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

Robert D. Stewart, Marc D. Auffret, Amanda Warr, Andrew H. Wiser, Maximillian O. Press, Kyle W. Langford, Ivan Liachko, Tim J Snelling, Richard J. Dewhurst, Alan W. Walker, Rainer Roehe, Mick Watson

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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.
Original languageEnglish
Article number870
Pages (from-to)1-11
Number of pages11
JournalNature Communications
Volume9
DOIs
Publication statusPublished - 28 Feb 2018

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Microbial Genome
Metagenomics
sequencing
genome
Rumen
assembly
Genes
draft
Microbiota
Genome
enzymes
carbohydrate metabolism
cattle
Archaeal Genome
Databases
Bacterial Genomes
nutrients
Enzymes
biomass
Nutrients

Keywords

  • Archaeal genomics
  • Bacterial genomics
  • Environmental microbiology
  • Metagenomics

Cite this

Stewart, R. D., Auffret, M. D., Warr, A., Wiser, A. H., Press, M. O., Langford, K. W., ... Watson, M. (2018). Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. Nature Communications, 9, 1-11. [870]. https://doi.org/10.1038/s41467-018-03317-6

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. / Stewart, Robert D.; Auffret, Marc D.; Warr, Amanda; Wiser, Andrew H.; Press, Maximillian O.; Langford, Kyle W.; Liachko, Ivan; Snelling, Tim J; Dewhurst, Richard J.; Walker, Alan W.; Roehe, Rainer; Watson, Mick.

In: Nature Communications, Vol. 9, 870, 28.02.2018, p. 1-11.

Research output: Contribution to journalArticle

Stewart, RD, Auffret, MD, Warr, A, Wiser, AH, Press, MO, Langford, KW, Liachko, I, Snelling, TJ, Dewhurst, RJ, Walker, AW, Roehe, R & Watson, M 2018, 'Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen' Nature Communications, vol. 9, 870, pp. 1-11. https://doi.org/10.1038/s41467-018-03317-6
Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW et al. Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. Nature Communications. 2018 Feb 28;9:1-11. 870. https://doi.org/10.1038/s41467-018-03317-6
Stewart, Robert D. ; Auffret, Marc D. ; Warr, Amanda ; Wiser, Andrew H. ; Press, Maximillian O. ; Langford, Kyle W. ; Liachko, Ivan ; Snelling, Tim J ; Dewhurst, Richard J. ; Walker, Alan W. ; Roehe, Rainer ; Watson, Mick. / Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. In: Nature Communications. 2018 ; Vol. 9. pp. 1-11.
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