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Nat Commun. 2018 Feb 28;9(1):870. doi: 10.1038/s41467-018-03317-6.

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

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The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, EH25 9RG, UK.
Scotland's Rural College, Edinburgh, EH25 9RG, UK.
Phase Genomics, 4000 Mason Road, Seattle, WA, 98195, USA.
The Rowett Institute, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, EH25 9RG, UK.


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.

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