A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

Publikation: Bidrag til tidsskriftTidsskriftartikelfagfællebedømt

Standard

A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment. / Li, Junhua; Zhong, Huanzi; Ramayo-Caldas, Yuliaxis; Terrapon, Nicolas; Lombard, Vincent; Potocki-Veronese, Gabrielle; Estellé, Jordi; Popova, Milka; Yang, Ziyi; Zhang, Hui; Li, Fang; Tang, Shanmei; Yang, Fangming; Chen, Weineng; Chen, Bing; Li, Jiyang; Guo, Jing; Martin, Cécile; Maguin, Emmanuelle; Xu, Xun; Yang, Huanming; Wang, Jian; Madsen, Lise; Kristiansen, Karsten; Henrissat, Bernard; Ehrlich, Stanislav D.; Morgavi, Diego P.

I: GigaScience, Bind 9, Nr. 6, giaa057, 2020.

Publikation: Bidrag til tidsskriftTidsskriftartikelfagfællebedømt

Harvard

Li, J, Zhong, H, Ramayo-Caldas, Y, Terrapon, N, Lombard, V, Potocki-Veronese, G, Estellé, J, Popova, M, Yang, Z, Zhang, H, Li, F, Tang, S, Yang, F, Chen, W, Chen, B, Li, J, Guo, J, Martin, C, Maguin, E, Xu, X, Yang, H, Wang, J, Madsen, L, Kristiansen, K, Henrissat, B, Ehrlich, SD & Morgavi, DP 2020, 'A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment', GigaScience, bind 9, nr. 6, giaa057. https://doi.org/10.1093/gigascience/giaa057

APA

Li, J., Zhong, H., Ramayo-Caldas, Y., Terrapon, N., Lombard, V., Potocki-Veronese, G., Estellé, J., Popova, M., Yang, Z., Zhang, H., Li, F., Tang, S., Yang, F., Chen, W., Chen, B., Li, J., Guo, J., Martin, C., Maguin, E., ... Morgavi, D. P. (2020). A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment. GigaScience, 9(6), [giaa057]. https://doi.org/10.1093/gigascience/giaa057

Vancouver

Li J, Zhong H, Ramayo-Caldas Y, Terrapon N, Lombard V, Potocki-Veronese G o.a. A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment. GigaScience. 2020;9(6). giaa057. https://doi.org/10.1093/gigascience/giaa057

Author

Li, Junhua ; Zhong, Huanzi ; Ramayo-Caldas, Yuliaxis ; Terrapon, Nicolas ; Lombard, Vincent ; Potocki-Veronese, Gabrielle ; Estellé, Jordi ; Popova, Milka ; Yang, Ziyi ; Zhang, Hui ; Li, Fang ; Tang, Shanmei ; Yang, Fangming ; Chen, Weineng ; Chen, Bing ; Li, Jiyang ; Guo, Jing ; Martin, Cécile ; Maguin, Emmanuelle ; Xu, Xun ; Yang, Huanming ; Wang, Jian ; Madsen, Lise ; Kristiansen, Karsten ; Henrissat, Bernard ; Ehrlich, Stanislav D. ; Morgavi, Diego P. / A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment. I: GigaScience. 2020 ; Bind 9, Nr. 6.

Bibtex

@article{a8be591f9ee44e6f97e66b98d3157487,
title = "A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment",
abstract = "BACKGROUND: The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. RESULTS: Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes. CONCLUSIONS: These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.",
keywords = "bovine, carbohydrate-active enzymes, herbivory, metagenome, rumen",
author = "Junhua Li and Huanzi Zhong and Yuliaxis Ramayo-Caldas and Nicolas Terrapon and Vincent Lombard and Gabrielle Potocki-Veronese and Jordi Estell{\'e} and Milka Popova and Ziyi Yang and Hui Zhang and Fang Li and Shanmei Tang and Fangming Yang and Weineng Chen and Bing Chen and Jiyang Li and Jing Guo and C{\'e}cile Martin and Emmanuelle Maguin and Xun Xu and Huanming Yang and Jian Wang and Lise Madsen and Karsten Kristiansen and Bernard Henrissat and Ehrlich, {Stanislav D.} and Morgavi, {Diego P.}",
year = "2020",
doi = "10.1093/gigascience/giaa057",
language = "English",
volume = "9",
journal = "GigaScience",
issn = "2047-217X",
publisher = "Oxford Academic",
number = "6",

}

RIS

TY - JOUR

T1 - A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

AU - Li, Junhua

AU - Zhong, Huanzi

AU - Ramayo-Caldas, Yuliaxis

AU - Terrapon, Nicolas

AU - Lombard, Vincent

AU - Potocki-Veronese, Gabrielle

AU - Estellé, Jordi

AU - Popova, Milka

AU - Yang, Ziyi

AU - Zhang, Hui

AU - Li, Fang

AU - Tang, Shanmei

AU - Yang, Fangming

AU - Chen, Weineng

AU - Chen, Bing

AU - Li, Jiyang

AU - Guo, Jing

AU - Martin, Cécile

AU - Maguin, Emmanuelle

AU - Xu, Xun

AU - Yang, Huanming

AU - Wang, Jian

AU - Madsen, Lise

AU - Kristiansen, Karsten

AU - Henrissat, Bernard

AU - Ehrlich, Stanislav D.

AU - Morgavi, Diego P.

PY - 2020

Y1 - 2020

N2 - BACKGROUND: The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. RESULTS: Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes. CONCLUSIONS: These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.

AB - BACKGROUND: The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. RESULTS: Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes. CONCLUSIONS: These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.

KW - bovine

KW - carbohydrate-active enzymes

KW - herbivory

KW - metagenome

KW - rumen

U2 - 10.1093/gigascience/giaa057

DO - 10.1093/gigascience/giaa057

M3 - Journal article

C2 - 32473013

AN - SCOPUS:85085712340

VL - 9

JO - GigaScience

JF - GigaScience

SN - 2047-217X

IS - 6

M1 - giaa057

ER -

ID: 243149799