An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants

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. In this study, we used...
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Autor*in:	Xie, Fei [verfasserIn] 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

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	Ruminant Gastrointestinal microbiome Metagenome-assembled genomes Alphaproteobacteria Feed efficiency

Anmerkung:	© The Author(s) 2021. corrected publication 2022

Übergeordnetes Werk:	Enthalten in: Microbiome - London : Biomed Central, 2013, 9(2021), 1 vom: 12. Juni
Übergeordnetes Werk:	volume:9 ; year:2021 ; number:1 ; day:12 ; month:06

Links:	Volltext

DOI / URN:	10.1186/s40168-021-01078-x

Katalog-ID:	SPR051235900

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520			\|a 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. 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 composition and function. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. 4XTAn6fj9egk7xEPDHXbzgVideo abstract
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allfields	10.1186/s40168-021-01078-x doi (DE-627)SPR051235900 (SPR)s40168-021-01078-x-e DE-627 ger DE-627 rakwb eng Xie, Fei verfasserin aut An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2021. corrected publication 2022 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. 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 composition and function. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. 4XTAn6fj9egk7xEPDHXbzgVideo abstract Ruminant (dpeaa)DE-He213 Gastrointestinal microbiome (dpeaa)DE-He213 Metagenome-assembled genomes (dpeaa)DE-He213 Alphaproteobacteria (dpeaa)DE-He213 Feed efficiency (dpeaa)DE-He213 Jin, Wei aut Si, Huazhe aut Yuan, Yuan aut Tao, Ye aut Liu, Junhua aut Wang, Xiaoxu aut Yang, Chengjian aut Li, Qiushuang aut Yan, Xiaoting aut Lin, Limei aut Jiang, Qian aut Zhang, Lei aut Guo, Changzheng aut Greening, Chris aut Heller, Rasmus aut Guan, Le Luo aut Pope, Phillip B. aut Tan, Zhiliang aut Zhu, Weiyun aut Wang, Min aut Qiu, Qiang aut Li, Zhipeng aut Mao, Shengyong (orcid)0000-0002-0089-9314 aut Enthalten in Microbiome London : Biomed Central, 2013 9(2021), 1 vom: 12. Juni (DE-627)734146140 (DE-600)2697425-3 2049-2618 nnns volume:9 year:2021 number:1 day:12 month:06 https://dx.doi.org/10.1186/s40168-021-01078-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2021 1 12 06
spelling	10.1186/s40168-021-01078-x doi (DE-627)SPR051235900 (SPR)s40168-021-01078-x-e DE-627 ger DE-627 rakwb eng Xie, Fei verfasserin aut An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2021. corrected publication 2022 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. 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 composition and function. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. 4XTAn6fj9egk7xEPDHXbzgVideo abstract Ruminant (dpeaa)DE-He213 Gastrointestinal microbiome (dpeaa)DE-He213 Metagenome-assembled genomes (dpeaa)DE-He213 Alphaproteobacteria (dpeaa)DE-He213 Feed efficiency (dpeaa)DE-He213 Jin, Wei aut Si, Huazhe aut Yuan, Yuan aut Tao, Ye aut Liu, Junhua aut Wang, Xiaoxu aut Yang, Chengjian aut Li, Qiushuang aut Yan, Xiaoting aut Lin, Limei aut Jiang, Qian aut Zhang, Lei aut Guo, Changzheng aut Greening, Chris aut Heller, Rasmus aut Guan, Le Luo aut Pope, Phillip B. aut Tan, Zhiliang aut Zhu, Weiyun aut Wang, Min aut Qiu, Qiang aut Li, Zhipeng aut Mao, Shengyong (orcid)0000-0002-0089-9314 aut Enthalten in Microbiome London : Biomed Central, 2013 9(2021), 1 vom: 12. Juni (DE-627)734146140 (DE-600)2697425-3 2049-2618 nnns volume:9 year:2021 number:1 day:12 month:06 https://dx.doi.org/10.1186/s40168-021-01078-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2021 1 12 06
allfields_unstemmed	10.1186/s40168-021-01078-x doi (DE-627)SPR051235900 (SPR)s40168-021-01078-x-e DE-627 ger DE-627 rakwb eng Xie, Fei verfasserin aut An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2021. corrected publication 2022 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. 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 composition and function. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. 4XTAn6fj9egk7xEPDHXbzgVideo abstract Ruminant (dpeaa)DE-He213 Gastrointestinal microbiome (dpeaa)DE-He213 Metagenome-assembled genomes (dpeaa)DE-He213 Alphaproteobacteria (dpeaa)DE-He213 Feed efficiency (dpeaa)DE-He213 Jin, Wei aut Si, Huazhe aut Yuan, Yuan aut Tao, Ye aut Liu, Junhua aut Wang, Xiaoxu aut Yang, Chengjian aut Li, Qiushuang aut Yan, Xiaoting aut Lin, Limei aut Jiang, Qian aut Zhang, Lei aut Guo, Changzheng aut Greening, Chris aut Heller, Rasmus aut Guan, Le Luo aut Pope, Phillip B. aut Tan, Zhiliang aut Zhu, Weiyun aut Wang, Min aut Qiu, Qiang aut Li, Zhipeng aut Mao, Shengyong (orcid)0000-0002-0089-9314 aut Enthalten in Microbiome London : Biomed Central, 2013 9(2021), 1 vom: 12. Juni (DE-627)734146140 (DE-600)2697425-3 2049-2618 nnns volume:9 year:2021 number:1 day:12 month:06 https://dx.doi.org/10.1186/s40168-021-01078-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2021 1 12 06
allfieldsGer	10.1186/s40168-021-01078-x doi (DE-627)SPR051235900 (SPR)s40168-021-01078-x-e DE-627 ger DE-627 rakwb eng Xie, Fei verfasserin aut An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2021. corrected publication 2022 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. 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 composition and function. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. 4XTAn6fj9egk7xEPDHXbzgVideo abstract Ruminant (dpeaa)DE-He213 Gastrointestinal microbiome (dpeaa)DE-He213 Metagenome-assembled genomes (dpeaa)DE-He213 Alphaproteobacteria (dpeaa)DE-He213 Feed efficiency (dpeaa)DE-He213 Jin, Wei aut Si, Huazhe aut Yuan, Yuan aut Tao, Ye aut Liu, Junhua aut Wang, Xiaoxu aut Yang, Chengjian aut Li, Qiushuang aut Yan, Xiaoting aut Lin, Limei aut Jiang, Qian aut Zhang, Lei aut Guo, Changzheng aut Greening, Chris aut Heller, Rasmus aut Guan, Le Luo aut Pope, Phillip B. aut Tan, Zhiliang aut Zhu, Weiyun aut Wang, Min aut Qiu, Qiang aut Li, Zhipeng aut Mao, Shengyong (orcid)0000-0002-0089-9314 aut Enthalten in Microbiome London : Biomed Central, 2013 9(2021), 1 vom: 12. Juni (DE-627)734146140 (DE-600)2697425-3 2049-2618 nnns volume:9 year:2021 number:1 day:12 month:06 https://dx.doi.org/10.1186/s40168-021-01078-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2021 1 12 06
allfieldsSound	10.1186/s40168-021-01078-x doi (DE-627)SPR051235900 (SPR)s40168-021-01078-x-e DE-627 ger DE-627 rakwb eng Xie, Fei verfasserin aut An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2021. corrected publication 2022 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. 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 composition and function. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. 4XTAn6fj9egk7xEPDHXbzgVideo abstract Ruminant (dpeaa)DE-He213 Gastrointestinal microbiome (dpeaa)DE-He213 Metagenome-assembled genomes (dpeaa)DE-He213 Alphaproteobacteria (dpeaa)DE-He213 Feed efficiency (dpeaa)DE-He213 Jin, Wei aut Si, Huazhe aut Yuan, Yuan aut Tao, Ye aut Liu, Junhua aut Wang, Xiaoxu aut Yang, Chengjian aut Li, Qiushuang aut Yan, Xiaoting aut Lin, Limei aut Jiang, Qian aut Zhang, Lei aut Guo, Changzheng aut Greening, Chris aut Heller, Rasmus aut Guan, Le Luo aut Pope, Phillip B. aut Tan, Zhiliang aut Zhu, Weiyun aut Wang, Min aut Qiu, Qiang aut Li, Zhipeng aut Mao, Shengyong (orcid)0000-0002-0089-9314 aut Enthalten in Microbiome London : Biomed Central, 2013 9(2021), 1 vom: 12. Juni (DE-627)734146140 (DE-600)2697425-3 2049-2618 nnns volume:9 year:2021 number:1 day:12 month:06 https://dx.doi.org/10.1186/s40168-021-01078-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2021 1 12 06
language	English
source	Enthalten in Microbiome 9(2021), 1 vom: 12. Juni volume:9 year:2021 number:1 day:12 month:06
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authorswithroles_txt_mv	Xie, Fei @@aut@@ Jin, Wei @@aut@@ Si, Huazhe @@aut@@ Yuan, Yuan @@aut@@ Tao, Ye @@aut@@ Liu, Junhua @@aut@@ Wang, Xiaoxu @@aut@@ Yang, Chengjian @@aut@@ Li, Qiushuang @@aut@@ Yan, Xiaoting @@aut@@ Lin, Limei @@aut@@ Jiang, Qian @@aut@@ Zhang, Lei @@aut@@ Guo, Changzheng @@aut@@ Greening, Chris @@aut@@ Heller, Rasmus @@aut@@ Guan, Le Luo @@aut@@ Pope, Phillip B. @@aut@@ Tan, Zhiliang @@aut@@ Zhu, Weiyun @@aut@@ Wang, Min @@aut@@ Qiu, Qiang @@aut@@ Li, Zhipeng @@aut@@ Mao, Shengyong @@aut@@
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author	Xie, Fei
spellingShingle	Xie, Fei misc Ruminant misc Gastrointestinal microbiome misc Metagenome-assembled genomes misc Alphaproteobacteria misc Feed efficiency An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
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topic_title	An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants Ruminant (dpeaa)DE-He213 Gastrointestinal microbiome (dpeaa)DE-He213 Metagenome-assembled genomes (dpeaa)DE-He213 Alphaproteobacteria (dpeaa)DE-He213 Feed efficiency (dpeaa)DE-He213
topic	misc Ruminant misc Gastrointestinal microbiome misc Metagenome-assembled genomes misc Alphaproteobacteria misc Feed efficiency
topic_unstemmed	misc Ruminant misc Gastrointestinal microbiome misc Metagenome-assembled genomes misc Alphaproteobacteria misc Feed efficiency
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title	An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
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author_browse	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
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title_sort	integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
title_auth	An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
abstract	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. 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 composition and function. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. 4XTAn6fj9egk7xEPDHXbzgVideo abstract © The Author(s) 2021. corrected publication 2022
abstractGer	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. 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 composition and function. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. 4XTAn6fj9egk7xEPDHXbzgVideo abstract © The Author(s) 2021. corrected publication 2022
abstract_unstemmed	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. 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 composition and function. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. 4XTAn6fj9egk7xEPDHXbzgVideo abstract © The Author(s) 2021. corrected publication 2022
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container_issue	1
title_short	An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
url	https://dx.doi.org/10.1186/s40168-021-01078-x
remote_bool	true
author2	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
author2Str	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
ppnlink	734146140
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isOA_txt	true
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doi_str	10.1186/s40168-021-01078-x
up_date	2024-07-03T20:36:15.762Z
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