Prophages are regarded as one of the factors underlying bacterial virulence, genomic diversification, and fitness, and are ubiquitous in bacterial genomes. Information on Helicobacter sp. prophages remains scarce. In this study, sixteen prophages were identified and analyzed in detail. Eight of them are described for the first time. Based on a comparative genomic analysis, these sixteen prophag...

Bacteriophages (phages) infect many bacterial species, but little is known about the diversity of phages among the pneumococcus, a leading global pathogen. The objectives of this study were to determine the prevalence, diversity and molecular epidemiology of prophages (phage DNA integrated within the bacterial genome) among pneumococci isolated over the past 90 years. Nearly 500 pneumococcal ge...

Comparative genomics demonstrated that the chromosomes from bacteria and their viruses (bacteriophages) are coevolving. This process is most evident for bacterial pathogens where the majority contain prophages or phage remnants integrated into the bacterial DNA. Many prophages from bacterial pathogens encode virulence factors. Two situations can be distinguished: Vibrio cholerae, Shiga toxin-pr...

Shiga toxin (Stx) genes in Stx producing Escherichia coli (STEC) are encoded in prophages of the lambda family, such as H-19B. The subpopulation of STEC lysogens with induced prophages has been postulated to contribute significantly to Stx production and release. To study induced STEC, we developed a selectable in vivo expression technology, SIVET, a reporter system adapted from the RIVET syste...

Phages are the most abundant entity in the biosphere and outnumber bacteria by a factor of 10. Phage DNA may also constitute 20% of bacterial genomes; however, its role is ill defined. Here, we explore the impact of cryptic prophages on cell physiology by precisely deleting all nine prophage elements (166 kbp) using Escherichia coli. We find that cryptic prophages contribute significantly to re...

UNLABELLED Prophinder is a prophage prediction tool coupled with a prediction database, a web server and web service. Predicted prophages will help to fill the gaps in the current sparse phage sequence space, which should cover an estimated 100 million species. Systematic and reliable predictions will enable further studies of prophages contribution to the bacteriophage gene pool and to better ...

Bacteriophages are major genetic factors promoting horizontal gene transfer (HGT) between bacteria. Their roles in dynamic bacterial genome evolution have been increasingly highlighted by the fact that many sequenced bacterial genomes contain multiple prophages carrying a wide range of genes. Enterohemorrhagic Escherichia coli O157 is the most striking case. A sequenced strain (O157 Sakai) poss...

Integrated phages (prophages) are major contributors to the diversity of bacterial gene repertoires. Domestication of their components is thought to have endowed bacteria with molecular systems involved in secretion, defense, warfare, and gene transfer. However, the rates and mechanisms of domestication remain unknown. We used comparative genomics to study the evolution of prophages within the ...

Prophages are common in many bacterial genomes. Distinguishing putatively viable prophages from nonviable sequences can be a challenge, since some prophages are remnants of once-functional prophages that have been rendered inactive by mutational changes. In some cases, a putative prophage may be missed due to the lack of recognizable prophage loci. The genome of a marine roseobacter, Roseovariu...

Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographi...