Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement
Journal Articles The International Society of Microbiologial Ecology Journal Year : 2017

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

Olov Svartström
  • Function : Author
Johannes Alneberg
  • Function : Author
Nicolas Terrapon
Ino de Bruijn
  • Function : Author
Jonas Malmsten
  • Function : Author
Ann-Marie Dalin
  • Function : Author
Emilie El Muller
  • Function : Author
Pranjul Shah
  • Function : Author
Paul Wilmes
Anders Andersson
  • Function : Author

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.

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Olov Svartström, Johannes Alneberg, Nicolas Terrapon, Vincent Lombard, Ino de Bruijn, et al.. Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation. The International Society of Microbiologial Ecology Journal, 2017, 11 (11), pp.2538-2551. ⟨10.1038/ismej.2017.108⟩. ⟨hal-02328246⟩
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