Cited by 600Genomics and Phylogenetic StudiesRuminant Nutrition and Digestive PhysiologyAnaerobic Digestion and Biogas Production

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

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Stewart, Robert D., Auffret, Marc D., Warr, Amanda, Wiser, Andrew H., Press, Maximilian O., Langford, Kyle W., Liachko, Ivan, Snelling, Timothy J., Dewhurst, Richard J., Walker, Alan W., Roehe, Rainer, Watson, Mick·2018·Nature Communications

DOI 10.1038/s41467-018-03317-6PMC PMC5830445

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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.

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Fig. 1 Phylogenetic tree of 913 draft genomes from the cow rumen, and closely related public genomes including 15 binned genomes from Hess et al1. Coloured circles represent the RUGs. White circles represent public genomes and have corresponding labelsCC BY · PubMed Central

Fig. 2 Distribution of carbohydrate-active enzyme classes across the 913 RUGs. GH glycoside hydrolase, GT glycosyl transferase, PL polysaccharide lyases, CE carbohydrate esterases, AA auxiliary activities, CB carbohydrate binding. White = absent, dark red = abundantCC BY · PubMed Central

Fig. 3 Distribution of the maximum percentage identity of the RUG proteins against five public databases for six classes of carbohydrate-active enzymes. GH glycoside hydrolase, GT glycosyl transferase, PL polysaccharide lyases, CE carbohydrate esterases, AA auxiliary activities, CB carbohydrate bindingCC BY · PubMed Central

Fig. 4 Classification rate for three datasets against various Kraken databases. BFAP bacterial, archaeal, fungal and protozoan genomes from RefSeq, BGEB BFAP + 1003 GEBA genomes, BHIC BFAP + 63 hRUG genomes, BHUN BFAP + 410 genomes from the Hungate 1000 project, BRUG BFAP + 850 RUG MAGs, BRHI BFAP + all 913 genomes from this study, BRHH BFAP + 913 RUGs + 410 Hungate 1000 genomes. Addition of rumen-specific RUGs or Hungate 1000 genomes has the most dramatic effectCC BY · PubMed Central

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The characterization of lactic acid producing bacteria from the rumen of dairy cattle grazing on improved pasture supplemented with wheat and barley grain
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New insights from uncultivated genomes of the global human gut microbiome
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See all 600

Authors: Stewart, R. D., Auffret, M. D., Warr, A., Wiser, A. H., Press, M. O., Langford, K. W., Liachko, I., Snelling, T. J., Dewhurst, R. J., Walker, A. W., Roehe, R., & Watson, M.
Affiliations: Roslin Institute (GB)
Scotland's Rural College (GB)
University of Aberdeen (GB)
Corresponding author: Watson, Mick
ORCID: Auffret, Marc D.
Warr, Amanda
Press, Maximilian O.
Langford, Kyle W.
Liachko, Ivan
Snelling, Timothy J.
Dewhurst, Richard J.
Walker, Alan W.
Roehe, Rainer
Watson, Mick
Venue: Nature Communications
Publisher: Springer Science and Business Media LLC
Published: 2018-02-28
Volume: 9
Issue: 1
Pages: 870-870
ISSN: 2041-1723 (ISSN-L)
DOI: 10.1038/s41467-018-03317-6
PMC: PMC5830445
OpenAlex: W2786358949
Cited by: 559
References: 83
Citations by year: 2026: 39 · 2025: 48 · 2024: 77 · 2023: 69 · 2022: 64 · 2021: 73 · 2020: 89 · 2019: 73 · 2018: 27
FWCI: 24.09
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0 (tdm)
creativecommons.org/licenses/by/4.0 (vor)
Locations: Nature Communications (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Edinburgh Research Explorer (University of Edinburgh) (publishedVersion, cc-by)
RePEc: Research Papers in Economics (submittedVersion)
Aberdeen University Research Archive (Aberdeen University) (submittedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: Rural and Environment Science and Analytical Services Division
Scottish Government
Scotland’s Rural College
Directorate for Biological Sciences
Biotechnology and Biological Sciences Research Council (BBS/E/D/30002276, BB/M01844X/1, BB/J004235/1, BB/R015023/1, BB/P013732/1, BB/J004235, BB/N016742/1, BB/ J004243/1, BB/N01720X/1, P013759, BBP013759/1, BBS/E/D/20310000)
National Institute of Allergy and Infectious Diseases (R43AI122654, R44AI122654)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Ruminant Nutrition and Digestive Physiology
Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Anaerobic Digestion and Biogas Production
Keywords: rumen microbiome, draft genome sequence, metagenome binning, Hi-C, cattle, rumen bacteria, rumen archaea, carbohydrate metabolism, biomass-degrading enzymes, metagenome-assembled genomes, read classification
MeSH terms: Animals, Bacteria, Bacterial Proteins, Cattle, Phylogeny, Rumen, Genome, Bacterial, Metagenome, Metagenomics

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

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