Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation
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 microb...
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ftunivaixmarseil:oai:HAL:hal-02328246v1 2023-05-15T13:12:58+02:00 Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation 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 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) 2017-11 https://hal.science/hal-02328246 https://doi.org/10.1038/ismej.2017.108 en eng HAL CCSD Nature Publishing Group info:eu-repo/semantics/altIdentifier/doi/10.1038/ismej.2017.108 info:eu-repo/semantics/altIdentifier/pmid/28731473 info:eu-repo/grantAgreement/EC/FP7/322820/EU/Understanding and exploiting complex glycan metabolism in the human microbiota/HUMAN MICROBIOTA hal-02328246 https://hal.science/hal-02328246 doi:10.1038/ismej.2017.108 PRODINRA: 411028 PUBMED: 28731473 PUBMEDCENTRAL: PMC5648042 WOS: 000413240100011 ISSN: 1751-7362 EISSN: 1751-7370 ISME Journal https://hal.science/hal-02328246 ISME Journal, 2017, 11 (11), pp.2538-2551. ⟨10.1038/ismej.2017.108⟩ [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 info:eu-repo/semantics/article Journal articles 2017 ftunivaixmarseil https://doi.org/10.1038/ismej.2017.108 2023-02-07T23:55:10Z 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. Article in Journal/Newspaper Alces alces Aix-Marseille Université: HAL The ISME Journal 11 11 2538 2551 |
institution |
Open Polar |
collection |
Aix-Marseille Université: HAL |
op_collection_id |
ftunivaixmarseil |
language |
English |
topic |
[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 |
spellingShingle |
[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 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 Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation |
topic_facet |
[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 |
description |
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. |
author2 |
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 |
author |
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 |
author_facet |
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 |
author_sort |
Svartström, Olov |
title |
Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation |
title_short |
Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation |
title_full |
Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation |
title_fullStr |
Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation |
title_full_unstemmed |
Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation |
title_sort |
ninety-nine de novo assembled genomes from the moose (alces alces) rumen microbiome provide new insights into microbial plant biomass degradation |
publisher |
HAL CCSD |
publishDate |
2017 |
url |
https://hal.science/hal-02328246 https://doi.org/10.1038/ismej.2017.108 |
genre |
Alces alces |
genre_facet |
Alces alces |
op_source |
ISSN: 1751-7362 EISSN: 1751-7370 ISME Journal https://hal.science/hal-02328246 ISME Journal, 2017, 11 (11), pp.2538-2551. ⟨10.1038/ismej.2017.108⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1038/ismej.2017.108 info:eu-repo/semantics/altIdentifier/pmid/28731473 info:eu-repo/grantAgreement/EC/FP7/322820/EU/Understanding and exploiting complex glycan metabolism in the human microbiota/HUMAN MICROBIOTA hal-02328246 https://hal.science/hal-02328246 doi:10.1038/ismej.2017.108 PRODINRA: 411028 PUBMED: 28731473 PUBMEDCENTRAL: PMC5648042 WOS: 000413240100011 |
op_doi |
https://doi.org/10.1038/ismej.2017.108 |
container_title |
The ISME Journal |
container_volume |
11 |
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11 |
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2538 |
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2551 |
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