Characterization of Two Virulent Phages of Lactobacillus plantarum

ABSTRACTWe characterized twoLactobacillus plantarumvirulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eightL. plantarumstrains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least twoL. plantarumstrains, LMG9211 and WCSF1. The linear double-stranded DNA genome of thepac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that ofPediococcus damnosusphage clP1 and 77% identity with that ofL. plantarumphage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of thecos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those ofBacillusandLactobacillusstrains as well as phages. Some phage B2 genes were similar to ORFs fromL. plantarumphage LP65 of theMyoviridaefamily. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.

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Isolation and Characterization of Gardnerella Phage vB_Gva_AB1, a Bacteriophage Infecting a Clinical Strain of Gardnerella vaginalis

Microbiology Resource Announcements ◽

10.1128/mra.00053-21 ◽

2021 ◽

Vol 10 (12) ◽

Author(s):

Alexia Bordigoni ◽

Sonia Bouchard ◽

Christelle Desnues

Keyword(s):

Bacterial Vaginosis ◽

Gc Content ◽

Open Reading Frames ◽

Gardnerella Vaginalis ◽

Clinical Strain ◽

Content Type ◽

Isolation And Characterization ◽

Double Stranded Dna ◽

Reading Frames

ABSTRACT Gardnerella vaginalis is the presumed causative agent of bacterial vaginosis. Here, we describe the complete genome sequence of Gardnerella phage vB_Gva_AB1, induced from a vaginal bacterial strain from a woman suffering with bacterial vaginosis. The phage double-stranded DNA (dsDNA) genome is 50,268 bp long with a GC content of 39.55% and contains 62 predicted open reading frames.

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Bacteriophages LIMElight and LIMEzero of Pantoea agglomerans, Belonging to the “phiKMV-Like Viruses”

Applied and Environmental Microbiology ◽

10.1128/aem.00128-11 ◽

2011 ◽

Vol 77 (10) ◽

pp. 3443-3450 ◽

Cited By ~ 35

Author(s):

Evelien M. Adriaenssens ◽

Pieter-Jan Ceyssens ◽

Vincent Dunon ◽

Hans-Wolfgang Ackermann ◽

Johan Van Vaerenbergh ◽

...

Keyword(s):

Soil Samples ◽

Pantoea Agglomerans ◽

Open Reading Frames ◽

Human Pathogen ◽

Content Type ◽

Host Diversity ◽

Double Stranded Dna ◽

Opportunistic Human Pathogen ◽

Reading Frames

ABSTRACTPantoea agglomeransis a common soil bacterium used in the biocontrol of fungi and bacteria but is also an opportunistic human pathogen. It has been described extensively in this context, but knowledge of bacteriophages infecting this species is limited. Bacteriophages LIMEzero and LIMElight ofP. agglomeransare lytic phages, isolated from soil samples, belonging to thePodoviridaeand are the firstPantoeaphages of this family to be described. The double-stranded DNA (dsDNA) genomes (43,032 bp and 44,546 bp, respectively) encode 57 and 55 open reading frames (ORFs). Based on the presence of an RNA polymerase in their genomes and their overall genome architecture, these phages should be classified in the subfamily of theAutographivirinae, within the genus of the “phiKMV-like viruses.” Phylogenetic analysis of all the sequenced members of theAutographivirinaesupports the classification of phages LIMElight and LIMEzero as members of the “phiKMV-like viruses” and corroborates the subdivision into the different genera. These data expand the knowledge ofPantoeaphages and illustrate the wide host diversity of phages within the “phiKMV-like viruses.”

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Genome Sequence of a T4-like Phage, Escherichia Phage vB_EcoM-Sa45lw, Infecting Shiga Toxin-Producing Escherichia coli Strains

Microbiology Resource Announcements ◽

10.1128/mra.00804-19 ◽

2019 ◽

Vol 8 (32) ◽

Author(s):

Yen-Te Liao ◽

Yujie Zhang ◽

Alexandra Salvador ◽

Vivian C. H. Wu

Keyword(s):

Escherichia Coli ◽

Surface Water ◽

Genome Size ◽

Shiga Toxin ◽

Open Reading Frames ◽

Content Type ◽

E Coli ◽

Double Stranded Dna ◽

A Genome ◽

Reading Frames

Escherichia phage vB_EcoM-Sa45lw, a new member of the T4-like phages, was isolated from surface water in a produce-growing area. The phage, containing double-stranded DNA with a genome size of 167,353 bp and 282 predicted open reading frames (ORFs), is able to infect generic Escherichia coli and Shiga toxin-producing E. coli O45 and O157 strains.

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Characterization of the Enterobacter Phage vB_EclM_CIP9

Microbiology Resource Announcements ◽

10.1128/mra.01600-19 ◽

2020 ◽

Vol 9 (13) ◽

Author(s):

Klara Wang ◽

Marielou G. Tamayo ◽

Tiffany V. Penner ◽

Bradley W. M. Cook ◽

Deborah A. Court ◽

...

Keyword(s):

Enterobacter Cloacae ◽

Opportunistic Pathogen ◽

Multidrug Resistant ◽

Open Reading Frames ◽

Resistant Isolate ◽

Content Type ◽

Hospital Acquired Infections ◽

Hospital Acquired ◽

Reading Frames

Enterobacter cloacae is an opportunistic pathogen that causes hospital-acquired infections in immunocompromised patients. Here, we describe vB_EclM_CIP9, a novel Enterobacter phage that infects a multidrug-resistant isolate of E. cloacae. Phage vB_EclM_CIP9 is a myovirus that has a 174,924-bp genome, with 296 predicted open reading frames.

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Complete Genome Sequence of Salmonella Bacteriophage SS3e

Journal of Virology ◽

10.1128/jvi.01550-12 ◽

2012 ◽

Vol 86 (18) ◽

pp. 10253-10254 ◽

Cited By ~ 12

Author(s):

Sung-Hun Kim ◽

Jeong-Hyun Park ◽

Bok-Kwon Lee ◽

Hyuk-Joon Kwon ◽

Ji-Hyun Shin ◽

...

Keyword(s):

Escherichia Coli ◽

Sequence Analysis ◽

Genomic Sequence ◽

Enterobacter Cloacae ◽

Open Reading Frames ◽

Lytic Bacteriophage ◽

Content Type ◽

Double Stranded Dna ◽

Genomic Sequence Analysis ◽

Reading Frames

ASalmonellalytic bacteriophage, SS3e, was isolated, and its genome was sequenced completely. This phage is able to lyse not only variousSalmonellaserovars but alsoEscherichia coli,Shigella sonnei,Enterobacter cloacae, andSerratia marcescens, indicating a broad host specificity. Genomic sequence analysis of SS3e revealed a linear double-stranded DNA sequence of 40,793 bp harboring 58 open reading frames, which is highly similar toSalmonellaphages SETP13 and MB78.

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Genome Sequence of the Broad-Host-Range Pseudomonas Phage Φ-S1

Journal of Virology ◽

10.1128/jvi.01605-12 ◽

2012 ◽

Vol 86 (18) ◽

pp. 10239-10239 ◽

Cited By ~ 9

Author(s):

Sanna Sillankorva ◽

Andrew M. Kropinski ◽

Joana Azeredo

Keyword(s):

Host Range ◽

Genome Sequence ◽

Open Reading Frames ◽

Broad Host Range ◽

Content Type ◽

Double Stranded Dna ◽

The Family ◽

Reading Frames

The broad-host-range lyticPseudomonasphage Φ-S1 possess a 40,192 bp double-stranded DNA (dsDNA) genome of 47 open reading frames (ORFs) and belongs to the familyPodoviridae, subfamilyAutographivirinae, genusT7likevirus.

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A Virulent Phage Infecting Lactococcus garvieae, with Homology to Lactococcus lactis Phages

Applied and Environmental Microbiology ◽

10.1128/aem.02603-15 ◽

2015 ◽

Vol 81 (24) ◽

pp. 8358-8365 ◽

Cited By ~ 4

Author(s):

Giovanni Eraclio ◽

Denise M. Tremblay ◽

Alexia Lacelle-Côté ◽

Simon J. Labrie ◽

Maria Grazia Fortina ◽

...

Keyword(s):

Lactococcus Lactis ◽

Common Ancestor ◽

Burst Size ◽

Open Reading Frames ◽

Content Type ◽

Virulent Phage ◽

Lactococcus Garvieae ◽

Double Stranded Dna ◽

Compost Soil ◽

Reading Frames

ABSTRACTA new virulent phage belonging to theSiphoviridaefamily and able to infectLactococcus garvieaestrains was isolated from compost soil. Phage GE1 has a prolate capsid (56 by 38 nm) and a long noncontractile tail (123 nm). It had a burst size of 139 and a latent period of 31 min. Its host range was limited to only twoL. garvieaestrains out of 73 tested. Phage GE1 has a double-stranded DNA genome of 24,847 bp containing 48 predicted open reading frames (ORFs). Putative functions could be assigned to only 14 ORFs, and significant matches in public databases were found for only 17 ORFs, indicating that GE1 is a novel phage and its genome contains several new viral genes and encodes several new viral proteins. Of these 17 ORFs, 16 were homologous to deduced proteins of virulent phages infecting the dairy bacteriumLactococcus lactis, including previously characterized prolate-headed phages. Comparative genome analysis confirmed the relatedness ofL. garvieaephage GE1 toL. lactisphages c2 (22,172 bp) and Q54 (26,537 bp), although its genome organization was closer to that of phage c2. Phage GE1 did not infect any of the 58L. lactisstrains tested. This study suggests that phages infecting different lactococcal species may have a common ancestor.

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Complete Genome of a Novel Lytic Vibrio parahaemolyticus Phage VPp1 and Characterization of Its Endolysin for Antibacterial Activities

Journal of Food Protection ◽

10.4315/0362-028x.jfp-17-278 ◽

2018 ◽

Vol 81 (7) ◽

pp. 1117-1125 ◽

Cited By ~ 7

Author(s):

MENGZHE LI ◽

YANQIU JIN ◽

HONG LIN ◽

JINGXUE WANG ◽

XIUPING JIANG

Keyword(s):

Vibrio Parahaemolyticus ◽

Foodborne Pathogen ◽

Antibacterial Activities ◽

Nucleotide Metabolism ◽

Open Reading Frames ◽

Bacterial Cells ◽

Control Groups ◽

Double Stranded Dna ◽

Reading Frames

ABSTRACT Vibrio parahaemolyticus is an important foodborne pathogen that is generally transmitted via raw or undercooked seafood. Endolysins originating from bacteriophages offer a new way to control bacterial pathogens. The objectives of this study were to sequence a novel lytic V. parahaemolyticus phage VPp1 and determine the antibacterial activities of the recombinant endolysin (LysVPp1) derived from this phage. The complete VPp1 genome contained a double-stranded DNA of 50,431 bp with a total G+C content of 41.35%. The genome was predicted to encode 67 open reading frames (ORFs), which were organized as nucleotide metabolism, replication, structure, packaging, lysis, and some additional functions. Two tRNAs were encoded to carry anticodons UGG and CCA. Among the functional proteins, ORF33 was deduced to encode endolysin, whereas no holin/antiholin or Rz/Rz1 lysis gene equivalents were found in the VPp1 genome. ORF33 was cloned and expressed. The endolysin LysVPp1 could lyse 9 of 12 V. parahaemolyticus strains, showing its relatively broader host spectrum than phage VPp1, which lysed only 3 of 12 V. parahaemolyticus strains. Furthermore, for EDTA-pretreated bacterial cells, the optical density of the LysVPp1 treatment group decreased by 0.4 at 450 nm, compared with less than 0.1 in control groups, demonstrating enhanced hydrolytic properties. These results contribute to the potential for development of novel enzybiotics for controlling V. parahaemolyticus.

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Genetic Characterization of Plasmid-Borne blaOXA-58 in Distinct Acinetobacter Species

mSphere ◽

10.1128/msphere.00376-19 ◽

2019 ◽

Vol 4 (5) ◽

Cited By ~ 10

Author(s):

Adriana P. Matos ◽

Rodrigo Cayô ◽

Luiz G. P. Almeida ◽

Ana Paula Streling ◽

Carolina S. Nodari ◽

...

Keyword(s):

Open Reading Frames ◽

South American ◽

Acinetobacter Species ◽

Content Type ◽

Clinical Strains ◽

Carbapenem Resistant ◽

Encoding Genes ◽

Reading Frames ◽

Over Time

ABSTRACT We characterize by whole-plasmid-sequence (WPS) two-plasmid-borne blaOXA-58 obtained from Acinetobacter seifertii (Asp-1069) and A. baumannii (Acb-45063) clinical strains recovered 17 years apart from distinct Brazilian regions. Multilocus sequence type (MLST) analysis showed that the Asp-1069 and Acb-45063 strains belong to ST551 and ST15/CC15, respectively. WPS analysis demonstrated that blaOXA-58 was located in two distinct plasmids named pAs1069_a (24,672 bp/44 open reading frames [ORFs]) and pAb45063_b (19,808 bp/24 ORFs), which belong to the GR8/GR23 (repAci23) and GR4 (repAci4) incompatibility groups, respectively. The genetic environments surrounding blaOXA-58 revealed that it was flanked by two intact ISAba3 copies on pAb45063_b, which differed from pAs1069_a. In the latter, the upstream ISAba3 copy was truncated by insertion of ISAba825 element. Although Re27-specific recombination sites were found adjacent to ISAba3-blaOXA-58-ISAba3 arrangement on pAb45063_b, such structures were absent on pAs1069_a. The conserved ISAba125-araC1-lysE arrangement was disrupted by TnaphA6 harboring the aminoglycosides resistance gene aphA6 on pAs1069_a, while an IS26-blaTEM-1-aac(3)-IIa-IS26 genetic structure was found upstream from ISAba3-blaOXA-58-ISAba3 on pAb45063_b. Other two plasmids, pAb45063_a (183,767 bp/209 ORFs) and pAs1069_b (13,129 bp/14 ORFs), were also found in the OXA-58-producing Acinetobacter species strains, harboring the strA and strB genes and the sul2 gene, which confer resistance to streptomycin and sulfonamides, respectively. The plasmid-mediated virulence factors corresponding to genes tonB, spl, glmM, ppa, sulP, and map were found in both strains, as well distinct toxin-antitoxin system-encoding genes stbD and relE (pAs1069_a), brnT and brnA (pAb45063_b), and xreE (pAb45063_a). Although infrequently reported in Brazil, plasmid-borne blaOXA-58 showed a complex and diverse genetic backbone that confers stability in different Acinetobacter species that have been isolated from nosocomial settings over time. IMPORTANCE Although the blaOXA-58 gene has been infrequently described in Brazil, contrasting with other bordering South American countries, we verified the maintenance of this resistance determinant over time among carbapenem-resistant Acinetobacter species isolates, not only in nosocomial settings but also in the environment. In addition, to the best of our knowledge, this is the first study to have used WPS analysis to evaluate the genetic surroundings of blaOXA-58 in Brazil. Moreover, the A. seifertii and A. baumannii clinical strains evaluated in this study were recovered 17 years apart in hospitals located in distinct Brazilian geographic regions.

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Complete Genome Sequence of Acinetobacter baumannii Phage BS46

Microbiology Resource Announcements ◽

10.1128/mra.00398-20 ◽

2020 ◽

Vol 9 (22) ◽

Author(s):

Anastasia V. Popova ◽

Mikhail M. Shneider ◽

Yulia V. Mikhailova ◽

Andrey A. Shelenkov ◽

Dmitry A. Shagin ◽

...

Keyword(s):

Complete Genome Sequence ◽

Complete Genome ◽

Open Reading Frames ◽

Capsular Polysaccharides ◽

Bacterial Host ◽

Gene Encoding ◽

Content Type ◽

Double Stranded Dna ◽

A Genome ◽

Reading Frames

ABSTRACT Acinetobacter myovirus BS46 was isolated from sewage by J. S. Soothill in 1991. We have sequenced the genome of BS46 and found it to be almost unique. BS46 contains double-stranded DNA with a genome size of 94,068 bp and 176 predicted open reading frames. The gene encoding the tailspike that presumably possesses depolymerase activity toward the capsular polysaccharides of the bacterial host was identified.

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