Genomic diversity of phages infecting probiotic strains of Lactobacillus paracasei

MERCANTI DIEGO JAVIER; ROUSSEAU GM; CAPRA MARÍA LUJÁN; QUIBERONI ANDREA; TREMBLAY DM; LABRIE SJ; MOINEAU SYLVAIN

San Miguel de Tucumán

Simposio; V International Symposium on Lactic Acid Bacteria. Benefitting from lactic acid bacteria. Progress in health and food; 2016

CERELA - CONICET

The Lactobacillus casei group includes three closely related species: L. casei, L. paracasei, and L. rhamnosus. Although some strains of this group have been extensively studied because they are used as probiotics in foods, their phages have received less attention. The aim of this study was to sequence 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. Phages CL1 and CL2 were isolated from spontaneously lysed cultures of the commercial strain L. paracasei A. Prophage iA2 can be induced by mitomycin C from L. paracasei A, but cannot be propagated on any indicator strain. Phage iLp84 and iLp1308 were isolated from mitomycin C-induced strains (L. paracasei 84 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 commercial kits, and their nucleotidic sequences were determined using illumina's sequencing technology. 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 the five phage genomes ranged from 44.8 to 45.6%. As observed with many other phages, their genomes were organized as follows: genes coding for DNA packaging, morphogenesis, lysis, lysogeny, and replication. Phages CL1, CL2, and iLp1308 are highly related to each other. Phage iLp84 was also related to these three phages, but the similarities were limited to gene products involved in DNA packaging and structural proteins. Genomic fragments of phages CL1, CL2, iLp1308, and iLp84 were found in several genomes of L.casei strains. Prophage iA2 is unrelated to these four phages, but almost all of its genome was found in at least four L. casei strains. Overall, these phages are distinct from previously characterized Lactobacillus phages. Our results highlight the diversity of L. casei phages and indicate frequent DNA exchanges between phages and their hosts. Our comparative genomic analyses also suggest that the ample distribution of prophages in the genomes of L. paracasei strains offers a reservoir of genes that could be used by virulent phages to rapidly evolve. These phage-host interactions could affect phenotypes, probiotic properties and stability of the strains.