Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms

Jian Sun, Xiao-Ping Liao, Alaric W. D’Souza, Manish Boolchandani, Sheng-Hui Li, Ke Cheng, José Luis Martínez, Liang Li, You-Jun Feng, Liang-Xing Fang, Ting Huang, Jing Xia, Yang Yu, Yu-Feng Zhou, Yong-Xue Sun, Xian-Bo Deng, Zhen-Ling Zeng, Hong-Xia Jiang, Bing-Hu Fang, You-Zhi Tang, Xin-Lei Lian, Rong-Min Zhang, Zhi-Wei Fang, Qiu-Long Yan, Gautam Dantas () and Ya-Hong Liu ()
Additional contact information
Jian Sun: South China Agricultural University
Xiao-Ping Liao: South China Agricultural University
Alaric W. D’Souza: Washington University in St. Louis School of Medicine
Manish Boolchandani: Washington University in St. Louis School of Medicine
Sheng-Hui Li: South China Agricultural University
Ke Cheng: South China Agricultural University
José Luis Martínez: Consejo Superior de Investigaciones Científicas
Liang Li: South China Agricultural University
You-Jun Feng: South China Agricultural University
Liang-Xing Fang: South China Agricultural University
Ting Huang: South China Agricultural University
Jing Xia: South China Agricultural University
Yang Yu: South China Agricultural University
Yu-Feng Zhou: South China Agricultural University
Yong-Xue Sun: South China Agricultural University
Xian-Bo Deng: Guangdong Laboratory for Lingnan Modern Agriculture
Zhen-Ling Zeng: South China Agricultural University
Hong-Xia Jiang: South China Agricultural University
Bing-Hu Fang: South China Agricultural University
You-Zhi Tang: South China Agricultural University
Xin-Lei Lian: South China Agricultural University
Rong-Min Zhang: South China Agricultural University
Zhi-Wei Fang: Shenzhen Puensum Genetech Institute
Qiu-Long Yan: Shenzhen Puensum Genetech Institute
Gautam Dantas: Washington University in St. Louis School of Medicine
Ya-Hong Liu: South China Agricultural University

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-15222-y

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