%0 Journal Article
%T The multi-kingdom microbiome of the goat gastrointestinal tract.
%A Cao Y
%A Feng T
%A Wu Y
%A Xu Y
%A Du L
%A Wang T
%A Luo Y
%A Wang Y
%A Li Z
%A Xuan Z
%A Chen S
%A Yao N
%A Gao NL
%A Xiao Q
%A Huang K
%A Wang X
%A Cui K
%A Rehman SU
%A Tang X
%A Liu D
%A Han H
%A Li Y
%A Chen WH
%A Liu Q
%J Microbiome
%V 11
%N 1
%D 2023 10 2
%M 37779211
%F 16.837
%R 10.1186/s40168-023-01651-6
%X 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.<BR>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.<BR>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.