A number of ecological studies have revealed that microbial viruses predominate in the biosphere and outnumber their hosts by at least one order of magnitude. Due to their abundance and consequent influence on the composition and diversity of microbial communities, viruses can be rightfully considered to be the “major players in the global ecosystem”. Until recently, the majority of viruses in the environment were believed to possess double-stranded DNA genomes. However, technological advances in single-stranded (ss) DNA amplification and sequencing from environmental samples revealed that viruses with ssDNA genomes are more prevalent in both soil and marine environments than previously recognized. This realization precipitated an interest amongst environmental virologists in the diversity and distribution of ssDNA bacterial viruses in nature. Among ssDNA viruses that are most often identified in the environment using metagenomic approach are those belonging to the family Microviridae. However, the host organisms have yet to be determined.
Unexplored diversity and abundance of the Microviridae viruses in the environment fuels interest in this virus group. In order to obtain more information about these viruses, researchers analyzed the genomic sequences available in public databases for the presence of proviruses related to Microviridae. The rationale behind this approach is that a provirus, defective or not, represents a molecular record that a cell has been in contact with a particular virus. This study identified seven proviruses that are related to members of the Microviridae. The proviruses are integrated in the genomes of different species of the order Bacteroidales (phylum Bacteroidetes). The identified proviruses are only distantly related to the previously characterized microviruses and gokushoviruses and may represent a new group or subfamily within the Microviridae. Searches against metagenomic databases suggest that these new viruses might be associated with the human gut microbiota. This extends our knowledge of the evolution, diversity and host range of microviruses.
Microviridae Goes Temperate: Microvirus-Related Proviruses Reside in the Genomes of Bacteroidetes. 2011 PLoS ONE 6(5): e19893. doi:10.1371/journal.pone.0019893
The Microviridae comprises icosahedral lytic viruses with circular single-stranded DNA genomes. The family is divided into two distinct groups based on genome characteristics and virion structure. Viruses infecting enterobacteria belong to the genus Microvirus, whereas those infecting obligate parasitic bacteria, such as Chlamydia, Spiroplasma and Bdellovibrio, are classified into a subfamily, the Gokushovirinae. Recent metagenomic studies suggest that members of the Microviridae might also play an important role in marine environments. In this study we present the identification and characterization of Microviridae-related prophages integrated in the genomes of species of the Bacteroidetes, a phylum not previously known to be associated with microviruses. Searches against metagenomic databases revealed the presence of highly similar sequences in the human gut. This is the first report indicating that viruses of the Microviridae lysogenize their hosts. Absence of associated integrase-coding genes and apparent recombination with dif-like sequences suggests that Bacteroidetes-associated microviruses are likely to rely on the cellular chromosome dimer resolution machinery. Phylogenetic analysis of the putative major capsid proteins places the identified proviruses into a group separate from the previously characterized microviruses and gokushoviruses, suggesting that the genetic diversity and host range of bacteriophages in the family Microviridae is wider than currently appreciated.