title: Genomic Diversity of Phages Infecting Probiotic Strains of Lactobacillus paracasei.
abstract: Strains of the Lactobacillus casei group have been extensively studied because some are used as probiotics in foods. Conversely, their phages have received much less attention. We analyzed the complete genome sequences of five L. paracasei temperate phages: CL1, CL2, iLp84, iLp1308, and iA2. Only phage iA2 could not replicate in an indicator strain. 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.
authors.affiliation: Instituto de Lactología Industrial (Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas), Facultad de Ingeniería Química, Santa Fe, Argentina diegojav78@gmail.com sylvain.moineau@bcm.ulaval.ca.
authors.forename: Diego J
authors.identifier: http://orcid.org/0000-0001-5243-9259
authors.initials: DJ
authors.lastname: Mercanti
authors.affiliation: Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada.
authors.forename: Geneviève M
authors.initials: GM
authors.lastname: Rousseau
authors.affiliation: Instituto de Lactología Industrial (Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas), Facultad de Ingeniería Química, Santa Fe, Argentina.
authors.forename: María L
authors.initials: ML
authors.lastname: Capra
authors.affiliation: Instituto de Lactología Industrial (Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas), Facultad de Ingeniería Química, Santa Fe, Argentina.
authors.forename: Andrea
authors.initials: A
authors.lastname: Quiberoni
authors.affiliation: Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada.
authors.forename: Denise M
authors.initials: DM
authors.lastname: Tremblay
authors.affiliation: Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada.
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Labrie
authors.affiliation: Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada diegojav78@gmail.com sylvain.moineau@bcm.ulaval.ca.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Moineau
mesh_terms: D001435:Bacteriophages / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D001483:Base Sequence; D014644:Genetic Variation; D016679:Genome, Viral; D023281:Genomics; D007780:Lacticaseibacillus casei / Q000821:virology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D019936:Probiotics / Q000032:analysis; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins