The multi-kingdom microbiome of the goat gastrointestinal tract
Yanhong Cao,
Tong Feng,
Yingjian Wu,
Yixue Xu,
Li Du,
Teng Wang,
Yuhong Luo,
Yan Wang,
Zhipeng Li,
Zeyi Xuan,
Shaomei Chen,
Na Yao,
Na L. Gao,
Qian Xiao,
Kongwei Huang,
Xiaobo Wang,
Kuiqing Cui,
Saif ur Rehman,
Xiangfang Tang,
Dewu Liu,
Hongbing Han,
Ying Li,
Wei-Hua Chen,
Qingyou Liu
Affiliations
Yanhong Cao
Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University
Tong Feng
Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology
Yingjian Wu
Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology
Yixue Xu
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University
Li Du
Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University
Teng Wang
Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology
Yuhong Luo
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University
Yan Wang
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University
Zhipeng Li
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University
Zeyi Xuan
Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region
Shaomei Chen
Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region
Na Yao
Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region
Na L. Gao
Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology
Qian Xiao
Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University
Kongwei Huang
Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University
Xiaobo Wang
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University
Kuiqing Cui
Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University
Saif ur Rehman
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University
Xiangfang Tang
State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences
Dewu Liu
South China Agricultural University
Hongbing Han
College of Animal Science and Technology, China Agricultural University
Ying Li
Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University
Wei-Hua Chen
Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology
Qingyou Liu
Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University
Abstract Background Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT. Results We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network. Conclusions Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract
