Characterization of the Genome of the Dairy Lactobacillus helveticus Bacteriophage AQ113 (original) (raw)
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Characterization of the Genome of the Dairy Lactobacillus helveticus Bacteriophage ΦAQ113
Applied and Environmental Microbiology, 2013
The complete genomic sequence of the dairy Lactobacillus helveticus bacteriophage ΦAQ113 was determined. Phage ΦAQ113 is a Myoviridae bacteriophage with an isometric capsid and a contractile tail. The final assembled consensus sequence revealed a linear, circularly permuted, double-stranded DNA genome with a size of 36,566 bp and a G+C content of 37%. Fifty-six open reading frames (ORFs) were predicted, and a putative function was assigned to approximately 90% of them. The ΦAQ113 genome shows functionally related genes clustered together in a genome structure composed of modules for DNA replication/regulation, DNA packaging, head and tail morphogenesis, cell lysis, and lysogeny. The identification of genes involved in the establishment of lysogeny indicates that it may have originated as a temperate phage, even if it was isolated from natural cheese whey starters as a virulent phage, because it is able to propagate in a sensitive host strain. Additionally, we discovered that the ΦAQ...
There is a lack of fundamental knowledge about the influence of bacteriophage on probiotic bacteria and other commensals in the gut. Here, we present the isolation and morphological and genetic characterization of a virulent narrow-host-range bacteriophage, φLb338-1. This phage was isolated from fresh sewage and was shown to infect the probiotic cheese strain Lactobacillus paracasei NFBC 338. Electron microscopy studies revealed that φLb338-1 is a member of the Myoviridae family, with an isometric head, a mediumsized contractile tail, and a complex base plate. Genome sequencing revealed a 142-kb genome with 199 open reading frames. Putative functions could be assigned to 22% of the open reading frames; these had significant homology to genes found in the broad-host-range SPO1-like group of phages which includes the Enterococcus faecalis phage φEF24C, Listeria phage A511, and Lactobacillus plantarum phage LP65. Interestingly, no significant genomic similarity was observed between the phage and the probiotic host strain. Future studies will determine if the presence of bacteriophage φLb338-1 or others in the human or animal gut plays an antagonistic role against the probiotic effect of beneficial bacteria.
Genome Sequences of Eight Prophages Isolated from Lactococcus lactis Dairy Strains
Genome announcements, 2016
P335 group phages represent the most divergent phage group infecting dairy Lactococcus lactis strains and have significant implications for the dairy processing industry. Here, we report the complete genome sequences of eight lactococcal prophages chemically induced from industrial lactococcal strains that propagate lytically on one of two laboratory strains.
Biodiversity and Classification of Phages Infecting Lactobacillus brevis
Frontiers in Microbiology
Lactobacillus brevis is a lactic acid bacterium that is known as a food and beverage spoilage organism, and more specifically as a beer-spoiler. Phages of L. brevis have been described, but very limited data is available regarding temperate phages of L. brevis. Temperate phages may exert benefits to the host, while they may also be employed to combat beer spoilage. The current study reports on the incidence of prophage sequences present in nineteen distinct L. brevis genomes. Prophage induction was evaluated using mitomycin C exposure followed by genome targeted-PCR, electron microscopy and structural proteome analysis. The morphological and genome sequence analyses revealed significant diversity among L. brevis prophages, which appear to be dominated by members of the Myoviridae phage family. Based on this analysis, we propose a classification of L. brevis phages into five groups.
Analysis of the complete nucleotide sequence of the lactococcal phage 4268, which is lytic for the cheese starter Lactococcus lactis DPC4268, is presented. Phage 4268 has a linear genome of 36,596 bp, which is modularly organised and encompasses 49 open reading frames. Putative functions were assigned to approximately 45% of the predicted products of these open reading frames based on sequence similarity with known proteins, N-terminal sequence analysis and identification of conserved domains. Significantly, a segment of the genome has homology to the recently sequenced lysogenic module in lactococcal phage ϕ31 that contains a lytic switch but no phage integrase or attachment site. This suggests that it is derived from a prophage. A phage 4268-encoded and a host-encoded methylase were found to be highly similar, having only two nucleotide mismatches, suggesting that the phage acquired the methylase gene to protect it from a host endonuclease. Comparative genomic analysis revealed significant homology between phage 4268 and the lactococcal phage BK5-T. The comparative analysis also supported the classification of phage 4268 and other BK5-T-related phage as separate from the proposed P335 species of lactococcal phage.
Isolation and Characterization of Lactobacillus brevis Phages
Viruses, 2019
Lactobacillus brevis has been widely used in industry for fermentation purposes. However, it is also associated with the spoilage of foods and beverages, in particular, beer. There is an increasing demand for natural food preservation methods, and in this context, bacteriophages possess the potential to control such spoilage bacteria. Just a few studies on phages infecting Lactobacillus brevis have been performed to date and in the present study, we report the isolation and characterization of five virulent phages capable of infecting Lb. brevis strains. The analysis reveals a high diversity among the isolates, with members belonging to both, the Myoviridae and Siphoviridae families. One isolate, designated phage 3-521, possesses a genome of 140.8 kb, thus representing the largest Lb. brevis phage genome sequenced to date. While the isolated phages do not propagate on Lb. brevis beer-spoiling strains, phages showed activity against these strains, impairing the growth of some Lb. brevis strains. The results highlight the potential of bacteriophage-based treatments as an effective approach to prevent bacterial spoilage of beer.
Genomic diversity of phages infecting probiotic strains of Lactobacillus paracasei
Applied and Environmental Microbiology, 2015
Strains of theLactobacillus caseigroup 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 fiveL. paracaseitemperate 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 theL. caseigroup. 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 p...
Bulgarian Journal of Agricultural Science, 2013
The modular evolution of phage genomes makes their classifi cation extremely diffi cult. Still in dairy industry, the identifi cation of the phage species that disturbs the fermentation process is of crucial importance in the selection of a strategy to avoid or eliminate phage infections. Phages attacking Lactobacillus delbrueckii are currently divided into four groups assigned as "a", "b", "c" and "d" which have substantial differences in their virion morphology and DNA homology. Lactobacillus delbrueckii ssp. bulgaricus phage Gb1 was isolated in 2005 from yoghurt production. Restriction fragments of phage Gb1 DNA were cloned into pIL253 in Lactococcus lctis IL1403 and PCR amplifi ed with vector-specifi c primers. The resulting amplicons were sequenced and identities with existing sequence databases were searched. All of the obtained sequences showed homology only to regions within the genome of phages LL-Ku and c5 with levels of nucleotide identity of 80-99%. No signifi cant sequence matches were found with other L. delbrueckii phages. The sequenced fragments from the genome of phage Gb1 were homologous to key genes in phages LL-Ku and c5 encoding a major head protein, the tape-measure protein, tail proteins, the single strand binding protein and a diesterase. As phages LL-Ku and c5 are typical representatives of group "b" L. delbrueckii bacteriophages that do not share DNA homology with L. delbrueckii phages from other groups we could classify phage Gb1 into group "b" L. delbrueckii phages. This is the fi rst report of a bacteriophage from this group isolated in Bulgaria. Further studies of phage Gb1 will facilitate the work on the selection of phage resistant starters and prevention of phage infections in yoghurt production.