scholarly journals Genome Organization and Characterization of the Virulent Lactococcal Phage 1358 and Its Similarities to Listeria Phages

2010 ◽  
Vol 76 (5) ◽  
pp. 1623-1632 ◽  
Author(s):  
Marie-�ve Dupuis ◽  
Sylvain Moineau
Keyword(s):  
Burst Size ◽  
Gc Content ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Origin And Evolution ◽  
Sds Page ◽  
Liquid Chromatography Tandem Mass ◽  
Icosahedral Capsid ◽  
Rare Group

ABSTRACT Virulent phage 1358 is the reference member of a rare group of phages infecting Lactococcus lactis. Electron microscopy revealed a typical icosahedral capsid connected to one of the smallest noncontractile tails found in a lactococcal phage of the Siphoviridae family. Microbiological characterization identified a burst size of 72 virions released per infected host cell and a latent period of 90 min. The host range of phage 1358 was limited to 3 out of the 60 lactococcal strains tested. Moreover, this phage was insensitive to four Abi systems (AbiK, AbiQ, AbiT, and AbiV). The genome of phage 1358 consisted of a linear, double-stranded, 36,892-bp DNA molecule containing 43 open reading frames (ORFs). At least 14 ORFs coded for structural proteins, as identified by SDS-PAGE coupled to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses. The genomic organization was similar to those of other siphophages. All genes were on the same coding strand and in the same orientation. This lactococcal phage was unique, however, in its 51.4% GC content, much higher than those of other phages infecting this low-GC Gram-positive host. A bias for GC-rich codons was also observed. Comparative analyses showed that several phage 1358 structural proteins shared similarity with two Listeria monocytogenes phages, P35 and P40. The possible origin and evolution of lactococcal phage 1358 is discussed.

scholarly journals Isolation and Characterization of a Bacteriophage Infecting Pseudomonas Aeruginosa and Its Application as a Potential Decontaminating Agent

2021 ◽  
Author(s):  
Sonika Sharma ◽  
Sibnarayan Datta ◽  
Soumya Chatterjee ◽  
Moumita Dutta ◽  
Jhuma Samanta ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Burst Size ◽  
Gc Content ◽  
Alginate Beads ◽  
Open Reading Frames ◽  
Isolation And Characterization ◽  
The Family ◽  
Infected Cells

Abstract To treat antibiotic resistance bacteria, bacteriophage (also called 'phage') application has recently drawn considerable attention from researchers globally. Bacteria like Pseudomonas aeruginosa are known to be associated with nosocomial infections especially in patients with compromised immune systems. In the present work, phage against P. aeruginosa (named 'DRLP1') was isolated from wastewater, enriched and characterized. Morphologically DRLP1 belongs to the family Myoviridae with a high lytic ability. DRLP1 has a burst size of approximately 100 PFU/infected cells, a rapid adsorption time when supplemented with MgCl2, and has viability in a wide temperature range and pH. Genomic sequencing and bioinformatics analysis showed that the phage genome is linear double-stranded, 66,243 bp in length and have a GC content of 54.9%. the genome encodes 93 phage related ORFs open reading frames (ORFs). Phage stability in lyophilized state, adsorption study on sodium alginate beads, and in-vitro pathogen reduction assays were also investigated. Study carried out with artificially contaminated fomites suggests that this phage has the potential for application as a biological decontaminant agent against P. aeruginosa in different conditions.

Isolation, Characterization, and Application in Poultry Product of a Specific Salmonella Bacteriophage S55

2021 ◽  
Author(s):  
Haojie Ge ◽  
Yanping Xu ◽  
Kai Zhang ◽  
Shuxuan Zhang ◽  
Maozhi Hu ◽  
...  
Keyword(s):  
Prevention And Control ◽  
Burst Size ◽  
Gc Content ◽  
Skin Surface ◽  
Open Reading Frames ◽  
Lytic Phage ◽  
Trna Genes ◽  
Host Bacterium ◽  
Salmonella Pullorum ◽  
And Control

Salmonellosis occurs frequently worldwide, causing serious threats to public health safety. The abuse of antibiotics is increasing the antibiotic resistance in bacteria, thereby making the prevention and control of Salmonella more difficult. A phage can help control the spread of bacteria. In this study, S55, a lytic phage, was isolated from faecal samples obtained from poultry farms using Salmonella Pullorum ( S . Pullorum) as the host bacterium. This phage belongs to Siphoviridae and has a polyhedral head and a retraction-free tail. S55 showed a strong ability to lyse Salmonella serovars, such as S . Pullorum (58/60, 96.67%) and S . Enteritidis (97/104, 93.27%). One-step growth kinetics showed that the latent period was 10 min, burst period was 80 min and burst size was 40 pfu/cell. The optimal multiplicity of infection was 0.01, and the phage was able to survive at a pH of 4–11 and temperature of 40°C–60°C for 60 min. Complete genome sequence analysis revealed that the S55 genome length is 42,781 bp (GC content, 50.28%) and it contains 58 open reading frames (ORF), including 25 ORFs with known or assumed functions, without tRNA genes. Moreover, S55 does not carry genes that encode virulence or resistance factors. At different temperatures (4°C or 25°C), S55 was found to lower the populations of S . Pullorum and S . Enteritidis on chicken skin surface. Its bacteriostatic effect at 4°C was higher than that at 25°C. In conclusion, S55 can be considered a promising biological agent for the prevention and control of Salmonella .

scholarly journals Characterization of Lactococcus lactis Phage 949 and Comparison with Other Lactococcal Phages

2010 ◽  
Vol 76 (20) ◽  
pp. 6843-6852 ◽  
Author(s):  
Julie E. Samson ◽  
Sylvain Moineau
Keyword(s):  
Lactococcus Lactis ◽  
Defense Mechanisms ◽  
Gc Content ◽  
Tail Length ◽  
Open Reading Frames ◽  
Phage Group ◽  
Double Stranded Dna ◽  
Group I ◽  
Sds Page ◽  
Genetic Clusters

ABSTRACT The virulent Lactococcus lactis phage 949 was isolated in 1975 from cheese whey in New Zealand. This phage is a member of the Siphoviridae family and of a rare lactococcal phage group that bears its name (949 group). It has an icosahedral capsid (79-nm diameter) and a very long noncontractile tail (length, 500 nm; width, 12 nm). It infected 7 of 59 tested L. lactis strains, a somewhat expanded host range for a rare lactococcal phage. The abortive phage infection defense mechanisms AbiQ and AbiT strongly inhibited the multiplication of phage 949, but AbiK and AbiV did not. Its double-stranded DNA (dsDNA) genome of 114,768 bp is, to date, the largest among lactococcal phages. Its GC content was calculated at 32.7%, which is the lowest reported for a lactococcal phage. Its 154 open reading frames (ORFs) share limited identity with database sequences. In addition, terminal redundancy was observed as well as the presence of six tRNAs, one group I intron, and putative recombinases. SDS-PAGE coupled with mass spectrometry identified 13 structural proteins. The genomes of the members of the 10 currently known L. lactis phage groups were used to construct a proteomic tree. Each L. lactis phage group separated into distinct genetic clusters, validating the current classification scheme. Of note, members of the polythetic P335 groups were clearly separated into subgroups.

scholarly journals Characterization and Genomic Analysis of Phage asccφ28, a Phage of the Family Podoviridae Infecting Lactococcus lactis

2008 ◽  
Vol 74 (11) ◽  
pp. 3453-3460 ◽  
Author(s):  
Steven E. Kotsonis ◽  
Ian B. Powell ◽  
Christopher J. Pillidge ◽  
Gaëtan K. Y. Limsowtin ◽  
Alan J. Hillier ◽  
...  
Keyword(s):  
Lactococcus Lactis ◽  
Dna Hybridization ◽  
Burst Size ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Full Genome Sequence ◽  
The Family ◽  
Reading Frames ◽  
Dairy Fermentation

ABSTRACT Bacteriophage asccφ28 infects dairy fermentation strains of Lactococcus lactis. This report describes characterization of asccφ28 and its full genome sequence. Phage asccφ28 has a prolate head, whiskers, and a short tail (C2 morphotype). This morphology and DNA hybridization to L. lactis phage P369 DNA showed that asccφ28 belongs to the P034 phage species, a group rarely encountered in the dairy industry. The burst size of asccφ28 was found to be 121 ± 18 PFU per infected bacterial cell after a latent period of 44 min. The linear genome (18,762 bp) contains 28 possible open reading frames (ORFs) comprising 90% of the total genome. The ORFs are arranged bidirectionally in recognizable functional modules. The genome contains 577 bp inverted terminal repeats (ITRs) and putatively eight promoters and four terminators. The presence of ITRs, a phage-encoded DNA polymerase, and a terminal protein that binds to the DNA, along with BLAST and morphology data, show that asccφ28 more closely resembles streptococcal phage Cp-1 and the φ29-like phages that infect Bacillus subtilis than it resembles common lactococcal phages. The sequence of this phage is the first published sequence of a P034 species phage genome.

scholarly journals Isolation and Characterization of Phages InfectingBacillus subtilis

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Anna Krasowska ◽  
Anna Biegalska ◽  
Daria Augustyniak ◽  
Marcin Łoś ◽  
Malwina Richert ◽  
...  
Keyword(s):  
Food Production ◽  
Burst Size ◽  
Industrial Applications ◽  
Isolation And Characterization ◽  
Latent Time ◽  
Food Borne ◽  
Alternative Approach ◽  
Sds Page

Bacteriophages have been suggested as an alternative approach to reduce the amount of pathogens in various applications. Bacteriophages of various specificity and virulence were isolated as a means of controlling food-borne pathogens. We studied the interaction of bacteriophages withBacillusspecies, which are very often persistent in industrial applications such as food production due to their antibiotic resistance and spore formation. A comparative study using electron microscopy, PFGE, and SDS-PAGE as well as determination of host range, pH and temperature resistance, adsorption rate, latent time, and phage burst size was performed on three phages of theMyoviridaefamily and one phage of theSiphoviridaefamily which infectedBacillus subtilisstrains. The phages are morphologically different and characterized by icosahedral heads and contractile (SIOΦ, SUBω, and SPOσphages) or noncontractile (ARπphage) tails. The genomes of SIOΦ and SUBωare composed of 154 kb. The capsid of SIOΦ is composed of four proteins. Bacteriophages SPOσand ARπhave genome sizes of 25 kbp and 40 kbp, respectively. Both phages as well as SUBωphage have 14 proteins in their capsids. Phages SIOΦ and SPOσare resistant to high temperatures and to the acid (4.0) and alkaline (9.0 and 10.0) pH.

scholarly journals ISOLATION, CHARACTERIZATION AND GENOME ANALYSIS OF A NOVEL VIRULENT ESCHERICHIA COLI BACTERIOPHAGE VB_ECOM_011D4

2021 ◽  
Vol 6 ◽  
pp. 27-35
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Phage Therapy ◽  
Burst Size ◽  
Large Subunit ◽  
Alternative Therapy ◽  
Gc Content ◽  
Open Reading Frames ◽  
Promising Alternative ◽  
E Coli

Phage therapy is a promising alternative therapy for the treatment of E. coli infection. Although the total number of phages on the earth is as high as 10 31 , the reported phages and thoroughly studied are very limited. Therefore, the continuous discovery of new phages and in-depth research will provide materials for the wide application of phage therapy in the future. In this study, a novel E. coli phage vB_EcoM_011D4 was isolated from sewage samples, and the biological characteristics were studied. Electron microscopy and homology analysis results showed that vB_EcoM_011D4 belongs to the family Myoviridae. One-step growth curve showing the latent period of vB_EcoM_011D4 was 10 min, with the burst size of 115 PFU/cell. Additionally, Phage vB_EcoM_011D4 was highly stabled under different temperatures (range 4 – 70 ℃) and pH conditions (range 6 – 10). At the same time, its genome was subjected to high-throughput sequencing and compared with the reported phages. The results of high-throughput sequencing assembly showed that vB_EcoM_011D4 is a linear, double-stranded DNA virus containing 163764 bp, with an average GC content of 40.50%, and a total of 273 open reading frames (ORFs). Genomic comparison analysis revealed that most of the ORFs were similar to Enterobacteria phage Phi1 and RB49. However, ORF147 and ORF148 putative DNA methylase family protein is less than 67% homology with already published phages. In addition, the phylogenetic analysis of terminates large subunit showed that it belongs to a new branch and shows less than 50 similarities to reported phages. There is no lysogenic, toxin or antibiotic-resistant related gene was found in the genome of vB_EcoM_011D4. In summary, vB_EcoM_011D4 is a newly discovered phage, which can be further studied for elucidating the phage diversity and it is benefits for the wide application of phage therapy.

scholarly journals Genomic and Proteomic Characterization of Bacteriophage BH1 Spontaneously Released from Probiotic Lactobacillus rhamnosus Pen

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1163 ◽  
Author(s):  
Piotr Jarocki ◽  
Elwira Komoń-Janczara ◽  
Marcin Podleśny ◽  
Oleksandr Kholiavskyi ◽  
Monika Pytka ◽  
...  
Keyword(s):  
Lactobacillus Rhamnosus ◽  
Gc Content ◽  
Probiotic Strain ◽  
Open Reading Frames ◽  
Potential Threat ◽  
Genetic Switch ◽  
Important Virulence Factor ◽  
Inducing Factors ◽  
Reading Frames

Lactobacillus rhamnosus Pen is a human endogenous strain used for the production of probiotic formula, which is effective in the prevention of antibiotic-associated diarrhoea. Our study showed that this probiotic strain releases bacteriophage BH1 without the addition of any inducing agent. Our research revealed that phage BH1 has a circular genome with a length of 40721 nt and a GC content of 44.8%. The genome of phage BH1 possesses 57 open reading frames which could be divided into functional modules associated with DNA packaging, morphogenesis, lysis, integration, genetic switch, and replication. In spite of similarity in morphology and genomic organization, comparative analysis revealed substantial genetic diversity and mosaic genomic architecture among phages described for the Lactobacillus casei group. Additionally, qPCR and ddPCR analysis confirmed earlier microscopic observations indicating that L. rhamnosus Pen liberates bacteriophage particles during growth. This occurs spontaneously, and is not a result of external inducing factors. For samples collected after 4 and 24 h of L. rhamnosus Pen culture, the number of attB and attP copies increased 2.5 and 12 times, respectively. This phenomenon, by introducing resistance to other phages or enhancing the biofilm-forming capabilities, may increase the survivability of microorganisms in their natural ecological niche. Conversely, spontaneous phage induction may be an important virulence factor for bacteria, posing a potential threat for the human host.

scholarly journals Isolation of New Stenotrophomonas Bacteriophages and Genomic Characterization of Temperate Phage S1

2008 ◽  
Vol 74 (24) ◽  
pp. 7552-7560 ◽  
Author(s):  
Pilar García ◽  
Cristina Monjardín ◽  
Rebeca Martín ◽  
Carmen Madera ◽  
Nora Soberón ◽  
...  
Keyword(s):  
Burst Size ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Virus Particles ◽  
Bacterial Titer ◽  
Genes Encoding ◽  
Replication Gene ◽  
Genomic Characterization ◽  
Phosphoadenosine Phosphosulfate

ABSTRACT Twenty-two phages that infect Stenotrophomonas species were isolated through sewage enrichment and prophage induction. Of them, S1, S3, and S4 were selected due to their wide host ranges compared to those of the other phages. S1 and S4 are temperate siphoviruses, while S3 is a virulent myovirus. The genomes of S3 and S4, about 33 and 200 kb, were resistant to restriction digestion. The lytic cycles lasted 30 min for S3 and about 75 min for S1 and S4. The burst size for S3 was 100 virions/cell, while S1 and S4 produced about 75 virus particles/cell. The frequency of bacteriophage-insensitive host mutants, calculated by dividing the number of surviving colonies by the bacterial titer of a parallel, uninfected culture, ranged between 10−5 and 10−6 for S3 and 10−3 and 10−4 for S1 and S4. The 40,287-bp genome of S1 contains 48 open reading frames (ORFs) and 12-bp 5′ protruding cohesive ends. By using a combination of bioinformatics and experimental evidence, functions were ascribed to 21 ORFs. The morphogenetic and lysis modules are well-conserved, but no lysis-lysogeny switch or DNA replication gene clusters were recognized. Two major clusters of genes with respect to transcriptional orientation were observed. Interspersed among them were lysogenic conversion genes encoding phosphoadenosine phosphosulfate reductase and GspM, a protein involved in the general secretion system II. The attP site of S1 may be located within a gene that presents over 75% homology to a Stenotrophomonas chromosomal determinant.

scholarly journals Characterization of Nora Virus Structural Proteins via Western Blot Analysis

Scientifica ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Brad L. Ericson ◽  
Darby J. Carlson ◽  
Kimberly A. Carlson
Keyword(s):  
Western Blot ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Polypeptide Composition ◽  
Virus Particles ◽  
E Coli ◽  
Nora Virus ◽  
Monospecific Antisera ◽  
Reading Frames

Nora virus is a single stranded RNA picorna-like virus with four open reading frames (ORFs). The coding potentials of the ORFs are not fully characterized, but ORF3 and ORF4 are believed to encode the capsid proteins (VP3, VP4a, VP4b, and VP4c) comprising the virion. To determine the polypeptide composition of Nora virus virions, polypeptides from purified virus were compared to polypeptides detected in Nora virus infectedDrosophila melanogaster. Nora virus was purified from infected flies and used to challenge mice for the production of antisera.ORF3,ORF4a,ORF4b, andORF4cwere individually cloned and expressed inE. coli; resultant recombinant proteins purified and were used to make monospecific antisera. Antisera were evaluated via Western blot against whole virus particles and Nora virus infected fly lysates. Viral purification yielded two particle types with densities of ~1.31 g/mL (empty particles) and ~1.33 g/mL (complete virions). Comparison of purified virus polypeptide composition to Nora virus infectedD. melanogasterlysate showed the number of proteins in infected cell lysates is less than purified virus. Our results suggest the virion is composed of 6 polypeptides, VP3, VP4a, two forms of VP4b, and two forms of VP4c. This polypeptide composition is similar to other small RNA insect viruses.

scholarly journals Evolution of Lactococcus lactis Phages within a Cheese Factory

2009 ◽  
Vol 75 (16) ◽  
pp. 5336-5344 ◽  
Author(s):  
Geneviève M. Rousseau ◽  
Sylvain Moineau
Keyword(s):  
Lactococcus Lactis ◽  
High Performance ◽  
Core Genome ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Tandem Mass ◽  
Double Stranded Dna ◽  
Chromatography Tandem Mass Spectrometry ◽  
Liquid Chromatography Tandem Mass ◽  
Reading Frames

ABSTRACT We have sequenced the double-stranded DNA genomes of six lactococcal phages (SL4, CB13, CB14, CB19, CB20, and GR7) from the 936 group that were isolated over a 9-year period from whey samples obtained from a Canadian cheese factory. These six phages infected the same two industrial Lactococcus lactis strains out of 30 tested. The CB14 and GR7 genomes were found to be 100% identical even though they were isolated 14 months apart, indicating that a phage can survive in a cheese plant for more than a year. The other four genomes were related but notably different. The length of the genomes varied from 28,144 to 32,182 bp, and they coded for 51 to 55 open reading frames. All five genomes possessed a 3′ overhang cos site that was 11 nucleotides long. Several structural proteins were also identified by nano-high-performance liquid chromatography-tandem mass spectrometry, confirming bioinformatic analyses. Comparative analyses suggested that the most recently isolated phages (CB19 and CB20) were derived, in part, from older phage isolates (CB13 and CB14/GR7). The organization of the five distinct genomes was similar to the previously sequenced lactococcal phage genomes of the 936 group, and from these sequences, a core genome was determined for lactococcal phages of the 936 group.

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