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

RD Stewart, MD Auffret, A Warr, AH Wiser, MO Press, KW Langford, I Liachko, TJ Snelling, RJ Dewhurst, AW Walker, R Roehe, M Watson

Research output: Contribution to journalArticle

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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-Cbased 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
JournalNature Communications
Volume9
Early online date28 Feb 2018
DOIs
Publication statusFirst published - 28 Feb 2018

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rumen
cows
genome
carbohydrate metabolism
cattle
biomass
energy
nutrients
enzymes
proteins
microbiome

Bibliographical note

1030565

Keywords

  • Archaeal genomics
  • Bacterial genomics
  • Environmental microbiology
  • Metagenomics

Cite this

Stewart, RD ; Auffret, MD ; Warr, A ; Wiser, AH ; Press, MO ; Langford, KW ; Liachko, I ; Snelling, TJ ; Dewhurst, RJ ; Walker, AW ; Roehe, R ; Watson, M. / Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. In: Nature Communications. 2018 ; Vol. 9.
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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. https://doi.org/10.1038/s41467-018-03317-6

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. / Stewart, RD; Auffret, MD; Warr, A; Wiser, AH; Press, MO; Langford, KW; Liachko, I; Snelling, TJ; Dewhurst, RJ; Walker, AW; Roehe, R; Watson, M.

In: Nature Communications, Vol. 9, 870, 28.02.2018.

Research output: Contribution to journalArticle

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AU - Liachko, I

AU - Snelling, TJ

AU - Dewhurst, RJ

AU - Walker, AW

AU - Roehe, R

AU - Watson, M

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