Genomic diversity of phages infecting probiotic strains of Lactobacillus paracasei

MERCANTI, DIEGO JAVIER; QUIBERONI, ANDREA DEL LUJÁN; MOINEAU, SYLVAIN; CAPRA, MARÍA LUJÁN; ROUSSEAU, GENEVIÈVE M; LABRIE, SIMON J; TREMBLAY, DENISE M

Tucumán

Simposio; V Simposio Internacional de Bacterias Lácticas; 2016

Cerela

TheLactobacillus casei group includesthree closely related species: L. casei,L. paracasei, and L. rhamnosus. Although some strains ofthis group have been extensively studied because they are used as probiotics infoods, their phages have received less attention. The aim of this study was tosequence and analyze the genomes of five temperate phages (CL1, CL2,iA2, iLp84, and iLp1308) infecting probiotic strains of L. paracasei, to shed light on their genetic relationships. PhagesCL1 and CL2 were isolated from spontaneously lysedcultures of the commercial strain L.paracasei A. Prophage iA2 can be induced by mitomycin C from L. paracasei A, but cannot be propagatedon any indicator strain. Phage iLp84and iLp1308 were isolated frommitomycin C-induced strains (L. paracasei84 and L. paracasei CNRZ 1308,respectively), and propagated on the indicator strains L. paracasei INL3 and L.paracasei A14, respectively). Phage DNA was extracted using commercialkits, and their nucleotidic sequences were determined using Illumina's sequencingtechnology. The genome lengths ranged from 34,155 bp (iA2) to 39,474 bp (CL1).Phages iA2 and iLp1308 (34,176 bp)possess the smallest genomes reported, thus far, for phages of the L. casei group. The GC contents of thefive phage genomes ranged from 44.8 to 45.6%. As observed with many otherphages, their genomes were organized as follows: genes coding for DNApackaging, morphogenesis, lysis, lysogeny, and replication. Phages CL1,CL2, and iLp1308 arehighly related to each other. Phage iLp84was also related to these three phages, but the similarities were limited togene products involved in DNA packaging and structural proteins. Genomicfragments of phages CL1, CL2, iLp1308, and iLp84 werefound in several genomes of L. caseistrains. Prophage iA2 is unrelated to these four phages, but almost all of itsgenome was found in at least four L.casei strains. Overall, these phages are distinct from previouslycharacterized Lactobacillus phages.Our results highlight the diversity of L.casei phages and indicate frequent DNA exchanges between phages and theirhosts. Our comparative genomic analyses also suggest that the ampledistribution of prophages in the genomes of L.paracasei strains offers a reservoir of genes that could be used byvirulent phages to rapidly evolve. These phage-host interactions could affectphenotypes, probiotic properties and stability of the strains.