Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

Robert D. Stewart; Marc D. Auffret; Amanda Warr; Alan W. Walker; Rainer Roehe; Mick Watson

doi:10.1101/489443

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

Robert D. Stewart, Marc D. Auffret, Amanda Warr, Alan W. Walker, Rainer Roehe, Mick Watson^* (Corresponding Author)

^*Corresponding author for this work

The Rowett Institute of Nutrition and Health

Research output: Contribution to journal › Article › peer-review

263 Citations (Scopus)

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Abstract

Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialized stomach that is adapted to the breakdown of plant-derived complex polysaccharides. The genomes of the rumen microbiota encode thousands of enzymes adapted to digestion of the plant matter that dominates the ruminant diet. We assembled 4,941 rumen microbial metagenome-assembled genomes (MAGs) using approximately 6.5 terabases of short- and long-read sequence data from 283 ruminant cattle. We present a genome-resolved metagenomics workflow that enabled assembly of bacterial and archaeal genomes that were at least 80% complete. Of note, we obtained three single-contig, whole-chromosome assemblies of rumen bacteria, two of which represent previously unknown rumen species, assembled from long-read data. Using our rumen genome collection we predicted and annotated a large set of rumen proteins. Our set of rumen MAGs increases the rate of mapping of rumen metagenomic sequencing reads from 15% to 50–70%. These genomic and protein resources will enable a better understanding of the structure and functions of the rumen microbiota.

Original language	English
Pages (from-to)	953–961
Number of pages	9
Journal	Nature Biotechnology
Volume	37
Early online date	2 Aug 2019
DOIs	https://doi.org/10.1101/489443 https://doi.org/10.1038/s41587-019-0202-3
Publication status	Published - 31 Aug 2019

Bibliographical note

The Rowett Institute and SRUC are core funded by the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government. The Roslin Institute forms part of the Royal (Dick) School of Veterinary Studies, University of Edinburgh. This project was supported by the Biotechnology and Biological Sciences Research Council (BBSRC; BB/N016742/1, BB/N01720X/1), including institute strategic programme and national capability awards to The Roslin Institute (BBSRC: BB/P013759/1, BB/P013732/1, BB/J004235/1,
BB/J004243/1); and by the Scottish Government as part of the 2016–2021 commission.

Keywords

applied microbiology
microbial communities
databases
environmental microbiology
genome informatics

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Cite this

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abstract = "Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialized stomach that is adapted to the breakdown of plant-derived complex polysaccharides. The genomes of the rumen microbiota encode thousands of enzymes adapted to digestion of the plant matter that dominates the ruminant diet. We assembled 4,941 rumen microbial metagenome-assembled genomes (MAGs) using approximately 6.5 terabases of short- and long-read sequence data from 283 ruminant cattle. We present a genome-resolved metagenomics workflow that enabled assembly of bacterial and archaeal genomes that were at least 80% complete. Of note, we obtained three single-contig, whole-chromosome assemblies of rumen bacteria, two of which represent previously unknown rumen species, assembled from long-read data. Using our rumen genome collection we predicted and annotated a large set of rumen proteins. Our set of rumen MAGs increases the rate of mapping of rumen metagenomic sequencing reads from 15% to 50–70%. These genomic and protein resources will enable a better understanding of the structure and functions of the rumen microbiota.",

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note = "The Rowett Institute and SRUC are core funded by the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government. The Roslin Institute forms part of the Royal (Dick) School of Veterinary Studies, University of Edinburgh. This project was supported by the Biotechnology and Biological Sciences Research Council (BBSRC; BB/N016742/1, BB/N01720X/1), including institute strategic programme and national capability awards to The Roslin Institute (BBSRC: BB/P013759/1, BB/P013732/1, BB/J004235/1, BB/J004243/1); and by the Scottish Government as part of the 2016–2021 commission.",

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AU - Roehe, Rainer

AU - Watson, Mick

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Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

Abstract

Bibliographical note

Keywords

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Alan Walker

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Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

Abstract

Bibliographical note

Keywords

Access to Document

Other files and links

Fingerprint

Profiles

Alan Walker

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