Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Rekha Seshadri, Sinead C. Leahy, Graeme T. Attwood, Koon Hoong Teh, Suzanne C. Lambie, Adrian L. Cookson, Emiley A. Eloe-Fadrosh, Georgios A. Pavlopoulos, Michalis Hadjithomas, Neha J. Varghese, David Paez-Espino, Nikola Palevich, Peter H Janssen, Ron S Ronimus, Samantha Noel, Priya Soni, Kerri Reilly, Todd Atherly, Cherie Ziemer, Andre-denis WrightSuzanne Ishaq, Michael Cotta, Stephanie Thompson, Katie Crosley, Nest Mckain, R John Wallace, Harry J Flint, Jennifer C Martin, Robert J Forster, Robert J Gruninger, Tim Mcallister, Rosalind Gilbert, Diane Ouwerkerk, Athol Klieve, Rafat Al Jassim, Stuart Denman, Chris Mcsweeney, Carly Rosewarne, Satoshi Koike, Yasuo Kobayashi, Makoto Mitsumori, Takumi Shinkai, Silvio Cravero, María Cerón Cucchi, Rechelle Perry, Gemma Henderson, Christopher J Creevey, Nicolas Terrapon, Pascal Lapebie, Elodie Drula, Vincent Lombard, Edward Rubin, Nikos C. Kyrpides, Bernard Henrissat, Tanja Woyke, Natalia N. Ivanova, William J. Kelly

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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 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.
Original languageEnglish
Article number4110
Pages (from-to)359-367
Number of pages9
JournalNature Biotechnology
Volume36
DOIs
Publication statusPublished - 19 Mar 2018

Keywords

  • computational biology and bioinformatics
  • ecology
  • genome
  • microbial ecology
  • microbiology

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