Human Virome Variation

Bacteriophages, (a virus that infects and replicates within bacteria) are the most abundant biological entity on earth with an estimated population of ∼10^31 particles (Weinbauer, 2004).  Humans are also colonized by an immense population of viruses whose identities vary greatly from person to person. Many of the members of gut viromes are bacteriophages that infect bacterial species found in humans that harbor that particular bacteria. A new study by Minot et al., 2013 demonstrates that in addition to the variability introduced by different bacterial species in the gut, viral populations undergo rapid evolution giving rise to new bacteriophage species. Minot et al., follow an adult male for 2.5 years and examine his viral community by extreme deep sequencing (56 billion bases of purified viral sequence from 24 longitudinal fecal samples). Purified viral DNA was linearly amplified using Φ29 DNA polymerase which showed that bacterial 16S sequences were reduced to less than 10 copies per nanogram of DNA. Paired end reads were then obtained using Illumina HiSeq sequencing yielding more than 573 million reads, with 15-39 million reads per sample. Data analysis identified 478 contigs that were assumed to be DNA viruses. While 60 of these contgs assemble into circles, 87% showed no overlap with previously identified viruses.Taxonomic analysis of these contigs indicated recovery of Microviridae, Podoviridae, Myoviridae, and Siphoviridae, but contigs with taxonomic attributions were a minority, only 13%, emphasizing the enormous sequence variation present in bacteriophages. Interestingly, no human viruses were recovered, suggesting that the gut virome of healthy humans consists of mostly bacteriophages.

So while one factor for viral differences between populations is related to difference in bacterial populations, the authors point out that rapid within-host viral evolution is another contributing factor. Their data suggests that multiple new viral species will commonly arise in the gut of a typical human over the course of a human life.

Minot, S. et al. Rapid evolution of the human gut virome. Proc. Natl Acad. Sci. USA pnas.1300833110 (2013)


Weinbauer MG, Review Ecology of prokaryotic viruses, FEMS Microbiol Rev. May; 28(2):127-81 (2004)

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