Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation

• Published in: The ISME Journal
• Main Authors: Svartström, Olov, Alneberg, Johannes, Terrapon, Nicolas, Lombard, Vincent, de Bruijn, Ino, Malmsten, Jonas, Dalin, Ann-Marie, El Muller, Emilie, Shah, Pranjul, Wilmes, Paul, Henrissat, Bernard, Aspeborg, Henrik, Andersson, Anders
• Other Authors: Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg Luxembourg, AlbaNova University Center (ALBANOVA), Stockholm University, wedish Research Council Formas 213-2012-1513 213-2014-176 European Union's Seventh Framework Program (FP), European Project: 322820,EC:FP7:ERC,ERC-2012-ADG_20120314,HUMAN MICROBIOTA(2013)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2017
• Subjects: [SDE.BE]Environmental Sciences/Biodiversity and Ecology; [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry; Molecular Biology/Genomics [q-bio.GN]; [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics; Phylogenetics and taxonomy; Alces alces
• Online Access: https://hal.science/hal-02328246; https://doi.org/10.1038/ismej.2017.108

International audience The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.