Viral metagenomics

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Abstract

Viruses, most of which infect microorganisms, are the most abundant biological entities on the planet. Identifying and measuring the community dynamics of viruses in the environment is complicated because less than one percent of microbial hosts have been cultivated. Also, there is no single gene that is common to all viral genomes, so total uncultured viral diversity cannot be monitored using approaches analogous to ribosomal DNA profiling. Metagenomic analyses of uncultured viral communities circumvent these limitations and can provide insights into the composition and structure of environmental viral communities.

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Figure 1: Comparison of viral metagenomic libraries to the GenBank non-redundant database.
Figure 2: The Phage Proteomic Tree.
Figure 3: Metagenomics and viral diversity, community structure and ecology.

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Acknowledgements

Support from the National Science Foundation and Moore Foundation is gratefully acknowledged.

Author information

Correspondence to Forest Rohwer.

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Competing interests

The authors declare no competing financial interests.

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DATABASES

Entrez

ΦX147

Streptococcus pyogenes strain MGAS315

Xylella fastidiosa strain Temecula1

FURTHER INFORMATION

Forest Rohwer's laboratory

BLAST

FASTA

GenBank

PHACCS

Phrap computer program

Phred computer program

Sequencher

Glossary

BIOME

An important ecosystem type, usually used to describe a distinctive primary producer assemblage such as a temperate forest.

BLAST

Comparisons of sequences with databases are commonly done with BLAST and/or FASTA. Both programs allow comparison of either a nucleotide or protein query sequence with either a nucleotide or protein database.

COMMUNITY

A group of different populations within a specific area.

COMMUNITY STRUCTURE

The relative abundance of different populations in relation to each other, often graphed as a rank–abundance curve.

EXPECT VALUE (E-VALUE)

A parameter that describes the number of hits that would be 'expected' to occur by chance when searching a sequence database of a particular size. An E-value of 1 means that it would be expected to find a match with a similar score simply by chance. The lower the E-value, the more significant the match.

OPEN READING FRAME

Open reading frames (ORFs) are essentially the same as genes. They are also referred to as protein-coding regions. ORFs are identified in genomes by several algorithms, most of which search for stretches of DNA sequence without stop codons.

PHAGE

A virus that infects bacteria. Because bacteria are the most common targets on a global scale, most environmental viruses are phages.

POPULATION

The total count of individuals belonging to one species in a specific area.

RANK–ABUNDANCE CURVE

Graphs of community structure. In these graphs, the most abundant species has a rank of 1, the next most abundant is 2, and so on, on the x-axis. The y-axis represents the abundance of each species.

SUBSURFACE

The geological zone below the surface of the Earth. It is not exposed to the Earth's surface.

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Edwards, R., Rohwer, F. Viral metagenomics. Nat Rev Microbiol 3, 504–510 (2005) doi:10.1038/nrmicro1163

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