Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
Rumen microbiome biology gets a boost with the release of 410 high-quality reference genomes from the Hungate1000 project. Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions...
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| Veröffentlicht in: | Nature biotechnology Jg. 36; H. 4; S. 359 - 367 |
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| Hauptverfasser: | , , , , , , , , , , , , , , , , , , , , , , , |
| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
New York
Nature Publishing Group US
01.04.2018
Nature Publishing Group Springer Nature |
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| ISSN: | 1087-0156, 1546-1696, 1546-1696 |
| Online-Zugang: | Volltext |
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| Abstract | Rumen microbiome biology gets a boost with the release of 410 high-quality reference genomes from the Hungate1000 project.
Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding
de novo
synthesis of vitamin B
12
, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen. |
|---|---|
| AbstractList | Rumen microbiome biology gets a boost with the release of 410 high-quality reference genomes from the Hungate1000 project. Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen. Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B , ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen. Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12 , ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen. Rumen microbiome biology gets a boost with the release of 410 high-quality reference genomes from the Hungate1000 project. Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12 , ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen. Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen.Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen. Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. As a result, we estimate that our Hungate genome resource represents ~75% of the genus-level bacterial and archaeal taxa present in the rumen. |
| Author | Woyke, Tanja Seshadri, Rekha Attwood, Graeme T Ivanova, Natalia N Cookson, Adrian L Pavlopoulos, Georgios A Varghese, Neha J Perry, Rechelle Paez-Espino, David Henderson, Gemma Kelly, William J Kyrpides, Nikos C Creevey, Christopher J Drula, Elodie Teh, Koon Hoong Henrissat, Bernard Lambie, Suzanne C Eloe-Fadrosh, Emiley A Lapebie, Pascal Hadjithomas, Michalis Leahy, Sinead C Lombard, Vincent Rubin, Edward Terrapon, Nicolas |
| Author_xml | – sequence: 1 givenname: Rekha orcidid: 0000-0003-3219-2900 surname: Seshadri fullname: Seshadri, Rekha email: rseshadri@lbl.gov organization: Department of Energy, Joint Genome Institute – sequence: 2 givenname: Sinead C orcidid: 0000-0002-5461-6738 surname: Leahy fullname: Leahy, Sinead C email: sinead.leahy@nzagrc.org.nz organization: AgResearch Limited, Grasslands Research Centre, New Zealand Agricultural Greenhouse Gas Research Centre – sequence: 3 givenname: Graeme T surname: Attwood fullname: Attwood, Graeme T organization: AgResearch Limited, Grasslands Research Centre – sequence: 4 givenname: Koon Hoong surname: Teh fullname: Teh, Koon Hoong organization: AgResearch Limited, Grasslands Research Centre, Massey University – sequence: 5 givenname: Suzanne C surname: Lambie fullname: Lambie, Suzanne C organization: AgResearch Limited, Grasslands Research Centre, Hill Laboratories – sequence: 6 givenname: Adrian L surname: Cookson fullname: Cookson, Adrian L organization: AgResearch Limited, Grasslands Research Centre – sequence: 7 givenname: Emiley A surname: Eloe-Fadrosh fullname: Eloe-Fadrosh, Emiley A organization: Department of Energy, Joint Genome Institute – sequence: 8 givenname: Georgios A surname: Pavlopoulos fullname: Pavlopoulos, Georgios A organization: Department of Energy, Joint Genome Institute – sequence: 9 givenname: Michalis surname: Hadjithomas fullname: Hadjithomas, Michalis organization: Department of Energy, Joint Genome Institute – sequence: 10 givenname: Neha J surname: Varghese fullname: Varghese, Neha J organization: Department of Energy, Joint Genome Institute – sequence: 11 givenname: David orcidid: 0000-0002-2939-5398 surname: Paez-Espino fullname: Paez-Espino, David organization: Department of Energy, Joint Genome Institute – sequence: 13 givenname: Rechelle surname: Perry fullname: Perry, Rechelle organization: AgResearch Limited, Grasslands Research Centre – sequence: 14 givenname: Gemma surname: Henderson fullname: Henderson, Gemma organization: AgResearch Limited, Grasslands Research Centre, Chr. Hansen A/S – sequence: 15 givenname: Christopher J surname: Creevey fullname: Creevey, Christopher J organization: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University – sequence: 16 givenname: Nicolas orcidid: 0000-0002-3693-6017 surname: Terrapon fullname: Terrapon, Nicolas organization: Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Institut National de la Recherche Agronomique – sequence: 17 givenname: Pascal surname: Lapebie fullname: Lapebie, Pascal organization: Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Institut National de la Recherche Agronomique – sequence: 18 givenname: Elodie surname: Drula fullname: Drula, Elodie organization: Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Institut National de la Recherche Agronomique – sequence: 19 givenname: Vincent surname: Lombard fullname: Lombard, Vincent organization: Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Institut National de la Recherche Agronomique – sequence: 20 givenname: Edward surname: Rubin fullname: Rubin, Edward organization: Department of Energy, Joint Genome Institute – sequence: 21 givenname: Nikos C surname: Kyrpides fullname: Kyrpides, Nikos C organization: Department of Energy, Joint Genome Institute – sequence: 22 givenname: Bernard surname: Henrissat fullname: Henrissat, Bernard organization: Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Institut National de la Recherche Agronomique, Department of Biological Sciences, King Abdulaziz University – sequence: 23 givenname: Tanja orcidid: 0000-0002-9485-5637 surname: Woyke fullname: Woyke, Tanja organization: Department of Energy, Joint Genome Institute – sequence: 24 givenname: Natalia N surname: Ivanova fullname: Ivanova, Natalia N organization: Department of Energy, Joint Genome Institute – sequence: 25 givenname: William J orcidid: 0000-0001-8982-066X surname: Kelly fullname: Kelly, William J email: bill.kelly.donvis@gmail.com organization: AgResearch Limited, Grasslands Research Centre, Donvis Ltd |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29553575$$D View this record in MEDLINE/PubMed https://amu.hal.science/hal-02094598$$DView record in HAL https://www.osti.gov/servlets/purl/1489281$$D View this record in Osti.gov |
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| Snippet | Rumen microbiome biology gets a boost with the release of 410 high-quality reference genomes from the Hungate1000 project.
Productivity of ruminant livestock... Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth.... Rumen microbiome biology gets a boost with the release of 410 high-quality reference genomes from the Hungate1000 project. Productivity of ruminant livestock... |
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| Title | Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection |
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