Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China
Chunlai Wang,
Peng Li,
Qiulong Yan,
Liping Chen,
Tiantian Li,
Wanjiang Zhang,
He Li,
Changming Chen,
Xiuyan Han,
Siyi Zhang,
Miao Xu,
Bo Li,
Xiaoxuan Zhang,
Hongbo Ni,
Yufang Ma,
Bo Dong,
Shenghui Li,
Siguo Liu
Affiliations
Chunlai Wang
State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
Peng Li
Shenzhen Puensum Genetech Institute, Shenzhen, China
Qiulong Yan
Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
Liping Chen
State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
Tiantian Li
State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
Wanjiang Zhang
State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
He Li
State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
Changming Chen
Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
Xiuyan Han
Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
Siyi Zhang
Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
Miao Xu
Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
Bo Li
Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
Xiaoxuan Zhang
College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
Hongbo Ni
College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
Yufang Ma
Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
Bo Dong
Shenzhen Puensum Genetech Institute, Shenzhen, China
Shenghui Li
Shenzhen Puensum Genetech Institute, Shenzhen, China
Siguo Liu
State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
ABSTRACT 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.
