Ninety-nine de novo assembled genomes from the moose ( Alces alces ) rumen microbiome provide new insights into microbial plant biomass degradation
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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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Svartstrom et al. (2017) assembled 99 microbial genomes from the moose rumen, Stewart et al. (2018) assembled 913 microbial genomes from the rumen of cattle, and Parks et al. (2017) assembled over 8,000 novel microbial genomes from 1,500 public datasets, some of which originated from the rumen.
“Subsequently, Svartstrom et al. (2017) assembled 99 microbial genomes from the moose rumen, Stewart et al. (2018) assembled 913 microbial genomes from the rumen of cattle, and Parks et al. (2017) assembled over 8,000 novel microbial genomes from 1,500 public datasets, some of which originated from the rumen.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Svartstrom et al., 2017
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- Authors
- Svartström, O., Alneberg, J., Terrapon, N., Lombard, V., de Bruijn, I., Malmsten, J., Dalin, A.-M., EL Muller, E., Shah, P., Wilmes, P., Henrissat, B., Aspeborg, H., & Andersson, A. F.
- Affiliations
- KTH Royal Institute of Technology (SE)
- Science for Life Laboratory (SE)
- Centre National de la Recherche Scientifique (FR)
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory , Stockholm, Sweden
- Swedish Veterinary Agency (SE)
- Swedish University of Agricultural Sciences (SE)
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg , Esch-sur-Alzette, Luxembourg
- University of Luxembourg (LU)
- Corresponding author
- Aspeborg, Henrik
- Andersson, Anders F
- ORCID
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-07-21
- Volume
- 11
- Issue
- 11
- Pages
- 2538-2551
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- PMC
- PMC5648042
- OpenAlex
- W2737166528
- Cited by
- 161
- References
- 81
- Citations by year
- 2026: 7 · 2025: 9 · 2024: 16 · 2023: 18 · 2022: 34 · 2021: 17 · 2020: 20 · 2019: 16 · 2018: 23 · 2017: 1
- FWCI
- 29.02
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- The ISME Journal (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Open Repository and Bibliography (University of Luxembourg) (submittedVersion, cc-by-nc-sa)
- HAL (submittedVersion)
- Funders
- European Commission
- Svenska Forskningsrådet Formas (2012-1513, 2014-176)
- Vetenskapsrådet (2014-176, 2012-1513)
- FP7 Ideas: European Research Council (322820)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Ruminant Nutrition and Digestive Physiology
- Physical Sciences › Engineering › Building and Construction › Anaerobic Digestion and Biogas Production
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- moose, rumen microbiome, metagenome-assembled genomes, carbohydrate-active enzymes, lignocellulose degradation, plant biomass degradation, pectin degradation, spirochetes, Bacteroidetes, dockerin, polysaccharide utilization loci, cellulosome, Ruminococcus, Fibrobacteres, ruminant digestion
- MeSH terms
- Gastrointestinal Microbiome, Animals, Animal Feed, Bacteria, Deer, Poaceae, Lignin, Phylogeny, Rumen, Genome, Bacterial, Biomass, Metagenome, Metagenomics
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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