Abstract
| Original language | English |
|---|---|
| Pages (from-to) | 953–961 |
| Number of pages | 9 |
| Journal | Nature Biotechnology |
| Volume | 37 |
| DOIs | |
| Publication status | Published - 2 Aug 2019 |
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Keywords
- applied microbiology
- microbial communities
- databases
- environmental microbiology
- genome informatics
Cite this
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. / Stewart, Robert D.; Auffret, Marc D.; Warr, Amanda; Walker, Alan W.; Roehe, Rainer; Watson, Mick (Corresponding Author).
In: Nature Biotechnology, Vol. 37, 02.08.2019, p. 953–961.Research output: Contribution to journal › Article
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TY - JOUR
T1 - Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
AU - Stewart, Robert D.
AU - Auffret, Marc D.
AU - Warr, Amanda
AU - Walker, Alan W.
AU - Roehe, Rainer
AU - Watson, Mick
N1 - 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.
PY - 2019/8/2
Y1 - 2019/8/2
N2 - 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.
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.
KW - applied microbiology
KW - microbial communities
KW - databases
KW - environmental microbiology
KW - genome informatics
UR - https://www.biorxiv.org/content/early/2018/12/08/489443
UR - http://www.mendeley.com/research/genomic-proteomic-landscape-rumen-microbiome-revealed-comprehensive-genomeresolved-metagenomics
U2 - 10.1101/489443
DO - 10.1101/489443
M3 - Article
VL - 37
SP - 953
EP - 961
JO - Nature Biotechnology
JF - Nature Biotechnology
SN - 1087-0156
ER -