Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

Robert D. Stewart, Marc D. Auffret, Amanda Warr, Andrew H. Wiser, Maximilian O. Press, Kyle W. Langford, Ivan Liachko, Timothy J. Snelling, Richard J. Dewhurst, Alan W. Walker, Rainer Roehe and Mick Watson ()
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Robert D. Stewart: University of Edinburgh
Marc D. Auffret: Scotland’s Rural College
Amanda Warr: University of Edinburgh
Andrew H. Wiser: Phase Genomics
Maximilian O. Press: Phase Genomics
Kyle W. Langford: Phase Genomics
Ivan Liachko: Phase Genomics
Timothy J. Snelling: University of Aberdeen
Richard J. Dewhurst: Scotland’s Rural College
Alan W. Walker: University of Aberdeen
Rainer Roehe: Scotland’s Rural College
Mick Watson: University of Edinburgh

Nature Communications, 2018, vol. 9, issue 1, 1-11

Abstract: Abstract The cow rumen is adapted for the breakdown of plant material into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiome. Here we present 913 draft bacterial and archaeal genomes assembled from over 800 Gb of rumen metagenomic sequence data derived from 43 Scottish cattle, using both metagenomic binning and Hi-C-based proximity-guided assembly. Most of these genomes represent previously unsequenced strains and species. The draft genomes contain over 69,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in public databases. Inclusion of the 913 genomes presented here improves metagenomic read classification by sevenfold against our own data, and by fivefold against other publicly available rumen datasets. Thus, our dataset substantially improves the coverage of rumen microbial genomes in the public databases and represents a valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome.

Date: 2018
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03317-6

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DOI: 10.1038/s41467-018-03317-6

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