Phages are now acknowledged as the most abundant microorganisms on the planet and are also possibly the most diversified. This diversity is mostly driven by their dynamic adaptation when facing selective pressure such as phage resistance mechanisms, which are widespread in bacterial hosts. When infecting bacterial cells, phages face a range of antiviral mechanisms, and they have evolved multiple tactics to avoid, circumvent or subvert these mechanisms in order to thrive in most environments. In this Review, we highlight the most important antiviral mechanisms of bacteria as well as the counter-attacks used by phages to evade these systems.

For this study, an in-depth review of the classification of Lactococcus lactis phages was performed. Reference phages as well as unclassified phages from international collections were analyzed by stringent DNA-DNA hybridization studies, electron microscopy observations, and sequence analyses. A new classification scheme for lactococcal phages is proposed that reduces the current 12 groups to 8. However, two new phages (Q54 and 1706), which are unrelated to known lactococcal phages, may belong to new emerging groups. The multiplex PCR method currently used for the rapid identification of phages from the three main lactococcal groups (936, c2, and P335) was improved and tested against the other groups, none of which gave a PCR product, confirming the specificity of this detection tool. However, this method does not detect all members of the highly diverse P335 group. The lactococcal phages characterized here were deposited in the Félix d'Hérelle Reference Center for Bacterial Viruses and represent a highly diverse viral community from the dairy environment.

Summary 23The marine cyanobacteria Prochlorococcus and Synechococcus are highly abundant in the global 24 oceans, as are the cyanophage with which they co-evolve. While genomic analyses have been

Bacteriophages display remarkable genetic diversity and host specificity. In this study, we explore phages infecting bacterial strains of the Enterobacteriaceae family because of their ability to infect related but distinct hosts. We isolated and characterized two novel virulent phages, SH6 and SH7, using a strain of Shigella flexneri as host bacterium. Morphological and genomic analyses revealed that phage SH6 belongs to the T1virus genus of the Siphoviridae family. Conversely, phage SH7 was classified in the T4virus genus of the Myoviridae family. Phage SH6 had a short latent period of 16 min and a burst size of 103 ± 16 PFU/infected cell while the phage SH7 latent period was 23 min with a much lower burst size of 26 ± 5 PFU/infected cell. Moreover, phage SH6 was sensitive to acidic conditions (pH < 5) while phage SH7 was stable from pH 3 to 11 for 1 hour. Of the 35 bacterial strains tested, SH6 infected its S. flexneri host strain and 8 strains of E. coli. Phage SH7 lysed additionally strains of E. coli O157:H7, Salmonella Paratyphi, and Shigella dysenteriae. The broader host ranges of these two phages as well as their microbiological properties suggest that they may be useful for controlling bacterial populations.

In this study, we demonstrated the remarkable genome plasticity of lytic lactococcal phages that allows them to rapidly adapt to the dynamic dairy environment. The lytic double-stranded DNA phage ul36 was used to sequentially infect a wild-type strain of Lactococcus lactis and two isogenic derivatives with genes encoding two phage resistance mechanisms, AbiK and AbiT. Four phage mutants resistant to one or both Abi mechanisms were isolated. Comparative analysis of their complete genomes, as well as morphological observations, revealed that phage ul36 extensively evolved by large-scale homologous and nonhomologous recombination events with the inducible prophage present in the host strain. One phage mutant exchanged as much as 79% of its genome compared to the core genome of ul36. Thus, natural phage defense mechanisms and prophage elements found in bacterial chromosomes contribute significantly to the evolution of the lytic phage population.Bacteria and phages are linked by a long history of coevolution as prophage elements are found in the majority of the bacterial genomes that have been sequenced (11). Not all of the prophages are functional as many appear to be defective or in a state of partial decay. However, genes in both intact and decaying prophage genomes can have important effects on the bacterial cell, such as providing protection against phage infection or fitness factors that increase the selective advantage of the host in a particular niche (9). On the other hand, the diversification of a phage genome is driven by the accumulation of point mutations, gene disruption, and recombination (1). Because of the latter process, phages can significantly benefit from the acquisition of genetic modules from other phages or hosts (2). In fact, comparative analyses have shown that phage genomes are composed of mosaics of conserved modules (2) interspersed with nonhomologous sequences (12,23,25). It should be noted that our ideas about how bacteriophages, particularly bacteriophages with a double-stranded DNA (dsDNA) genome, evolved are often inferred from bioinformatic analyses of the structures and sequences of the phage genomes and not from direct observations of the evolution process.The evolution of phages infecting the low-GϩC-content gram-positive bacterium Lactococcus lactis is the subject of ongoing studies because of the economic value of the host strains in fermented dairy products, as well as the frequent emergence of new virulent phages that are responsible for delays in milk fermentation. Lactococcal phages have been reclassified recently into 10 genetically distinct groups of dsDNA and tail-containing phages (15). However, members of only three L. lactis phage groups (936, c2, and P335) are regularly isolated. While virulent members of the 936 and c2 groups are rather homogeneous, there is considerable genetic heterogeneity in members of the P335 group, which contains both temperate and lytic phages (15).One effective way to control lactococcal phages in dairy processes is through the use, in rota...