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Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation
KTH, School of Biotechnology (BIO), Industrial Biotechnology.
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
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2017 (English)In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 11, no 11, p. 2538-2551Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017. Vol. 11, no 11, p. 2538-2551
National Category
Environmental Sciences Ecology Microbiology
Identifiers
URN: urn:nbn:se:kth:diva-217180DOI: 10.1038/ismej.2017.108ISI: 000413240100011PubMedID: 28731473Scopus ID: 2-s2.0-85031798353OAI: oai:DiVA.org:kth-217180DiVA, id: diva2:1154436
Funder
Swedish Research Council Formas, 213-2012-1513 213-2014-176EU, FP7, Seventh Framework ProgrammeEU, European Research Council, 322820Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20171102

Available from: 2017-11-02 Created: 2017-11-02 Last updated: 2017-11-02Bibliographically approved

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Svartström, OlovAlneberg, Johannesde Bruijn, InoAspeborg, HenrikAndersson, Anders F.
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