Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.

Autor: Seshadri R; Department of Energy, Joint Genome Institute, Walnut Creek, California, USA., Leahy SC; AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand., Attwood GT; AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand., Teh KH; AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand., Lambie SC; AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand., Cookson AL; AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand., Eloe-Fadrosh EA; Department of Energy, Joint Genome Institute, Walnut Creek, California, USA., Pavlopoulos GA; Department of Energy, Joint Genome Institute, Walnut Creek, California, USA., Hadjithomas M; Department of Energy, Joint Genome Institute, Walnut Creek, California, USA., Varghese NJ; Department of Energy, Joint Genome Institute, Walnut Creek, California, USA., Paez-Espino D; Department of Energy, Joint Genome Institute, Walnut Creek, California, USA., Perry R; AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand., Henderson G; AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand., Creevey CJ; Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, UK., Terrapon N; Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France.; Institut National de la Recherche Agronomique, Marseille, France., Lapebie P; Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France.; Institut National de la Recherche Agronomique, Marseille, France., Drula E; Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France.; Institut National de la Recherche Agronomique, Marseille, France., Lombard V; Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France.; Institut National de la Recherche Agronomique, Marseille, France., Rubin E; Department of Energy, Joint Genome Institute, Walnut Creek, California, USA., Kyrpides NC; Department of Energy, Joint Genome Institute, Walnut Creek, California, USA., Henrissat B; Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France.; Institut National de la Recherche Agronomique, Marseille, France.; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia., Woyke T; Department of Energy, Joint Genome Institute, Walnut Creek, California, USA., Ivanova NN; Department of Energy, Joint Genome Institute, Walnut Creek, California, USA., Kelly WJ; AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
Jazyk: angličtina
Zdroj: Nature biotechnology [Nat Biotechnol] 2018 Apr; Vol. 36 (4), pp. 359-367. Date of Electronic Publication: 2018 Mar 19.
DOI: 10.1038/nbt.4110
Abstrakt: 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.
Databáze: MEDLINE
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