Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery: Comprehensive resource of cow rumen genomes and a database of predicted proteins.

Robert Stewart, MD Auffret, Amanda Warr, Alan Walker, R Roehe, Mick Watson*

*Corresponding author for this work

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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 languageEnglish
Pages (from-to)953-961
Number of pages9
JournalNature Biotechnology
Volume37
Early online date2 Aug 2019
DOIs
Publication statusPrint publication - 2 Aug 2019

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Metagenome
Protein Databases
Microbiota
Rumen
Enzymes
Genes
Genome
Proteins
Nutrition
Ruminants
Metagenomics
Polysaccharides
Chromosomes
Archaeal Genome
Bacteria
Bacterial Genomes
Workflow
Digestion
Stomach

Cite this

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title = "Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery: Comprehensive resource of cow rumen genomes and a database of predicted proteins.",
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.",
author = "Robert Stewart and MD Auffret and Amanda Warr and Alan Walker and R Roehe and Mick Watson",
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AU - Stewart, Robert

AU - Auffret, MD

AU - Warr, Amanda

AU - Walker, Alan

AU - Roehe, R

AU - Watson, Mick

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AB - 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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