Functional metagenomic profiling of nine biomes
Abstract
Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.
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Viruses are incredibly abundant and diverse, numerically outnumbering cells by a factor of 10.
“If viruses are classified as a life-form, the tree of life would need to be fundamentally restructured, as viruses are incredibly abundant and diverse, numerically outnumbering cells by a factor of 10 (Dinsdale et al., 2008).”
From The Astrobiology Primer v2.0 (2016) · cites this paper as Dinsdale et al., 2008
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Self-citation
- Authors
- Dinsdale, E. A., Edwards, R. A., Hall, D., Angly, F., Breitbart, M., Brulc, J. M., Furlan, M., Desnues, C., Haynes, M., Li, L., McDaniel, L., Moran, M. A., Nelson, K. E., Nilsson, C., Olson, R., Paul, J., Brito, B. R., Ruan, Y., Swan, B. K., Stevens, R., Valentine, D. L., Thurber, R. V., Wegley, L., White, B. A., & Rohwer, F.
- Affiliations
- San Diego State University (US)
- Argonne National Laboratory (US)
- University of South Florida (US)
- University of Georgia (US)
- J. Craig Venter Institute (US)
- Genome Institute of Singapore (SG)
- University of California, Santa Barbara (US)
- University of Illinois Urbana-Champaign (US)
- Corresponding author
- Dinsdale, Elizabeth A.
- ORCID
- Venue
- Nature
- Published
- 2008-03-12
- Volume
- 452
- Issue
- 7187
- Pages
- 629-632
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2131342905
- Cited by
- 980
- References
- 1
- Citations by year
- 2026: 15 · 2025: 18 · 2024: 20 · 2023: 25 · 2022: 43 · 2021: 37 · 2020: 33 · 2019: 40 · 2018: 64 · 2017: 55 · 2016: 50 · 2015: 76 · 2014: 62 · 2013: 78 · 2012: 76
- FWCI
- 82.52
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Digital Commons - University of South Florida (University of South Florida) (submittedVersion)
- HAL (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Keywords
- virome, bacteriophages, functional metagenomics, biogeochemical conditions, viral gene delivery, ecosystem types, coral reefs, deep mines, rivers, functional diversity
- MeSH terms
- Animals, Archaea, Bacteria, Chemotaxis, Fishes, Fresh Water, Microbiology, Culicidae, Seawater, Viruses, Genome, Viral, Genome, Bacterial, Ecosystem, Computational Biology, Genome, Archaeal, Gene Expression Profiling, Genomics, Anthozoa
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