggested that the within diversity (=alpha) was lower in Enterobacteriaceae VAP patients between days two to five of mechanical ventilation when compared to controls. Detection of Enterobacteriaceae in the oropharynx occurred on day two of follow-up and consisted of a single operational taxonomic unit in 2/3 patients with enterobacterial VAP. Conclusions In acutely-ill patients who developed enterobacterial VAP the causative pathogen gained access to the oropharynx early after starting mechanical ventilation and outgrew the commensal members of the microbiome. Whether a specific pattern of the oropharyngeal microbiome between days three to five of mechanical ventilation may predict VAP enterobacterial VAP has to be evaluated in further studies. Electronic supplementary material The online version of this article (10.1186/s13756-019-0530-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rami Sommerstein
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Freiburgstrasse; 4, 3010 Bern, Switzerland
| | - Tobias M Merz
- Department of Intensive Care, Bern University Hospital, University of Bern, Bern, Switzerland.,3Cardiovascular Intensive Care Unit, Auckland City Hospital, Auckland, New Zealand
| | - Sabine Berger
- Department of Intensive Care, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Julia G Kraemer
- 4Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Freiburgstrasse; 4, 3010 Bern, Switzerland
| | - Markus Hilty
- 4Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland
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Wang T, He Q, Yao W, Shao Y, Li J, Huang F. The Variation of Nasal Microbiota Caused by Low Levels of Gaseous Ammonia Exposure in Growing Pigs. Front Microbiol 2019; 10:1083. [PMID: 31156592 PMCID: PMC6532555 DOI: 10.3389/fmicb.2019.01083] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 04/29/2019] [Indexed: 01/24/2023] Open
Abstract
Exposure to gaseous ammonia, even at low levels, can be harmful to pigs and human health. However, less is known about the effects of sustained exposure to gaseous ammonia on nasal microbiota colonization in growing pigs. A total of 120 Duroc×Landrace×Yorkshire pigs were housed in 24 separate chambers and continuously exposed to gaseous ammonia at 0,5, 10, 15, 20, and 25 ppm (four groups per exposure level) for 4 weeks. Then, we used high-throughput sequencing to perform 16S rRNA gene analysis in nasal swabs samples from 72 pigs (n = 12). The results of the nasal microbiota analysis showed that an increase in ammonia concentration, especially at 20 and 25 ppm, decreased the alpha diversity and relative abundance of nasal microbiota. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Chloroflexi were the most abundant phyla. In addition, the relative abundances of 24 microbial genera significantly changed as the ammonia level increased. Four microbial genera (Pseudomonas, Lactobacillus, Prevotella, and Bacteroides) were significantly decreased at 25 ppm, while only two genera (Moraxella and Streptococcus) were increased at 25 ppm. PICRUSt analyses showed that the relative abundances of the nasal microbiota involved in cell motility, signal transduction, the nervous system, environmental adaptation, and energy and carbohydrate metabolism were significantly decreased, while genes involved in the immune system, endocrine system, circulatory system, immune system diseases and metabolism of vitamins, lipid, and amino acids were increased with increased ammonia levels. The results of in vivo tests showed that an increase in ammonia levels, especially an ammonia level of 25 ppm, caused respiratory tract injury and increase the number of Moraxella and Streptococcus species, while simultaneously decreasing respiratory immunity and growth performance, consistent with the increased presence of harmful bacteria identified by nasal microbiota analysis. Herein, this study also indicted that the threshold concentration of ammonia in pig farming is 20 ppm.
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Affiliation(s)
- Tongxin Wang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qiongyu He
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weilei Yao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yafei Shao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ji Li
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Feiruo Huang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
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The Indoor-Air Microbiota of Pig Farms Drives the Composition of the Pig Farmers' Nasal Microbiota in a Season-Dependent and Farm-Specific Manner. Appl Environ Microbiol 2019; 85:AEM.03038-18. [PMID: 30824439 DOI: 10.1128/aem.03038-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/19/2019] [Indexed: 12/20/2022] Open
Abstract
Prior studies have demonstrated an influence of the built environment on the human nasal microbiota. However, very little is known about the influences of working on a pig farm on the human nasal microbiota. We longitudinally collected samples from 30 pig farms (air and nasal swabs from humans and pigs) in Switzerland from 2014 to 2015. As controls, nasal swabs from cow farmers and individuals with no contact with farm animals were included. An analysis of the microbiota for all samples (n = 609) was performed based on 16S rRNA gene sequencing (MiSeq) and included the investigations of source-sink dynamics. The numbers of indoor airborne particles and bacterial loads in pig farms were also investigated and were highest in winter. Similarly, the microbiota analyses revealed that the alpha diversity values of the nares of pig farmers were increased in winter in contrast to those of samples from the nonexposed controls, which displayed low alpha diversity values throughout the seasons. Source-sink analyses revealed that bacteria from the noses of pigs are more commonly coidentified within the pig farmers' microbiota in winter but to a less extent in summer. In addition, in winter, there was a stronger intrasimilarity for samples that originated from the same farm than for samples from different farms, and this farm specificity was partially or completely lost in spring, summer, and fall. In conclusion, in contrast to nonexposed controls, a pig farmer's nasal microbiota is dynamic, as the indoor-air microbiota of pig farms drives the composition of the pig farmer's nasal microbiota in a season-dependent manner.IMPORTANCE The airborne microbiota of pig farms poses a potential health hazard and impacts both livestock and humans working in this environment. Therefore, a more thorough understanding of the microbiota composition and dynamics in this setting is needed. This study was of a prospective design (12 months) and used samples from different sites. This means that the microbiota of air, animals (pigs), and humans was simultaneously investigated. Our findings highlight that the potential health hazard might be particularly high in winter compared to that in summer.
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