Functional metagenomic profiling of nine biomes

@article{Dinsdale2008FunctionalMP,
  title={Functional metagenomic profiling of nine biomes},
  author={Elizabeth A. Dinsdale and Robert A. Edwards and Dana Hall and Florent E. Angly and Mya Breitbart and Jennifer M. Brulc and Mike Furlan and Christelle Desnues and Matthew Haynes and Linlin Li and L Mcdaniel and Mary Ann Moran and Karen E. Nelson and Christina Nilsson and Robert Olson and J H Paul and Beltran Rodriguez Brito and Yijun Ruan and Brandon K. Swan and Rick L. Stevens and David L. Valentine and Rebecca Vega Thurber and Linda Wegley and Bryan A. White and Forest L. Rohwer},
  journal={Nature},
  year={2008},
  volume={452},
  pages={629-632}
}
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… 

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References

SHOWING 1-10 OF 41 REFERENCES

Global patterns in bacterial diversity

This work reports the most comprehensive analysis of the environmental distribution of bacteria to date, based on 21,752 16S rRNA sequences compiled from 111 studies of diverse physical environments, and finds that sediments are more phylogenetically diverse than any other environment type.

Geomicrobiology: How Molecular-Scale Interactions Underpin Biogeochemical Systems

Genome-enabled biogeochemical modeling may provide an opportunity to determine how communities function, and how they shape and are shaped by their environments.

Using pyrosequencing to shed light on deep mine microbial ecology

BackgroundContrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence

Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil

In this first study to comprehensively survey viral communities using a metagenomic approach, it is found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach.

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes that is stable, extensible, and freely available to all researchers.

Microbial Ecology of Four Coral Atolls in the Northern Line Islands

Four coral atolls in the Northern Line Islands, central Pacific used as a baseline for future studies of coral reef microbes had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati.

Metagenomic analysis of the microbial community associated with the coral Porites astreoides.

A metabolic and taxonomic snapshot of microbes associated with the reef-building coral Porites astreoides is provided and presents a basis for understanding how coral-microbial interactions structure the holobiont and coral reefs.

Genomic Islands and the Ecology and Evolution of Prochlorococcus

Genomic islands in this free-living photoautotroph share features with pathogenicity islands of parasitic bacteria, suggesting a general mechanism for niche differentiation in microbial species.

Metagenomics: DNA sequencing of environmental samples

Although genomics has classically focused on pure, easy-to-obtain samples, such as microbes that grow readily in culture or large animals and plants, these organisms represent only a fraction of the

Genomic analysis of uncultured marine viral communities

Diversity of the viral communities was extremely high, and the results showed that it would be possible to sequence the entire genome of an uncultured marine viral community.