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Chen D, Cheng K, Wan L, Cui C, Li G, Zhao D, Yu Y, Liao X, Liu Y, D'Souza AW, Lian X, Sun J. Daily occupational exposure in swine farm alters human skin microbiota and antibiotic resistome. IMETA 2024; 3:e158. [PMID: 38868515 PMCID: PMC10989081 DOI: 10.1002/imt2.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 06/14/2024]
Abstract
Antimicrobial resistance (AMR) is a major threat to global public health, and antibiotic resistance genes (ARGs) are widely distributed across humans, animals, and environment. Farming environments are emerging as a key research area for ARGs and antibiotic resistant bacteria (ARB). While the skin is an important reservoir of ARGs and ARB, transmission mechanisms between farming environments and human skin remain unclear. Previous studies confirmed that swine farm environmental exposures alter skin microbiome, but the timeline of these changes is ill defined. To improve understanding of these changes and to determine the specific time, we designed a cohort study of swine farm workers and students through collected skin and environmental samples to explore the impact of daily occupational exposure in swine farm on human skin microbiome. Results indicated that exposure to livestock-associated environments where microorganisms are richer than school environment can reshape the human skin microbiome and antibiotic resistome. Exposure of 5 h was sufficient to modify the microbiome and ARG structure in workers' skin by enriching microorganisms and ARGs. These changes were preserved once formed. Further analysis indicated that ARGs carried by host microorganisms may transfer between the environment with workers' skin and have the potential to expand to the general population using farm workers as an ARG vector. These results raised concerns about potential transmission of ARGs to the broader community. Therefore, it is necessary to take corresponding intervention measures in the production process to reduce the possibility of ARGs and ARB transmission.
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Affiliation(s)
- Dong‐Rui Chen
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
- Veterinary CenterGuangxi State Farms Yongxin Animal Husbandry Group Co., Ltd.NanningChina
| | - Ke Cheng
- Veterinary CenterGuangxi State Farms Yongxin Animal Husbandry Group Co., Ltd.NanningChina
| | - Lei Wan
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Chao‐Yue Cui
- Laboratory Animal CentreWenzhou Medical UniversityWenzhouChina
| | - Gong Li
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Dong‐Hao Zhao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Yang Yu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Xiao‐Ping Liao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Ya‐Hong Liu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Alaric W. D'Souza
- Department of PediatricsBoston Children's HospitalBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Xin‐Lei Lian
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
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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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3
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Ruthsatz K, Lyra ML, Lambertini C, Belasen AM, Jenkinson TS, da Silva Leite D, Becker CG, Haddad CFB, James TY, Zamudio KR, Toledo LF, Vences M. Skin microbiome correlates with bioclimate and Batrachochytrium dendrobatidis infection intensity in Brazil's Atlantic Forest treefrogs. Sci Rep 2020; 10:22311. [PMID: 33339839 PMCID: PMC7749163 DOI: 10.1038/s41598-020-79130-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/04/2020] [Indexed: 12/20/2022] Open
Abstract
In Brazil’s Atlantic Forest (AF) biodiversity conservation is of key importance since the fungal pathogen Batrachochytrium dendrobatidis (Bd) has led to the rapid loss of amphibian populations here and worldwide. The impact of Bd on amphibians is determined by the host's immune system, of which the skin microbiome is a critical component. The richness and diversity of such cutaneous bacterial communities are known to be shaped by abiotic factors which thus may indirectly modulate host susceptibility to Bd. This study aimed to contribute to understanding the environment-host–pathogen interaction determining skin bacterial communities in 819 treefrogs (Anura: Hylidae and Phyllomedusidae) from 71 species sampled across the AF. We investigated whether abiotic factors influence the bacterial community richness and structure on the amphibian skin. We further tested for an association between skin bacterial community structure and Bd co-occurrence. Our data revealed that temperature, precipitation, and elevation consistently correlate with richness and diversity of the skin microbiome and also predict Bd infection status. Surprisingly, our data suggest a weak but significant positive correlation of Bd infection intensity and bacterial richness. We highlight the prospect of future experimental studies on the impact of changing environmental conditions associated with global change on environment-host–pathogen interactions in the AF.
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Affiliation(s)
- Katharina Ruthsatz
- Institute of Zoology, Universität Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany. .,Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106, Brunswick, Germany.
| | - Mariana L Lyra
- Laboratório de Herpetologia, Depto de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista - UNESP, Rio Claro, São Paulo, Brazil
| | - Carolina Lambertini
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Anat M Belasen
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-2701, USA
| | - Thomas S Jenkinson
- Department of Wildlife, Fish and Conservation Biology, University of California, Davis, Davis, CA, USA
| | - Domingos da Silva Leite
- Laboratório de Antígenos Bacterianos II, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Caixa Postal 6109, Campinas, São Paulo, CEP 13083-862, Brazil
| | - C Guilherme Becker
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35847, USA
| | - Célio F B Haddad
- Laboratório de Herpetologia, Depto de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista - UNESP, Rio Claro, São Paulo, Brazil
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-2701, USA
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106, Brunswick, Germany
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Hooper R, Brealey JC, van der Valk T, Alberdi A, Durban JW, Fearnbach H, Robertson KM, Baird RW, Bradley Hanson M, Wade P, Gilbert MTP, Morin PA, Wolf JBW, Foote AD, Guschanski K. Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin. Mol Ecol 2019; 28:484-502. [PMID: 30187987 PMCID: PMC6487819 DOI: 10.1111/mec.14860] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/15/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.
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Affiliation(s)
- Rebecca Hooper
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Jaelle C. Brealey
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Tom van der Valk
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Antton Alberdi
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
| | - John W. Durban
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | - Holly Fearnbach
- SR3, SeaLife Response, Rehabilitation, and ResearchSeattleWashington
| | - Kelly M. Robertson
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | | | - M. Bradley Hanson
- Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashington
| | - Paul Wade
- National Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashington
| | - M. Thomas P. Gilbert
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
- NTNU University MuseumTrondheimNorway
| | - Phillip A. Morin
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | - Jochen B. W. Wolf
- Science of Life Laboratories and Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
- Section of Evolutionary BiologyFaculty of BiologyLMU MunichMunichGermany
| | - Andrew D. Foote
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological SciencesBangor UniversityBangorGwyneddUK
| | - Katerina Guschanski
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
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Lemieux-Labonté V, Simard A, Willis CKR, Lapointe FJ. Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome. MICROBIOME 2017; 5:115. [PMID: 28870257 PMCID: PMC5584028 DOI: 10.1186/s40168-017-0334-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/28/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Infectious diseases of wildlife are increasing worldwide with implications for conservation and human public health. The microbiota (i.e. microbial community living on or in a host) could influence wildlife disease resistance or tolerance. White-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans (Pd), has killed millions of hibernating North American bats since 2007. We characterized the skin microbiota of naïve, pre-WNS little brown bats (Myotis lucifugus) from three WNS-negative hibernation sites and persisting, previously exposed bats from three WNS-positive sites to test the hypothesis that the skin microbiota of bats shifts following WNS invasion. RESULTS Using high-throughput 16S rRNA gene sequencing on 66 bats and 11 environmental samples, we found that hibernation site strongly influenced the composition and diversity of the skin microbiota. Bats from WNS-positive and WNS-negative sites differed in alpha and beta diversity, as well as in microbiota composition. Alpha diversity was reduced in persisting, WNS-positive bats, and the microbiota profile was enriched with particular taxa such Janthinobacterium, Micrococcaceae, Pseudomonas, Ralstonia, and Rhodococcus. Some of these taxa are recognized for their antifungal activity, and specific strains of Rhodococcus and Pseudomonas are known to inhibit Pd growth. Composition of the microbial community in the hibernaculum environment and the community on bat skin was superficially similar but differed in relative abundance of some bacterial taxa. CONCLUSIONS Our results are consistent with the hypothesis that Pd invasion leads to a shift in the skin microbiota of surviving bats and suggest the possibility that the microbiota plays a protective role for bats facing WNS. The detection of what appears to be enrichment of beneficial bacteria in the skin microbiota of persisting bats is a promising discovery for species re-establishment. Our findings highlight not only the potential value of management actions that might encourage transmission, growth, and establishment of beneficial bacteria on bats, and within hibernacula, but also the potential risks of such management actions.
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Affiliation(s)
- Virginie Lemieux-Labonté
- Département de Sciences Biologiques, Université de Montréal, CP 6182, Succursale Centre-ville, Montréal, Québec, H2V 2S9, Canada.
- Quebec Centre for Biodiversity Science, CP 6182, Succursale Centre-ville, Montréal, Québec, H2V 2S9, Canada.
| | - Anouk Simard
- Direction de l'expertise sur la faune terrestre, l'herpétofaune et l'avifaune, Ministère des Forêts, de la Faune et des Parcs, Québec, Canada
- Quebec Centre for Biodiversity Science, CP 6182, Succursale Centre-ville, Montréal, Québec, H2V 2S9, Canada
| | - Craig K R Willis
- Department of Biology and Centre for Forest Interdisciplinary Research, University of Winnipeg, Winnipeg, Manitoba, Canada
| | - François-Joseph Lapointe
- Département de Sciences Biologiques, Université de Montréal, CP 6182, Succursale Centre-ville, Montréal, Québec, H2V 2S9, Canada
- Quebec Centre for Biodiversity Science, CP 6182, Succursale Centre-ville, Montréal, Québec, H2V 2S9, Canada
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Dumas SE, French HM, Lavergne SN, Ramirez CR, Brown LJ, Bromfield CR, Garrett EF, French DD, Aldridge BM. Judicious use of prophylactic antimicrobials to reduce abdominal surgical site infections in periparturient cows: part 1 - a risk factor review. Vet Rec 2017; 178:654-60. [PMID: 27339926 DOI: 10.1136/vr.i103677] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Surgical site infections (SSI) are an uncommon, but significant, consequence of surgical interventions. There are very few studies investigating SSI risk in veterinary medicine, and even fewer in cattle, despite the fact that major surgeries are commonly conducted on livestock. Furthermore, the suboptimal conditions under which such surgeries are frequently performed on livestock could be considered an important risk factor for the development of SSIs. With increasing public concern over the contribution of veterinary-prescribed antimicrobials to the emergence of antimicrobial-resistant bacteria in people, there is widespread scrutiny and criticism of antimicrobial use in livestock production medicine systems. While the causal link between antimicrobial resistance in livestock and people is heavily debated, it is clear that the prevalence of antimicrobial resistance, in any population, is closely correlated with the antimicrobial 'consumption' within that population. As the veterinary profession explores ways of addressing the emergence and selection of antimicrobial-resistant bacteria in food-producing animals, there is a need for veterinarians and producers to carefully consider all areas of antimicrobial use, and employ an evidence-based approach in designing appropriate clinical protocols. This paper aims to review current knowledge regarding the risk factors related to abdominal SSI in periparturient cows, and to encourage practitioners to judiciously evaluate both their standard operating procedures and their use of antimicrobials in these situations. In a second paper, to be published in a subsequent issue of Veterinary Record, these principles will be used to provide specific evidence-based recommendations for antimicrobial use in bovine abdominal surgery.
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Affiliation(s)
- S E Dumas
- Integrated Food Animal Management Systems (IFAMS), Department of Veterinary Clinical Medicine, College of Veterinary Medicine
| | - H M French
- Integrated Food Animal Management Systems (IFAMS), Department of Veterinary Clinical Medicine, College of Veterinary Medicine
| | - S N Lavergne
- Comparative Biosciences, College of Veterinary Medicine
| | - C R Ramirez
- Integrated Food Animal Management Systems (IFAMS), Department of Veterinary Clinical Medicine, College of Veterinary Medicine
| | - L J Brown
- Agricultural Animal Care and Use Program, Department of Animal Sciences, College of Agriculture, Consumer and Environmental Sciences, University of Illnois - Urbana-Champaign, Urbana, IL 61802, USA Dr Dumas's current address is the College of Veterinary Medicine, Cornell University, Ithaca, NY, USA Dr H. M. French is also at Ross University School of Veterinary Medicine, St Kitts, West Indies
| | - C R Bromfield
- Agricultural Animal Care and Use Program, Department of Animal Sciences, College of Agriculture, Consumer and Environmental Sciences, University of Illnois - Urbana-Champaign, Urbana, IL 61802, USA Dr Dumas's current address is the College of Veterinary Medicine, Cornell University, Ithaca, NY, USA Dr H. M. French is also at Ross University School of Veterinary Medicine, St Kitts, West Indies
| | - E F Garrett
- Integrated Food Animal Management Systems (IFAMS), Department of Veterinary Clinical Medicine, College of Veterinary Medicine
| | - D D French
- Integrated Food Animal Management Systems (IFAMS), Department of Veterinary Clinical Medicine, College of Veterinary Medicine
| | - B M Aldridge
- Integrated Food Animal Management Systems (IFAMS), Department of Veterinary Clinical Medicine, College of Veterinary Medicine
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7
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Lemieux-Labonté V, Tromas N, Shapiro BJ, Lapointe FJ. Environment and host species shape the skin microbiome of captive neotropical bats. PeerJ 2016; 4:e2430. [PMID: 27688962 PMCID: PMC5036103 DOI: 10.7717/peerj.2430] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/10/2016] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND A wide range of microorganisms inhabit animal skin. This microbial community (microbiome) plays an important role in host defense against pathogens and disease. Bats (Chiroptera: Mammalia) are an ecologically and evolutionarily diversified group with a relatively unexplored skin microbiome. The bat skin microbiome could play a role in disease resistance, for example, to white nose syndrome (WNS), an infection which has been devastating North American bat populations. However, fundamental knowledge of the bat skin microbiome is needed before understanding its role in health and disease resistance. Captive neotropical frugivorous bats Artibeus jamaicensis and Carollia perspicillataprovide a simple controlled system in which to characterize the factors shaping the bat microbiome. Here, we aimed to determine the relative importance of habitat and host species on the bat skin microbiome. METHODS We performed high-throughput 16S rRNA gene sequencing of the skin microbiome of two different bat species living in captivity in two different habitats. In the first habitat, A. jamaicensis and C. perspicillata lived together, while the second habitat contained only A. jamaicensis. RESULTS We found that both habitat and host species shape the composition and diversity of the skin microbiome, with habitat having the strongest influence. Cohabitating A. jamaicensis and C. perspicillata shared more similar skin microbiomes than members of the same species (A. jamaicensis) across two habitats. DISCUSSION These results suggest that in captivity, the skin microbial community is homogenised by the shared environments and individual proximities of bats living together in the same habitat, at the expense of the innate host species factors. The predominant influence of habitat suggests that environmental microorganisms or pathogens might colonize bat skin. We also propose that bat populations could differ in pathogen susceptibility depending on their immediate environment and habitat.
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Affiliation(s)
| | - Nicolas Tromas
- Département de Sciences Biologiques, Université de Montréal , Montréal , Canada
| | - B Jesse Shapiro
- Département de Sciences Biologiques, Université de Montréal , Montréal , Canada
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