Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
Abstract
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.
- Authors:
- more »
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Contributing Org.:
- Hungate1000 Project Collaborators
- OSTI Identifier:
- 1489281
- Alternate Identifier(s):
- OSTI ID: 1542309
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Nature Biotechnology
- Additional Journal Information:
- Journal Volume: 36; Journal Issue: 4; Journal ID: ISSN 1087-0156
- Publisher:
- Springer Nature
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Seshadri, Rekha, Leahy, Sinead C., Attwood, Graeme T., Teh, Koon Hoong, Lambie, Suzanne C., Cookson, Adrian L., Eloe-Fadrosh, Emiley A., Pavlopoulos, Georgios A., Hadjithomas, Michalis, Varghese, Neha J., Paez-Espino, David, Palevich, Nikola, Janssen, Peter H., Ronimus, Ron S., Noel, Samantha, Soni, Priya, Reilly, Kerri, Atherly, Todd, Ziemer, Cherie, Wright, Andre-Denis, Ishaq, Suzanne, Cotta, Michael, Thompson, Stephanie, Crosley, Katie, McKain, Nest, Wallace, R. John, Flint, Harry J., Martin, Jennifer C., Forster, Robert J., Gruninger, Robert J., McAllister, Tim, Gilbert, Rosalind, Ouwerkerk, Diane, Klieve, Athol, Jassim, Rafat Al, Denman, Stuart, McSweeney, Chris, Rosewarne, Carly, Koike, Satoshi, Kobayashi, Yasuo, Mitsumori, Makoto, Shinkai, Takumi, Cravero, Silvio, Cucchi, María Cerón, Perry, Rechelle, Henderson, Gemma, Creevey, Christopher J., Terrapon, Nicolas, Lapebie, Pascal, Drula, Elodie, Lombard, Vincent, Rubin, Edward, Kyrpides, Nikos C., Henrissat, Bernard, Woyke, Tanja, Ivanova, Natalia N., and Kelly, William J. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. United States: N. p., 2018.
Web. doi:10.1038/nbt.4110.
Seshadri, Rekha, Leahy, Sinead C., Attwood, Graeme T., Teh, Koon Hoong, Lambie, Suzanne C., Cookson, Adrian L., Eloe-Fadrosh, Emiley A., Pavlopoulos, Georgios A., Hadjithomas, Michalis, Varghese, Neha J., Paez-Espino, David, Palevich, Nikola, Janssen, Peter H., Ronimus, Ron S., Noel, Samantha, Soni, Priya, Reilly, Kerri, Atherly, Todd, Ziemer, Cherie, Wright, Andre-Denis, Ishaq, Suzanne, Cotta, Michael, Thompson, Stephanie, Crosley, Katie, McKain, Nest, Wallace, R. John, Flint, Harry J., Martin, Jennifer C., Forster, Robert J., Gruninger, Robert J., McAllister, Tim, Gilbert, Rosalind, Ouwerkerk, Diane, Klieve, Athol, Jassim, Rafat Al, Denman, Stuart, McSweeney, Chris, Rosewarne, Carly, Koike, Satoshi, Kobayashi, Yasuo, Mitsumori, Makoto, Shinkai, Takumi, Cravero, Silvio, Cucchi, María Cerón, Perry, Rechelle, Henderson, Gemma, Creevey, Christopher J., Terrapon, Nicolas, Lapebie, Pascal, Drula, Elodie, Lombard, Vincent, Rubin, Edward, Kyrpides, Nikos C., Henrissat, Bernard, Woyke, Tanja, Ivanova, Natalia N., & Kelly, William J. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. United States. https://doi.org/10.1038/nbt.4110
Seshadri, Rekha, Leahy, Sinead C., Attwood, Graeme T., Teh, Koon Hoong, Lambie, Suzanne C., Cookson, Adrian L., Eloe-Fadrosh, Emiley A., Pavlopoulos, Georgios A., Hadjithomas, Michalis, Varghese, Neha J., Paez-Espino, David, Palevich, Nikola, Janssen, Peter H., Ronimus, Ron S., Noel, Samantha, Soni, Priya, Reilly, Kerri, Atherly, Todd, Ziemer, Cherie, Wright, Andre-Denis, Ishaq, Suzanne, Cotta, Michael, Thompson, Stephanie, Crosley, Katie, McKain, Nest, Wallace, R. John, Flint, Harry J., Martin, Jennifer C., Forster, Robert J., Gruninger, Robert J., McAllister, Tim, Gilbert, Rosalind, Ouwerkerk, Diane, Klieve, Athol, Jassim, Rafat Al, Denman, Stuart, McSweeney, Chris, Rosewarne, Carly, Koike, Satoshi, Kobayashi, Yasuo, Mitsumori, Makoto, Shinkai, Takumi, Cravero, Silvio, Cucchi, María Cerón, Perry, Rechelle, Henderson, Gemma, Creevey, Christopher J., Terrapon, Nicolas, Lapebie, Pascal, Drula, Elodie, Lombard, Vincent, Rubin, Edward, Kyrpides, Nikos C., Henrissat, Bernard, Woyke, Tanja, Ivanova, Natalia N., and Kelly, William J. 2018.
"Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection". United States. https://doi.org/10.1038/nbt.4110. https://www.osti.gov/servlets/purl/1489281.
@article{osti_1489281,
title = {Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection},
author = {Seshadri, Rekha and Leahy, Sinead C. and Attwood, Graeme T. and Teh, Koon Hoong and Lambie, Suzanne C. and Cookson, Adrian L. and Eloe-Fadrosh, Emiley A. and Pavlopoulos, Georgios A. and Hadjithomas, Michalis and Varghese, Neha J. and Paez-Espino, David and Palevich, Nikola and Janssen, Peter H. and Ronimus, Ron S. and Noel, Samantha and Soni, Priya and Reilly, Kerri and Atherly, Todd and Ziemer, Cherie and Wright, Andre-Denis and Ishaq, Suzanne and Cotta, Michael and Thompson, Stephanie and Crosley, Katie and McKain, Nest and Wallace, R. John and Flint, Harry J. and Martin, Jennifer C. and Forster, Robert J. and Gruninger, Robert J. and McAllister, Tim and Gilbert, Rosalind and Ouwerkerk, Diane and Klieve, Athol and Jassim, Rafat Al and Denman, Stuart and McSweeney, Chris and Rosewarne, Carly and Koike, Satoshi and Kobayashi, Yasuo and Mitsumori, Makoto and Shinkai, Takumi and Cravero, Silvio and Cucchi, María Cerón and Perry, Rechelle and Henderson, Gemma and Creevey, Christopher J. and Terrapon, Nicolas and Lapebie, Pascal and Drula, Elodie and Lombard, Vincent and Rubin, Edward and Kyrpides, Nikos C. and Henrissat, Bernard and Woyke, Tanja and Ivanova, Natalia N. and Kelly, William J.},
abstractNote = {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.},
doi = {10.1038/nbt.4110},
url = {https://www.osti.gov/biblio/1489281},
journal = {Nature Biotechnology},
issn = {1087-0156},
number = 4,
volume = 36,
place = {United States},
year = {Mon Mar 19 00:00:00 EDT 2018},
month = {Mon Mar 19 00:00:00 EDT 2018}
}
Web of Science
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Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities
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Use of a Fluorescent Analog of Glucose (2-NBDG) To Identify Uncultured Rumen Bacteria That Take Up Glucose
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Diversity and community of methanogens in the large intestine of finishing pigs
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Insights Into Culturomics of the Rumen Microbiome
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Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture
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Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches
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Effects of Chestnut Tannin Extract, Vescalagin and Gallic Acid on the Dimethyl Acetals Profile and Microbial Community Composition in Rumen Liquor: An In Vitro Study
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Cowpi: A Rumen Microbiome Focussed Version Of The Picrust Functional Inference Software
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Medium-Chain Fatty Acid Synthesis by “ Candidatus Weimeria bifida” gen. nov., sp. nov., and “ Candidatus Pseudoramibacter fermentans” sp. nov.
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Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes
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Metagenomic biomarker discovery and explanation
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Heterogeneous development of methanogens and the correlation with bacteria in the rumen and cecum of sika deer (Cervus nippon) during early life suggest different ecology relevance
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Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle
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Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future
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Cowpi: A Rumen Microbiome Focussed Version Of The Picrust Functional Inference Software
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Comparing the Microbial Community in Four Stomach of Dairy Cattle, Yellow Cattle and Three Yak Herds in Qinghai-Tibetan Plateau
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CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software
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Diverse hydrogen production and consumption pathways influence methane production in ruminants
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Characterization of antibiotic resistance genes in the species of the rumen microbiota
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Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem
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The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid
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Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities
journal, October 2019
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- Applied and Environmental Microbiology, Vol. 86, Issue 1
Medium-Chain Fatty Acid Synthesis by “ Candidatus Weimeria bifida” gen. nov., sp. nov., and “ Candidatus Pseudoramibacter fermentans” sp. nov.
journal, November 2019
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Diversity and community of methanogens in the large intestine of finishing pigs
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Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model
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Can rumen bacteria communicate to each other?
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Genomic insights into ruminant evolution: from past to future prospects
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Evaluating Established Methods for Rumen 16S rRNA Amplicon Sequencing With Mock Microbial Populations
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Humic Substances Alter Ammonia Production and the Microbial Populations Within a RUSITEC Fed a Mixed Hay – Concentrate Diet
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Insights Into Culturomics of the Rumen Microbiome
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Comparing the Microbial Community in Four Stomach of Dairy Cattle, Yellow Cattle and Three Yak Herds in Qinghai-Tibetan Plateau
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Use of Lactic Acid Bacteria to Reduce Methane Production in Ruminants, a Critical Review
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Comparison of Ruminal Degradability, Indigestible Neutral Detergent Fiber, and Total-Tract Digestibility of Three Main Crop Straws with Alfalfa Hay and Corn Silage
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Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches
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Effects of Chestnut Tannin Extract, Vescalagin and Gallic Acid on the Dimethyl Acetals Profile and Microbial Community Composition in Rumen Liquor: An In Vitro Study
journal, July 2019
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Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework
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