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Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
Open accessAbstract
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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“Subsequently, Svartstrom et al. (2017) assembled 99 microbial genomes from the moose rumen, Stewart et al. (2018) assembled 913 microbial genomes from the rumen of cattle, and Parks et al. (2017) assembled over 8,000 novel microbial genomes from 1,500 public datasets, some of which originated from the rumen.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Stewart et al., 2018
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“Hi-C binning has been used effectively on human feces (Press et al., 2017) as well as in ruminants (Stewart et al., 2018).”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Stewart et al., 2018
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“Similar results were obtained from a BLAST search analysis of the predicted ORFs from 913 cattle rumen MAGs [27].”
BackgroundMethodResultInfluentialDiet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas
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“MAGs have been constructed in many mammalian species, such as humans [14], mice [15], and livestock, including cows [16, 17], goats [18], pigs [19, 20], buffalo [21], and chickens [22, 23].”
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“an additional 63 draft genomes could be assembled (Stewart et al. 2018).”
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“The advances in computational techniques, such as metagenome binning, have enabled the generation of metagenome-assembled genomes (MAGs) [3, 4].”
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To Dereplicate or Not To Dereplicate?
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MethodRumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits
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Trait biases in microbial reference genomes
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“Our ability to detect these changes in abundance, and, more generally, microbial players that are present at lower frequencies, is restricted by depth of sequencing and biases of methods such as 16S rRNA gene and shotgun libraries (Stewart et al., 2018), thus, yielding a limited view of bovine ruminal bacteria.”
BackgroundViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data
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“Searches for CAZymes, scaffolding proteins, and susCD gene pairs were performed as previously described (7, 86).”
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Association between Rumen Microbiota and Marbling Score in Korean Native Beef Cattle
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“These genera are phylogenetically located within the Erysipelotrichaceae family, which was recently expanded based on genome recovery from the metagenome of the cow rumen [55].”
BackgroundAdoption of Climate Smart Agriculture by Communal Livestock Farmers in South Africa
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“One of these includes rumen fermentation, which is the process that converts ingested feed into energy sources for the host [53].”
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A metagenomic catalogue of the ruminant gut archaeome
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“Although extensive research has been conducted on the rumen and intestinal microbial communities of ruminants, with a primary focus onbacterialpopulations 29,57 – 60 ,systematicanalysesoftheruminantgut archaeome remain insuf fi cient.”
Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome
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“Hybrid approaches are also possible in many cases, as binning of the individual and grouped assemblies may be combined and dereplicated to obtain the most robust MAGs of both rare and abundant species [80].”
BackgroundCurrent Status and Potential Applications of Underexplored Prokaryotes
Goh, K., Shahar, S., Chan, K.-G., Chong, C., Amran, S., Sani, M. H., Zakaria, I. I., & Kahar, U. M. (2019) · Microorganisms · doi:10.3390/microorganisms7100468 · Cited by 29
A rather dry subject; investigating the study of arid-associated microbial communities
Osborne, P., Hall, L. J., Kronfeld‐Schor, N., Thybert, D., & Haerty, W. (2020) · Environmental Microbiome · doi:10.1186/s40793-020-00367-6 · Cited by 35
Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity
Wilbanks, E. G., Doré, H., Ashby, M., Heiner, C. R., Roberts, R. J., & Eisen, J. A. (2022) · The ISME Journal · doi:10.1038/s41396-022-01242-7 · Cited by 33
“Recent advances in binning leverage information about the genome orthogonal to its sequence, such as chromosomal conformation [21, 22] or DNA methylation [23].”
BackgroundThe phenotype and genotype of fermentative prokaryotes
Hackmann, T. J., & Zhang, B. (2023) · Science Advances · doi:10.1126/sciadv.adg8687 · Cited by 36
Qi, W., Xue, M., Jia, M., Zhang, S., Yan, Q., & Sun, H. (2023) · Animal Bioscience · doi:10.5713/ab.23.0308 · Cited by 43
“For example, 43 Scottish cattle, 913 bacterial and archaeal MAGs were assembled using more than 800 G of metagenomics data [5]; most of these strains had never been sequenced.”
MethodBaudry, L., Foutel-Rodier, T., Thierry, A., Koszul, R., & Marbouty, M. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00753 · Cited by 32
“Meta3C-like methods have only been applied to microbial rich samples so far (mice and human gut, cow rumen, sewage) (Marbouty et al., 2017; Stewart et al., 2018; Stalder et al., 2019) and still need to be improved in order to be applied to sample with low concentration of microorganisms.”
MethodMetagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs
Liu, G., Li, P., Hou, L., Niu, Q., Pu, G., Wang, B., Du, T., Kim, S. W., Niu, P., Li, Q., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.746717 · Cited by 36
Liang, J., Chang, J., Zhang, R., Fang, W., Chen, L., Ma, W., Zhang, Y., Yang, W., Li, Y., Zhang, P., et al. (2023) · Chemosphere · doi:10.1016/j.chemosphere.2023.139242 · Cited by 32
Dias, B. D. C., Lamarca, A. P., Machado, D. T., Klôh, V., de Carvalho, F. M., & de Vasconcelos, A. T. R. (2025) · Animal Microbiome · doi:10.1186/s42523-025-00379-y · Cited by 31
“For example, within the Firmicutes phylum, Clostridia taxa have been reported as key species in microbial consortia assembly in the chicken caecum [88], human gut [6], swine intestine [6, 89] and bovine rumen [90].”
Stergiadis, S., Luna, I. C., Mora-Ortiz, M., Stewart, R. D., Dewhurst, R. J., Humphries, D. J., Watson, M., Roehe, R., & Auffret, M. D. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.590441 · Cited by 32
Ivanova, V. A., Chernevskaya, E., Vasiluev, P. A., Ivanov, A. B., Tolstoganov, I., Shafranskaya, D. D., Игоревич, У. В., Korobeynikov, A., Razin, S. V., Nv, B., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.770323 · Cited by 31
“The networks were visualized in Cytoscape (Su et al., 2014).”
Huang, G., Shi, W., Wang, L., Qu, Q., Zuo, Z., Wang, J., Zhao, F., & Wei, F. (2023) · Microbiome · doi:10.1186/s40168-023-01657-0 · Cited by 32
“…gene catalogs and metagenome-assembled genome collections of microbiomes from several model organisms, including humans [32–40], non-human primates [41], mice [42–44], pigs [45, 46], dogs [47], chickens [48], and ruminants [49–54]; however, it still remains lacking for the threatened mammal.”
BackgroundJiao, J., Wu, J., Zhou, C., He, Z., Tan, Z., & Wang, M. (2024) · The ISME Journal · doi:10.1093/ismejo/wrae002 · Cited by 28
“Discoveries enabled by this technology in ruminants have focused on MAGs recovered from rumen microbial consortia from dairy cows and beef cattle [7, 22, 23].”
The multi-kingdom microbiome catalog of the chicken gastrointestinal tract
Wang, Y., Qu, M., Bi, Y., Liu, W. J., Ma, S., Wan, B., Hu, Y., Zhu, B., Zhang, G., & Gao, G. F. (2024) · Biosafety and Health · doi:10.1016/j.bsheal.2024.02.006 · Cited by 30
Fu, R., Lin, H., Li, Q., Li, Z., Dai, Y., & Leng, J. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1554271 · Cited by 36
Tikariha, H., & Purohit, H. J. (2018) · Genomics · doi:10.1016/j.ygeno.2018.12.005 · Cited by 30
Zhang, Z., Wei, W., Yang, S., Huang, Z., Li, C., Yu, X., Qi, R., Liu, W., Loor, J. J., Wang, M., et al. (2022) · Nutrients · doi:10.3390/nu14142972 · Cited by 32
“The host digests plant feed primarily through fermentation mediated by the microorganisms in these three phyla levels [38].”
BackgroundGuo, W., Zhou, M., Li, F., Neves, A. L. A., Ma, T., Bi, S., Wang, W., Long, R., & Guan, L. L. (2024) · BMC Biology · doi:10.1186/s12915-024-02035-4 · Cited by 32
“Venn diagrams were created by Venny 2.1 (https://bioinfogp.cnb.csic.es/tools/venny/), the taxonomic information of sequences (host both ARGs and CAZymes) were obtained by aligning the corresponding contigs to rumen metagenome-assembled genomes (MAGs) [5] using Kraken2 [113].”
MethodInfluentialEffect of slow-release urea on the composition of ruminal bacteria and fungi communities in yak
Yan, X., Yan, B. Y., Ren, Q., Dou, J., Wang, W. W., Zhang, J. J., Zhou, J., Long, R., Ding, L., Han, J., et al. (2018) · Animal Feed Science and Technology · doi:10.1016/j.anifeedsci.2018.07.016 · Cited by 29
Deng, C., Zhao, R., Qiu, Z. G., Li, B. J., Zhang, T., Guo, F., Mu, R., Wu, Y., Qiao, X., Zhang, L., et al. (2021) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2021.151635 · Cited by 29
Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice
Peeb, A., Dang, N. P., Truu, M., Nõlvak, H., Petrich, C., & Truu, J. (2022) · Microorganisms · doi:10.3390/microorganisms10020328 · Cited by 29
Characterization of metagenome-assembled genomes from the International Space Station
Singh, N. K., Wood, J. M., Patané, J. S. L., Moura, L. M. S., Lombardino, J., Setúbal, J. C., & Venkateswaran, K. (2023) · Microbiome · doi:10.1186/s40168-023-01545-7 · Cited by 29
“Projects retrieving thousands of MAGs have also been documented to understand yetto-be cultured microbiomes of cow rumens and other environmental samples [11].”
BackgroundZhao, Z. W., Ma, Z., Wang, H., & Zhang, C. F. (2021) · Animal Feed Science and Technology · doi:10.1016/j.anifeedsci.2021.114972 · Cited by 27
Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species
Stamboulian, M. H., Canderan, J., & Ye, Y. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009397 · Cited by 28
Unravelling microbial drivers of the sulfate-reduction process inside landfill using metagenomics
Hu, L., Wang, Y., Ci, M., & Long, Y. (2022) · Chemosphere · doi:10.1016/j.chemosphere.2022.137537 · Cited by 28
Zhang, H., Lang, X., Zhang, Y., & Wang, C. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1062077 · Cited by 30
Han, X., Lei, X., Xuexin, Y., Shen, J., Zheng, L., Jin, C., Cao, Y., & Yao, J. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.651631 · Cited by 27
“CAZymes-encoding gene abundance and KEGG enzyme gene abundance were helpful to characterize carbohydrate degradation for dairy goats (Stewart et al., 2018).”
BackgroundOladeinde, A., Abdo, Z., Press, M. O., Cook, K. L., Cox, N. A., Zwirzitz, B., Woyda, R., Lakin, S. M., Thomas, J. C., Looft, T. P., et al. (2021) · mSystems · doi:10.1128/msystems.00729-21 · Cited by 27
“Metagenome deconvolution was performed with ProxiMeta (82, 83), resulting in the creation of putative genome and genome fragment clusters.”
MethodWang, J., Liang, J., Li, Y., Tian, L., & Wei, Y. (2021) · AMB Express · doi:10.1186/s13568-020-01178-1 · Cited by 27
“Environmental biotechnology has recovered large amounts of functional genes from natural microbiota, however, most genes have not been characterized to date (Ariaeenejad et al. 2019; Stewart et al. 2018).”
Background
Metadata
- 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
- Venue
- Nature Communications
- Published
- 2018-02-28
- Volume
- 9
- Issue
- 1
- Pages
- 870-870
- ISSN
- 2041-1723 (ISSN-L)
- 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
- 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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