Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
Open accessAbstract
Rumen microbiome biology gets a boost with the release of 410 high-quality reference genomes from the Hungate1000 project. Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen.
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The Hungate1000 project sequenced 420 representatives of rumen microbes, mainly bacteria, providing a major tool for the community.
“The Hungate1000 project recently finished having sequenced 420 representatives of rumen microbes (mainly bacteria), and thus providing a major tool for the community (Seshadri et al., 2018).”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Seshadri et al., 2018
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- Authors
- Hungate1000 project collaborators, Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Hadjithomas, M., Varghese, N. J., Paez-Espino, D., Perry, R., Henderson, G., Creevey, C. J., Terrapon, N., Lapebie, P., Drula, E., Lombard, V., Rubin, E., Kyrpides, N. C., Henrissat, B., Woyke, T., Ivanova, N. N., & Kelly, W. J.
- Affiliations
- Joint Genome Institute (US)
- AgResearch (NZ)
- Johns Hopkins University (US)
- Aberystwyth University (GB)
- Aix-Marseille Université (FR)
- Los Alamos National Laboratory (US)
- Corresponding author
- Seshadri, Rekha
- Leahy, Sinead C
- Kelly, William J
- ORCID
- Seshadri, Rekha
- Leahy, Sinead C
- Attwood, Graeme T
- Lambie, Suzanne C
- Cookson, Adrian L
- Pavlopoulos, Georgios A
- Hadjithomas, Michalis
- Varghese, Neha J
- Paez-Espino, David
- Henderson, Gemma
- Creevey, Christopher J
- Terrapon, Nicolas
- Lombard, Vincent
- Rubin, Edward
- Kyrpides, Nikos C
- Henrissat, Bernard
- Woyke, Tanja
- Ivanova, Natalia N
- Kelly, William J
- Venue
- Nature Biotechnology
- Published
- 2018-03-19
- Volume
- 36
- Issue
- 4
- Pages
- 359-367
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC6118326
- OpenAlex
- W2792729061
- Cited by
- 624
- References
- 83
- Citations by year
- 2026: 59 · 2025: 69 · 2024: 103 · 2023: 85 · 2022: 95 · 2021: 76 · 2020: 65 · 2019: 50 · 2018: 20 · 2017: 1
- FWCI
- 92.09
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature Biotechnology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research Portal (Queen's University Belfast) (publishedVersion, cc-by)
- Aberdeen University Research Archive (Aberdeen University) (submittedVersion, cc-by)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, cc-by)
- HAL (submittedVersion, cc-by)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- Figshare (submittedVersion)
- Queensland Department of Agriculture and Fisheries archive of scientific and research publications (Queensland Department of Agriculture and Fisheries) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
- U.S. Department of Agriculture (DE-AC02-05CH11231)
- AgResearch
- University of Arizona
- University of Oregon
- New Zealand Government
- Joint Genome Institute (AC02-05CH11231, DE–AC02–05CH11231)
- European Commission (DE-AC02-05CH11231, FP/2007/2013)
- University of Aberdeen
- Commonwealth Scientific and Industrial Research Organisation
- Hokkaido University
- Instituto Nacional de Tecnología Agropecuaria
- Office of Science (DEAC02–05CH11231, AC02-05CH11231, DE-AC02, 05CH11231)
- Biotechnology and Biological Sciences Research Council (BBS/E/W/10964A01B, BBS/OS/GC/000011B, BBS/E/W/10964A01A)
- School of Agriculture and Food Sciences, University of Queensland
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland
- FP7 Ideas: European Research Council (322820)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Ruminant Nutrition and Digestive Physiology
- Physical Sciences › Engineering › Building and Construction › Anaerobic Digestion and Biogas Production
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- rumen microbiome, reference genome, rumen bacteria, rumen archaea, polysaccharide degradation, methanogenesis, vitamin B12 biosynthesis, gene loss, vertical transmission, ruminant livestock, greenhouse gas emissions reduction
- MeSH terms
- Gastrointestinal Microbiome, Animals, Archaea, Bacteria, Humans, Lignin, Rumen, Biofuels, Microbiota
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