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ISME J. 2017 Nov;11(11):2538-2551. doi: 10.1038/ismej.2017.108. Epub 2017 Jul 21.

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

Author information

1
School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden.
2
School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
3
CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.
4
INRA, USC 1408 AFMB, 13288 Marseille, France.
5
Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden.
6
Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
7
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
8
Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.

Abstract

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.

PMID:
28731473
PMCID:
PMC5648042
DOI:
10.1038/ismej.2017.108
[Indexed for MEDLINE]
Free PMC Article

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