Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms
Anthropogenic environments have been implicated in enrichment and exchange of antibiotic resistance genes and bacteria. Here we study the impact of confined and controlled swine farm environments on temporal changes in the gut microbiome and resistome of veterinary students with occupational exposur...
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| Published in | Nature communications Vol. 11; no. 1; pp. 1427 - 11 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
18.03.2020
Nature Publishing Group Nature Portfolio |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2041-1723 2041-1723 |
| DOI | 10.1038/s41467-020-15222-y |
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| Abstract | Anthropogenic environments have been implicated in enrichment and exchange of antibiotic resistance genes and bacteria. Here we study the impact of confined and controlled swine farm environments on temporal changes in the gut microbiome and resistome of veterinary students with occupational exposure for 3 months. By analyzing 16S rRNA and whole metagenome shotgun sequencing data in tandem with culture-based methods, we show that farm exposure shapes the gut microbiome of students, resulting in enrichment of potentially pathogenic taxa and antimicrobial resistance genes. Comparison of students’ gut microbiomes and resistomes to farm workers’ and environmental samples revealed extensive sharing of resistance genes and bacteria following exposure and after three months of their visit. Notably, antibiotic resistance genes were found in similar genetic contexts in student samples and farm environmental samples. Dynamic Bayesian network modeling predicted that the observed changes partially reverse over a 4-6 month period. Our results indicate that acute changes in a human’s living environment can persistently shape their gut microbiota and antibiotic resistome.
Environments where antibiotics are used indiscriminately exhibit microbial communities that can represent hot-spots of resistance gene enrichment, which in turn could spread to humans. Here, the authors characterize how exposure to swine farms environment lead to temporal changes in the gut microbiome and resistome of healthy veterinary students. |
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| AbstractList | Anthropogenic environments have been implicated in enrichment and exchange of antibiotic resistance genes and bacteria. Here we study the impact of confined and controlled swine farm environments on temporal changes in the gut microbiome and resistome of veterinary students with occupational exposure for 3 months. By analyzing 16S rRNA and whole metagenome shotgun sequencing data in tandem with culture-based methods, we show that farm exposure shapes the gut microbiome of students, resulting in enrichment of potentially pathogenic taxa and antimicrobial resistance genes. Comparison of students’ gut microbiomes and resistomes to farm workers’ and environmental samples revealed extensive sharing of resistance genes and bacteria following exposure and after three months of their visit. Notably, antibiotic resistance genes were found in similar genetic contexts in student samples and farm environmental samples. Dynamic Bayesian network modeling predicted that the observed changes partially reverse over a 4-6 month period. Our results indicate that acute changes in a human’s living environment can persistently shape their gut microbiota and antibiotic resistome.Environments where antibiotics are used indiscriminately exhibit microbial communities that can represent hot-spots of resistance gene enrichment, which in turn could spread to humans. Here, the authors characterize how exposure to swine farms environment lead to temporal changes in the gut microbiome and resistome of healthy veterinary students. Anthropogenic environments have been implicated in enrichment and exchange of antibiotic resistance genes and bacteria. Here we study the impact of confined and controlled swine farm environments on temporal changes in the gut microbiome and resistome of veterinary students with occupational exposure for 3 months. By analyzing 16S rRNA and whole metagenome shotgun sequencing data in tandem with culture-based methods, we show that farm exposure shapes the gut microbiome of students, resulting in enrichment of potentially pathogenic taxa and antimicrobial resistance genes. Comparison of students’ gut microbiomes and resistomes to farm workers’ and environmental samples revealed extensive sharing of resistance genes and bacteria following exposure and after three months of their visit. Notably, antibiotic resistance genes were found in similar genetic contexts in student samples and farm environmental samples. Dynamic Bayesian network modeling predicted that the observed changes partially reverse over a 4-6 month period. Our results indicate that acute changes in a human’s living environment can persistently shape their gut microbiota and antibiotic resistome. Anthropogenic environments have been implicated in enrichment and exchange of antibiotic resistance genes and bacteria. Here we study the impact of confined and controlled swine farm environments on temporal changes in the gut microbiome and resistome of veterinary students with occupational exposure for 3 months. By analyzing 16S rRNA and whole metagenome shotgun sequencing data in tandem with culture-based methods, we show that farm exposure shapes the gut microbiome of students, resulting in enrichment of potentially pathogenic taxa and antimicrobial resistance genes. Comparison of students’ gut microbiomes and resistomes to farm workers’ and environmental samples revealed extensive sharing of resistance genes and bacteria following exposure and after three months of their visit. Notably, antibiotic resistance genes were found in similar genetic contexts in student samples and farm environmental samples. Dynamic Bayesian network modeling predicted that the observed changes partially reverse over a 4-6 month period. Our results indicate that acute changes in a human’s living environment can persistently shape their gut microbiota and antibiotic resistome. Environments where antibiotics are used indiscriminately exhibit microbial communities that can represent hot-spots of resistance gene enrichment, which in turn could spread to humans. Here, the authors characterize how exposure to swine farms environment lead to temporal changes in the gut microbiome and resistome of healthy veterinary students. Anthropogenic environments have been implicated in enrichment and exchange of antibiotic resistance genes and bacteria. Here we study the impact of confined and controlled swine farm environments on temporal changes in the gut microbiome and resistome of veterinary students with occupational exposure for 3 months. By analyzing 16S rRNA and whole metagenome shotgun sequencing data in tandem with culture-based methods, we show that farm exposure shapes the gut microbiome of students, resulting in enrichment of potentially pathogenic taxa and antimicrobial resistance genes. Comparison of students' gut microbiomes and resistomes to farm workers' and environmental samples revealed extensive sharing of resistance genes and bacteria following exposure and after three months of their visit. Notably, antibiotic resistance genes were found in similar genetic contexts in student samples and farm environmental samples. Dynamic Bayesian network modeling predicted that the observed changes partially reverse over a 4-6 month period. Our results indicate that acute changes in a human's living environment can persistently shape their gut microbiota and antibiotic resistome.Anthropogenic environments have been implicated in enrichment and exchange of antibiotic resistance genes and bacteria. Here we study the impact of confined and controlled swine farm environments on temporal changes in the gut microbiome and resistome of veterinary students with occupational exposure for 3 months. By analyzing 16S rRNA and whole metagenome shotgun sequencing data in tandem with culture-based methods, we show that farm exposure shapes the gut microbiome of students, resulting in enrichment of potentially pathogenic taxa and antimicrobial resistance genes. Comparison of students' gut microbiomes and resistomes to farm workers' and environmental samples revealed extensive sharing of resistance genes and bacteria following exposure and after three months of their visit. Notably, antibiotic resistance genes were found in similar genetic contexts in student samples and farm environmental samples. Dynamic Bayesian network modeling predicted that the observed changes partially reverse over a 4-6 month period. Our results indicate that acute changes in a human's living environment can persistently shape their gut microbiota and antibiotic resistome. Environments where antibiotics are used indiscriminately exhibit microbial communities that can represent hot-spots of resistance gene enrichment, which in turn could spread to humans. Here, the authors characterize how exposure to swine farms environment lead to temporal changes in the gut microbiome and resistome of healthy veterinary students. |
| ArticleNumber | 1427 |
| Author | Luis Martínez, José Liu, Ya-Hong Dantas, Gautam Cheng, Ke Zhou, Yu-Feng Fang, Bing-Hu Tang, You-Zhi Li, Sheng-Hui Yu, Yang Li, Liang Feng, You-Jun Sun, Yong-Xue Fang, Zhi-Wei Xia, Jing Yan, Qiu-Long Zhang, Rong-Min Fang, Liang-Xing Liao, Xiao-Ping Zeng, Zhen-Ling Sun, Jian Boolchandani, Manish Lian, Xin-Lei Deng, Xian-Bo D’Souza, Alaric W. Huang, Ting Jiang, Hong-Xia |
| Author_xml | – sequence: 1 givenname: Jian surname: Sun fullname: Sun, Jian organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 2 givenname: Xiao-Ping orcidid: 0000-0002-4654-5837 surname: Liao fullname: Liao, Xiao-Ping organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 3 givenname: Alaric W. orcidid: 0000-0002-8744-8136 surname: D’Souza fullname: D’Souza, Alaric W. organization: The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine – sequence: 4 givenname: Manish orcidid: 0000-0001-6038-8957 surname: Boolchandani fullname: Boolchandani, Manish organization: The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine – sequence: 5 givenname: Sheng-Hui surname: Li fullname: Li, Sheng-Hui organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Shenzhen Puensum Genetech Institute – sequence: 6 givenname: Ke surname: Cheng fullname: Cheng, Ke organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 7 givenname: José orcidid: 0000-0001-8813-7607 surname: Luis Martínez fullname: Luis Martínez, José organization: Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas – sequence: 8 givenname: Liang surname: Li fullname: Li, Liang organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 9 givenname: You-Jun surname: Feng fullname: Feng, You-Jun organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 10 givenname: Liang-Xing surname: Fang fullname: Fang, Liang-Xing organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 11 givenname: Ting surname: Huang fullname: Huang, Ting organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 12 givenname: Jing surname: Xia fullname: Xia, Jing organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 13 givenname: Yang surname: Yu fullname: Yu, Yang organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 14 givenname: Yu-Feng surname: Zhou fullname: Zhou, Yu-Feng organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 15 givenname: Yong-Xue surname: Sun fullname: Sun, Yong-Xue organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University – sequence: 16 givenname: Xian-Bo surname: Deng fullname: Deng, Xian-Bo organization: Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 17 givenname: Zhen-Ling surname: Zeng fullname: Zeng, Zhen-Ling organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University – sequence: 18 givenname: Hong-Xia surname: Jiang fullname: Jiang, Hong-Xia organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University – sequence: 19 givenname: Bing-Hu surname: Fang fullname: Fang, Bing-Hu organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University – sequence: 20 givenname: You-Zhi surname: Tang fullname: Tang, You-Zhi organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University – sequence: 21 givenname: Xin-Lei surname: Lian fullname: Lian, Xin-Lei organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 22 givenname: Rong-Min surname: Zhang fullname: Zhang, Rong-Min organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture – sequence: 23 givenname: Zhi-Wei surname: Fang fullname: Fang, Zhi-Wei organization: Shenzhen Puensum Genetech Institute – sequence: 24 givenname: Qiu-Long surname: Yan fullname: Yan, Qiu-Long organization: Shenzhen Puensum Genetech Institute – sequence: 25 givenname: Gautam orcidid: 0000-0003-0455-8370 surname: Dantas fullname: Dantas, Gautam email: dantas@wustl.edu organization: The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, Department of Biomedical Engineering, Washington University in St. Louis, Department of Molecular Microbiology, Washington University in St. Louis School of Medicine – sequence: 26 givenname: Ya-Hong orcidid: 0000-0003-2915-2406 surname: Liu fullname: Liu, Ya-Hong email: lyh@scau.edu.cn organization: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/32188862$$D View this record in MEDLINE/PubMed |
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| Title | Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms |
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