Genomics of tailless bacteriophages in a complex lactic acid bacteria starter culture

Abstract

Background Our previous study on a model microbial community originating from artisanal cheese fermentation starter revealed that bacteriophages not only co-exist with bacteria but also are highly abundant. To gain more insight into the potential role of prophages in the microbial community, we analysed the genomic content of 6 phage crops released by different strains in the starter culture, performed comparative genome analysis, and demonstrated their roles in phage defence of respective hosts. Results The identified prophages belong to three different subgroups of the Siphoviridae P335 phage group. Remarkably, most analysed prophages show disruptions in different tail encoding genes, resulting in a common tailless phenotype. Furthermore, a number of potentially beneficial features for the host carried by prophages were identified. The prophages carry up to 3 different phage defence systems per genome that are functional in protecting the host from foreign phage infection. Conclusion We suggest that the presumably defective prophages are a result of bacteria-phage coevolution and convey advantages to host bacteria; knowledge on the ecological role of such (defective) prophages may contribute to a refreshed look in strain selection criteria in (dairy) industry.

Chronic release of tailless phage particles from Lactococcus lactis

“…2F). This conclusion is also supported by the previous study where the tailless phage particles were isolated with the same method and subjected to DNA sequencing, and full phage genomes were recovered with more than 100-fold higher coverage than background (6).…”

“…Examples are Tectiviridae phage PRD1 employing membrane protein P10 (49), and Corticoviridae phage PM2 employing membrane proteins P3 and P6 to interact with phage-specific areas on the cell membrane (42,50). For all above mentioned phage-encoded proteins, we did not find homology to any of the proteins encoded on proPhi1 or any of the other prophages found in lactococci isolated from the starter culture Ur (6).…”

“…However, it should be noted that other membrane-associated protein coding sequences were indeed predicted in the Ur prophages, namely ORF42 in proPhi1&5, ORF08 in proPhi2&4 and ORF49 in proPhi6 (6). Targeting phage particles to special areas of cell membrane by membrane-associated proteins could potentially be an explanation for the distinct lipid composition associated with released phage particles.…”

“…In cells actively replicating the phage particles, green fluorescence intensity was expected to increase. As mentioned, we used L. lactis TIFN1 as the model strain, which harbors the genome of prophage proPhi1 (6). The insertion site was selected within the prophage sequence between stop codons of open reading frames (ORFs) 48 and 49 encoded on opposite DNA strands (Fig.…”

“…However, they possess some peculiar features: phage particles are abundantly released spontaneously and further stimulated by mitomycin C induction (23). They appear to be tailless due to disruptions in tail-protein encoding genes (6).…”