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Gigascience

Title:		A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment
Author(s):		Li J; Zhong H; Ramayo-Caldas Y; Terrapon N; Lombard V; Potocki-Veronese G; Estelle 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;
Address:		"BGI-Shenzhen, Shenzhen 518083, China. China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China. School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China. Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen O, Denmark. INRAE, Genetique Animale et Biologie Integrative, AgroParisTech, Universite Paris-Saclay, 78350 Jouy-en-Josas, France. Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui 08140, Spain. CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France. INRAE, USC 1408 AFMB, 13288 Marseille, France. LISBP, Universite de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France. Universite Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes Champanelle, France. School of Future Technology, University of Chinese Academy of Sciences, Beijing 101408, China. INRAE, Micalis Institute, AgroParisTech, Universite Paris-Saclay, 78350 Jouy-en-Josas, France. James D. Watson Institute of Genome Sciences, Hangzhou 310058, China. Institute of Marine Research (IMR), Postboks 1870 Nordnes, 5817 Bergen, Norway. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. MGP MetaGenoPolis, INRAE, Universite Paris-Saclay, 78350 Jouy en Josas, France. Centre for Host Microbiome Interactions, Dental Institute, King's College London, London, UK"
Journal Title:		Gigascience
Year:		2020
Volume:		9
Issue:		6
Page Number:		-
DOI:		10.1093/gigascience/giaa057
ISSN/ISBN:		2047-217X (Electronic) 2047-217X (Linking)
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:		"Animals Biomass Cattle Diet Digestion Drug Resistance, Microbial Gastrointestinal Microbiome/*genetics Humans *Metagenome *Metagenomics/methods Mice Microbiota/*genetics Rumen/*microbiology Swine bovine carbohydrate-active enzymes herbivory metagenome rum;"
Notes:		"MedlineLi, Junhua Zhong, Huanzi Ramayo-Caldas, Yuliaxis Terrapon, Nicolas Lombard, Vincent Potocki-Veronese, Gabrielle Estelle, Jordi Popova, Milka Yang, Ziyi Zhang, Hui Li, Fang Tang, Shanmei Yang, Fangming Chen, Weineng Chen, Bing Li, Jiyang Guo, Jing Martin, Cecile Maguin, Emmanuelle Xu, Xun Yang, Huanming Wang, Jian Madsen, Lise Kristiansen, Karsten Henrissat, Bernard Ehrlich, Stanislav D Morgavi, Diego P eng 322820/ERC_/European Research Council/International Research Support, Non-U.S. Gov't 2020/05/31 Gigascience. 2020 Jun 1; 9(6):giaa057. doi: 10.1093/gigascience/giaa057"