The multi-kingdom microbiome of the goat gastrointestinal tract

BackgroundGoat 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, develo...

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Published in:Microbiome 2023-10, Vol.11 (1), p.1-219, Article 219
Main Authors: Cao, Yanhong, Feng, Tong, Wu, Yingjian, Xu, Yixue, Du, Li, Wang, Teng, Luo, Yuhong, Wang, Yan, Li, Zhipeng, Xuan, Zeyi, Chen, Shaomei, Yao, Na, Gao, Na L., Xiao, Qian, Huang, Kongwei, Wang, Xiaobo, Cui, Kuiqing, Rehman, Saif ur, Tang, Xiangfang, Liu, Dewu, Han, Hongbing, Li, Ying, Chen, Wei-Hua, Liu, Qingyou
Format: Article
Language:English
Subjects:
Archaeome
Bacteria
Bacteriome
Cloning
Developmental stages
Ecology
Food
Gastrointestinal tract
Genetic testing
Genomes
Goat
Goats
Large intestine
Livestock
Metagenome-assembled genomes
Methane
Microbiome
Microbiomes
Microbiota
Plasmids
Small intestine
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Summary:BackgroundGoat 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.ResultsWe 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.ConclusionsTogether, 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
ISSN:2049-2618
2049-2618
DOI:10.1186/s40168-023-01651-6