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Title: 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:
ORCiD logo; ORCiD logo; ; ; ; ; ; ; ; ; ORCiD logo; ; ; ; ; ; ; ; ; more »; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ORCiD logo; ; ; ; ; ; ; ORCiD logo; ; ORCiD logo « less
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
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. 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., and Kelly, William J. Mon . "Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection". United States. doi: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},
journal = {Nature Biotechnology},
issn = {1087-0156},
number = 4,
volume = 36,
place = {United States},
year = {2018},
month = {3}
}

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    Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture
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