Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Rekha Seshadri (1, 2) , Sinead Leahy (3) , Graeme Attwood (4) , Koon Hoong Teh (3) , Suzanne Lambie (5) , Adrian Cookson (4) , Emiley Eloe-Fadrosh (1, 2) , Georgios Pavlopoulos (1, 2) , Michalis Hadjithomas (6, 7) , Neha Varghese (7, 2) , David Páez-Espino (2) , Rechelle Perry (4) , Gemma Henderson (4) , Christopher J. Creevey (8, 9) , Nicolas Terrapon (10) , Pascal Lapébie (11) , Elodie Drula (12) , Vincent Lombard (10) , Edward M. Rubin (13) , Nikos Kyrpides (2) , Bernard Henrissat (10) , Tanja Woyke (13) , Natalia Ivanova (13) , William Kelly (4) , Nikola Palevich , Peter Janssen , Ron Ronimus , Samantha Noel , Priya Soni , Kerri Reilly , Todd Atherly , Cherie Ziemer , Andre-Denis Wright , Suzanne Ishaq , Michael Cotta , Stephanie Thompson , Katie Crosley , Nest Mckain , R John Wallace , Harry Flint (14) , Jennifer Martin (15) , Robert Forster , Robert Gruninger , Tim Mcallister , Rosalind Gilbert , Diane Ouwerkerk , Athol Klieve , Rafat Al Jassim , Stuart Denman , Chris Mcsweeney , Carly Rosewarne , Satoshi Koike (16) , Yasuo Kobayashi , Makoto Mitsumori , Takumi Shinkai , Silvio Cravero , María Cerón Cucchi , Chris Creevey (17)

1 US Department of Energy Joint Genome Institute, Walnut Creek CA, USA
2 DOE Joint Genome Institute [Walnut Creek]
3 Grasslands Research Centre
4 AgResearch Limited
5 Grasslands Res Ctr
6 Department of Biology [JHU Baltimore]
7 US Department of Energy Joint Genome Institute, Walnut Creek CA, USA
8 Animal & Grassland Research and Innovation Centre
9 Aberystwyth University
10 AFMB - Architecture et fonction des macromolécules biologiques
11 COM - Centre d'océanologie de Marseille
12 BBF - Biodiversité et Biotechnologie Fongiques
13 DOE - Department of Energy / Joint Genome Institute
14 Rowett Inst Nutr & Hlth, Microbial Ecol Grp
15 FAPSE - Laboratoire de Psycholinguistique Expérimentale
16 Tohoku University [Sendai]
17 Animal Bioscience Centre

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.

Domains: Life Sciences [q-bio]; Biochemistry, Molecular Biology; Genomics [q-bio.GN]

Rekha Seshadri, Sinead Leahy, Graeme Attwood, Koon Hoong Teh, Suzanne Lambie, et al.. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology, 2018, 36 (4), pp.359-367. ⟨10.1038/nbt.4110⟩. ⟨hal-02094598⟩