An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
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An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants. / Xie, Fei; Jin, Wei; Si, Huazhe; Yuan, Yuan; Tao, Ye; Liu, Junhua; Wang, Xiaoxu; Yang, Chengjian; Li, Qiushuang; Yan, Xiaoting; Lin, Limei; Jiang, Qian; Zhang, Lei; Guo, Changzheng; Greening, Chris; Heller, Rasmus; Guan, Le Luo; Pope, Phillip B.; Tan, Zhiliang; Zhu, Weiyun; Wang, Min; Qiu, Qiang; Li, Zhipeng; Mao, Shengyong.
In: Microbiome, Vol. 9, 137, 2021.Research output: Contribution to journal › Journal article › Research › peer-review
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T1 - An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
AU - Xie, Fei
AU - Jin, Wei
AU - Si, Huazhe
AU - Yuan, Yuan
AU - Tao, Ye
AU - Liu, Junhua
AU - Wang, Xiaoxu
AU - Yang, Chengjian
AU - Li, Qiushuang
AU - Yan, Xiaoting
AU - Lin, Limei
AU - Jiang, Qian
AU - Zhang, Lei
AU - Guo, Changzheng
AU - Greening, Chris
AU - Heller, Rasmus
AU - Guan, Le Luo
AU - Pope, Phillip B.
AU - Tan, Zhiliang
AU - Zhu, Weiyun
AU - Wang, Min
AU - Qiu, Qiang
AU - Li, Zhipeng
AU - Mao, Shengyong
PY - 2021
Y1 - 2021
N2 - Background: Gastrointestinal tract (GIT) microbiomes in ruminants play major roles in host health and thus animal production. However, we lack an integrated understanding of microbial community structure and function as prior studies. are predominantly biased towards the rumen. Therefore, to acquire a microbiota inventory of the discrete GIT compartments, In this study, we used shotgun metagenomics to profile the microbiota of 370 samples that represent 10 GIT regions of seven ruminant species.Results: Our analyses reconstructed a GIT microbial reference catalog with > 154 million nonredundant genes and identified 8745 uncultured candidate species from over 10,000 metagenome-assembled genomes. The integrated gene catalog across the GIT regions demonstrates spatial associations between the microbiome and physiological adaptations, and 8745 newly characterized genomes substantially expand the genomic landscape of ruminant microbiota, particularly those from the lower gut. This substantially expands the previously known set of endogenous microbial diversity and the taxonomic classification rate of the GIT microbiome. These candidate species encode hundreds of enzymes and novel biosynthetic gene clusters that improve our understanding concerning methane production and feed efficiency in ruminants. Overall, this study expands the characterization of the ruminant GIT microbiota at unprecedented spatial resolution and offers clues for improving ruminant livestock production in the future.Conclusions: Having access to a comprehensive gene catalog and collections of microbial genomes provides the ability to perform efficiently genome-based analysis to achieve a detailed classification of GIT microbial ecosystem composition. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production.
AB - Background: Gastrointestinal tract (GIT) microbiomes in ruminants play major roles in host health and thus animal production. However, we lack an integrated understanding of microbial community structure and function as prior studies. are predominantly biased towards the rumen. Therefore, to acquire a microbiota inventory of the discrete GIT compartments, In this study, we used shotgun metagenomics to profile the microbiota of 370 samples that represent 10 GIT regions of seven ruminant species.Results: Our analyses reconstructed a GIT microbial reference catalog with > 154 million nonredundant genes and identified 8745 uncultured candidate species from over 10,000 metagenome-assembled genomes. The integrated gene catalog across the GIT regions demonstrates spatial associations between the microbiome and physiological adaptations, and 8745 newly characterized genomes substantially expand the genomic landscape of ruminant microbiota, particularly those from the lower gut. This substantially expands the previously known set of endogenous microbial diversity and the taxonomic classification rate of the GIT microbiome. These candidate species encode hundreds of enzymes and novel biosynthetic gene clusters that improve our understanding concerning methane production and feed efficiency in ruminants. Overall, this study expands the characterization of the ruminant GIT microbiota at unprecedented spatial resolution and offers clues for improving ruminant livestock production in the future.Conclusions: Having access to a comprehensive gene catalog and collections of microbial genomes provides the ability to perform efficiently genome-based analysis to achieve a detailed classification of GIT microbial ecosystem composition. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production.
KW - Ruminant
KW - Gastrointestinal microbiome
KW - Metagenome-assembled genomes
KW - Alphaproteobacteria
KW - Feed efficiency
KW - RNA-SEQ DATA
KW - RUMEN MICROBIOME
KW - READ ALIGNMENT
KW - TOOL
KW - COW
KW - EFFICIENCY
KW - EVOLUTION
KW - INSIGHTS
KW - REVEALS
KW - COMPLEX
U2 - 10.1186/s40168-021-01078-x
DO - 10.1186/s40168-021-01078-x
M3 - Journal article
C2 - 34118976
VL - 9
JO - Microbiome
JF - Microbiome
SN - 2049-2618
M1 - 137
ER -
ID: 273372101