scholarly journals A Novel Benthic Phage Infecting Shewanella with Strong Replication Ability

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1081 ◽  
Author(s):  
Zengmeng Wang ◽  
Jiulong Zhao ◽  
Long Wang ◽  
Chengcheng Li ◽  
Jianhui Liu ◽  
...  
Keyword(s):  
Burst Size ◽  
Coastal Sediments ◽  
The Yellow Sea ◽  
Comparative Genomic ◽  
Lytic Phage ◽  
Host Interactions ◽  
Metabolic Genes ◽  
Double Stranded Dna ◽  
Auxiliary Metabolic Genes ◽  
Structure Assembly

The coastal sediments were considered to contain diverse phages playing important roles in driving biogeochemical cycles based on genetic analysis. However, till now, benthic phages in coastal sediments were very rarely isolated, which largely limits our understanding of their biological characteristics. Here, we describe a novel lytic phage (named Shewanella phage S0112) isolated from the coastal sediments of the Yellow Sea infecting a sediment bacterium of the genus Shewanella. The phage has a very high replication capability, with the burst size of ca. 1170 phage particles per infected cell, which is 5–10 times higher than that of most phages isolated before. Meanwhile, the latent period of this phage is relatively longer, which might ensure adequate time for phage replication. The phage has a double-stranded DNA genome comprising 62,286 bp with 102 ORFs, ca. 60% of which are functionally unknown. The expression products of 16 ORF genes, mainly structural proteins, were identified by LC-MS/MS analysis. Besides the general DNA metabolism and structure assembly genes in the phage genome, there is a cluster of auxiliary metabolic genes that may be involved in 7-cyano-7-deazaguanine (preQ0) biosynthesis. Meanwhile, a pyrophosphohydrolase (MazG) gene being considered as a regulator of programmed cell death or involving in host stringer responses is inserted in this gene cluster. Comparative genomic and phylogenetic analysis both revealed a great novelty of phage S0112. This study represents the first report of a benthic phage infecting Shewanella, which also sheds light on the phage–host interactions in coastal sediments.

scholarly journals Genome Analysis of Two Novel Synechococcus Phages That Lack Common Auxiliary Metabolic Genes: Possible Reasons and Ecological Insights by Comparative Analysis of Cyanomyoviruses

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 800
Author(s):  
Tong Jiang ◽  
Cui Guo ◽  
Min Wang ◽  
Meiwen Wang ◽  
Xinran Zhang ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Open Reading Frames ◽  
The Yellow Sea ◽  
Comparative Genomic ◽  
Genomic Context ◽  
Phytoplankton Primary Production ◽  
Metabolic Genes ◽  
Ecological Features ◽  
Auxiliary Metabolic Genes ◽  
Reading Frames

The abundant and widespread unicellular cyanobacteria Synechococcus plays an important role in contributing to global phytoplankton primary production. In the present study, two novel cyanomyoviruses, S-N03 and S-H34 that infected Synechococcus MW02, were isolated from the coastal waters of the Yellow Sea. S-N03 contained a 167,069-bp genome comprising double-stranded DNA with a G + C content of 50.1%, 247 potential open reading frames and 1 tRNA; S-H34 contained a 167,040-bp genome with a G + C content of 50.1%, 246 potential open reading frames and 5 tRNAs. These two cyanophages contain fewer auxiliary metabolic genes (AMGs) than other previously isolated cyanophages. S-H34 in particular, is currently the only known cyanomyovirus that does not contain any AMGs related to photosynthesis. The absence of such common AMGs in S-N03 and S-H34, their distinct evolutionary history and ecological features imply that the energy for phage production might be obtained from other sources rather than being strictly dependent on the maintenance of photochemical ATP under high light. Phylogenetic analysis showed that the two isolated cyanophages clustered together and had a close relationship with two other cyanophages of low AMG content. Comparative genomic analysis, habitats and hosts across 81 representative cyanomyovirus showed that cyanomyovirus with less AMGs content all belonged to Synechococcus phages isolated from eutrophic waters. The relatively small genome size and high G + C content may also relate to the lower AMG content, as suggested by the significant correlation between the number of AMGs and G + C%. Therefore, the lower content of AMG in S-N03 and S-H34 might be a result of viral evolution that was likely shaped by habitat, host, and their genomic context. The genomic content of AMGs in cyanophages may have adaptive significance and provide clues to their evolution.

A moderately halophilic Vibrio from a Spanish saltern and its lytic bacteriophage

1996 ◽  
Vol 42 (10) ◽  
pp. 1015-1023 ◽  
Author(s):  
Usha Goel ◽  
Tiiu Kauri ◽  
Donn J. Kushner ◽  
Hans-W. Ackermann
Keyword(s):  
Burst Size ◽  
Lytic Phage ◽  
Host Bacterium ◽  
Lytic Bacteriophage ◽  
Moderate Halophile ◽  
Double Stranded Dna ◽  
Halophilic Archaebacteria ◽  
Water Salt ◽  
Inhibitory Agents ◽  
Number Of Bacteria

A number of bacteria and their phages were isolated from a saltern near Alicante, Spain. One isolate, Vibrio B1, a moderate halophile that is probably a strain of Vibrio costicola, was host to a lytic phage, UTAK. Studies of the host bacterium included the effects of salt concentrations on the action of a number of inhibitory agents. Phage UTAK has a head, a tail, and a baseplate. It contains 80 kbp of double-stranded DNA with no unusual bases. It was stable for long periods in the absence of high salt concentrations and even in distilled water. Salt concentrations had little effect on adsorption of UTAK to its host but resulted in considerable changes in burst size. It appears that phages of halophilic and salt-tolerant eubacteria, and also of some marine bacteria, have much lower salt requirements for stability than the phages of halophilic archaebacteria. Our results suggest that ionic controls of phage replication in these eubacteria may differ from those of growth.Key words: halophiles, Vibrio sp., bacteriophage, salt responses.

scholarly journals Vibrio vulnificus Bacteriophage SSP002 as a Possible Biocontrol Agent

2013 ◽  
Vol 80 (2) ◽  
pp. 515-524 ◽  
Author(s):  
Hyun Sung Lee ◽  
Slae Choi ◽  
Hakdong Shin ◽  
Ju-Hoon Lee ◽  
Sang Ho Choi
Keyword(s):  
Vibrio Vulnificus ◽  
Burst Size ◽  
Genomic Analysis ◽  
The Yellow Sea ◽  
Comparative Genomic ◽  
Specific Gene ◽  
Growth Curve Analysis ◽  
Range Analysis ◽  
Content Type ◽  
One Step

ABSTRACTA novelVibrio vulnificus-infecting bacteriophage, SSP002, belonging to theSiphoviridaefamily, was isolated from the coastal area of the Yellow Sea of South Korea. Host range analysis revealed that the growth inhibition of phage SSP002 is relatively specific toV. vulnificusstrains from both clinical and environmental samples. In addition, a one-step growth curve analysis and a bacteriophage stability test revealed a latent period of 65 min, a burst size of 23 ± 2 PFU, as well as broad temperature (20°C to 60°C) and pH stability (pH 3 to 12) ranges. A Tn5random transposon mutation ofV. vulnificusand partial DNA sequencing of the inserted Tn5regions revealed that theflhA,flhB,fliF, andfleQmutants are resistant to SSP002 phage infection, suggesting that the flagellum may be the host receptor for infection. The subsequent construction of specific gene-inactivated mutants (flhA,flhB,fliF, andfleQ) and complementation experiments substantiated this. Previously, the genome of phage SSP002 was completely sequenced and analyzed. Comparative genomic analysis of phage SSP002 andVibrio parahaemolyticusphage vB_VpaS_MAR10 showed differences among their tail-related genes, supporting different host ranges at the species level, even though their genome sequences are highly similar. An additional mouse survival test showed that the administration of phage SSP002 at a multiplicity of infection of 1,000 significantly protects mice from infection byV. vulnificusfor up to 2 months, suggesting that this phage may be a good candidate for the development of biocontrol agents againstV. vulnificusinfection.

scholarly journals Lytic Myophage Abp53 Encodes Several Proteins Similar to Those Encoded by Host Acinetobacter baumannii and Phage phiKO2

2011 ◽  
Vol 77 (19) ◽  
pp. 6755-6762 ◽  
Author(s):  
Chia-Ni Lee ◽  
Tsai-Tien Tseng ◽  
Juey-Wen Lin ◽  
Yung-Chieh Fu ◽  
Shu-Fen Weng ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Burst Size ◽  
Sputum Sample ◽  
Polyacrylamide Gel Electrophoresis ◽  
Multiple Drug ◽  
Lytic Phage ◽  
Tail Fiber ◽  
Drug Resistant ◽  
Content Type ◽  
Multiple Drug Resistant

ABSTRACTAcinetobacter baumanniiis an important Gram-negative opportunistic pathogen causing nosocomial infections. The emergence of multiple-drug-resistantA. baumanniiisolates has increased in recent years. Directed toward phage therapy, a lytic phage ofA. baumannii, designated Abp53, was isolated from a sputum sample in this study. Abp53 has an isometric head and a contractile tail with tail fibers (belonging toMyoviridae), a latent period of about 10 min, and a burst size of approximately 150 PFU per infected cell. Abp53 could completely lyse 27% of theA. baumanniiisolates tested, which were all multiple drug resistant, but not other bacteria. Mg2+enhanced the adsorption and productivity of, and host lysis by, Abp53. Twenty Abp53 virion proteins were visualized in SDS-polyacrylamide gel electrophoresis, with a 47-kDa protein being the predicted major capsid protein. Abp53 has a double-stranded DNA genome of 95 kb. Sequence analyses of a 10-kb region revealed 8 open reading frames. Five of the encoded proteins, including 3 tail components and 2 hypothetical proteins, were similar to proteins encoded byA. baumanniistrain ACICU. ORF1176 (one of the tail components, 1,176 amino acids [aa]), which is also similar to tail protein gp21 ofKlebsiellaphage phiKO2, contained repeated domains similar to those within the ACICU_02717 protein ofA. baumanniiACICU and gp21. These findings suggest a common ancestry and horizontal gene transfer during evolution. As phages can expand the host range by domain duplication in tail fiber proteins, repeated domains in ORF1176 might have a similar significance in Abp53.

scholarly journals Characterization and Full Genome Sequence of Novel KPP-5 Lytic Phage against Klebsiella pneumoniae Responsible for Recalcitrant Infection

Biomedicines ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 342
Author(s):  
Ahmed R. Sofy ◽  
Noha K. El-Dougdoug ◽  
Ehab E. Refaey ◽  
Rehab A. Dawoud ◽  
Ahmed A. Hmed
Keyword(s):  
Klebsiella Pneumoniae ◽  
Burst Size ◽  
Phylogenetic Analyses ◽  
Foodborne Pathogen ◽  
Gc Content ◽  
Full Genome Sequence ◽  
Multiple Drug ◽  
Lytic Phage ◽  
Trna Genes ◽  
Bacteriophage Therapy

Klebsiella pneumoniae is a hazardous opportunistic pathogen that is involved in many serious human diseases and is considered to be an important foodborne pathogen found in many food types. Multidrug resistance (MDR) K. pneumoniae strains have recently spread and increased, making bacteriophage therapy an effective alternative to multiple drug-resistant pathogens. As a consequence, this research was conducted to describe the genome and basic biological characteristics of a novel phage capable of lysing MDR K. pneumoniae isolated from food samples in Egypt. The host range revealed that KPP-5 phage had potent lytic activity and was able to infect all selected MDR K. pneumoniae strains from different sources. Electron microscopy images showed that KPP-5 lytic phage was a podovirus morphology. The one-step growth curve exhibited that KPP-5 phage had a relatively short latent period of 25 min, and the burst size was about 236 PFU/infected cells. In addition, KPP-5 phage showed high stability at different temperatures and pH levels. KPP-5 phage has a linear dsDNA genome with a length of 38,245 bp with a GC content of 50.8% and 40 predicted open reading frames (ORFs). Comparative genomics and phylogenetic analyses showed that KPP-5 is most closely associated with the Teetrevirus genus in the Autographviridae family. No tRNA genes have been identified in the KPP-5 phage genome. In addition, phage-borne virulence genes or drug resistance genes were not present, suggesting that KPP-5 could be used safely as a phage biocontrol agent.

scholarly journals Individuals at risk for developing rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential

2021 ◽  
Author(s):  
Mihnea R. Mangalea ◽  
David Paez-Espino ◽  
Kristopher Kieft ◽  
Anushila Chatterjee ◽  
Jennifer A. Seifert ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
At Risk ◽  
Autoimmune Disease ◽  
Intestinal Microbiota ◽  
Disease Development ◽  
Metabolic Potential ◽  
Metabolic Genes ◽  
Auxiliary Metabolic Genes ◽  
Citrullinated Protein ◽  
Insight Into

SUMMARYRheumatoid arthritis (RA) is an autoimmune disease characterized in seropositive individuals by the presence of anti-cyclic citrullinated protein (CCP) antibodies. RA is linked to the intestinal microbiota, yet the association of microbes with CCP serology and their contribution to RA is unclear. We describe intestinal phage communities of individuals at risk for developing RA, with or without anti-CCP antibodies, whose first degree relatives have been diagnosed with RA. We show that at-risk individuals harbor intestinal phage compositions that diverge based on CCP serology, are dominated by Lachnospiraceae phages, and originate from disparate ecosystems. These phages encode unique repertoires of auxiliary metabolic genes (AMGs) which associate with anti-CCP status, suggesting that these phages directly influence the metabolic and immunomodulatory capability of the microbiota. This work sets the stage for the use of phages as preclinical biomarkers and provides insight into a possible microbial-based causation of RA disease development.

scholarly journals Interactions between the Prophage 919TP and Its Vibrio cholerae Host: Implications of gmd Mutation for Phage Resistance, Cell Auto-Aggregation, and Motility

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2342
Author(s):  
Na Li ◽  
Yigang Zeng ◽  
Bijie Hu ◽  
Tongyu Zhu ◽  
Sine Lo Svenningsen ◽  
...  
Keyword(s):  
Bacterial Pathogen ◽  
Genomic Analysis ◽  
Resistant Mutant ◽  
Resistance Mechanisms ◽  
Phage Resistance ◽  
Comparative Genomic ◽  
Lytic Phage ◽  
O Antigen ◽  
Trade Offs ◽  
Base Pair Deletion

Prophage 919TP is widely distributed among Vibrio cholera and is induced to produce free φ919TP phage particles. However, the interactions between prophage φ919TP, the induced phage particle, and its host remain unknown. In particular, phage resistance mechanisms and potential fitness trade-offs, resulting from phage resistance, are unresolved. In this study, we examined a prophage 919TP-deleted variant of V. cholerae and its interaction with a modified lytic variant of the induced prophage (φ919TP cI-). Specifically, the phage-resistant mutant was isolated by challenging a prophage-deleted variant with lytic phage φ919TP cI-. Further, the comparative genomic analysis of wild-type and φ919TP cI--resistant mutant predicted that phage φ919TP cI- selects for phage-resistant mutants harboring a mutation in key steps of lipopolysaccharide (LPS) O-antigen biosynthesis, causing a single-base-pair deletion in gene gmd. Our study showed that the gmd-mediated O-antigen defect can cause pleiotropic phenotypes, e.g., cell autoaggregation and reduced swarming motility, emphasizing the role of phage-driven diversification in V. cholerae. The developed approach assists in the identification of genetic determinants of host specificity and is used to explore the molecular mechanism underlying phage-host interactions. Our findings contribute to the understanding of prophage-facilitated horizontal gene transfer and emphasize the potential for developing new strategies to optimize the use of phages in bacterial pathogen control.

scholarly journals Characterization of a New and Efficient Polyvalent Phage Infecting E. coli O157:H7, Salmonella spp., and Shigella sonnei

2021 ◽  
Vol 9 (10) ◽  
pp. 2105
Author(s):  
Su-Hyeon Kim ◽  
Damilare Adeyemi ◽  
Mi-Kyung Park
Keyword(s):  
Burst Size ◽  
Genomic Analysis ◽  
Cesium Chloride ◽  
Shigella Sonnei ◽  
Health Concern ◽  
Lytic Phage ◽  
Salmonella Spp ◽  
E Coli ◽  
Significant Public Health ◽  
Ph Range

Ongoing outbreaks of foodborne diseases remain a significant public health concern. Lytic phages provide promising attributes as biocontrol agents. This study characterized KFS-EC3, a polyvalent and lytic phage, which was isolated from slaughterhouse sewage and purified by cesium chloride density centrifugation. Host range and efficiency of plating analyses revealed that KFS-EC3 is polyvalent and can efficiently infect E. coli O157:H7, Salmonella spp., and Shigella sonnei. KFS-EC3 had a latent time of 20 min and burst size of ~71 phages/infected cell. KFS-EC3 was stable and infectious following storage at a pH range of 3 to 11 and a temperature range of −70°C to 60°C. KFS-EC3 could inhibit E. coli O157:H7 growth by 2 logs up to 52 h even at the lowest MOI of 0.001. Genomic analysis of KFS-EC3 revealed that it consisted of 167,440 bp and 273 ORFs identified as functional genes, without any genes associated with antibiotic resistance, virulence, allergenicity, and lysogenicity. This phage was finally classified into the Tequatrovirus genus of the Myoviridae family. In conclusion, KFS-EC3 could simultaneously infect E. coli O157:H7, S. sonnei, and Salmonella spp. with the lowest MOI values over long periods, suggesting its suitability for simultaneous pathogen control in foods.

scholarly journals The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses

Virology ◽  
2016 ◽  
Vol 499 ◽  
pp. 219-229 ◽  
Author(s):  
Lisa T. Crummett ◽  
Richard J. Puxty ◽  
Claudia Weihe ◽  
Marcia F. Marston ◽  
Jennifer B.H. Martiny
Keyword(s):  
Metabolic Genes ◽  
Auxiliary Metabolic Genes

Occurrence and microscopic analyses of multicellular magnetotactic prokaryotes from coastal sediments in the Yellow Sea

2011 ◽  
Vol 29 (2) ◽  
pp. 246-251 ◽  
Author(s):  
Ke Zhou ◽  
Hongmiao Pan ◽  
Shengda Zhang ◽  
Haidong Yue ◽  
Tian Xiao ◽  
...  
Keyword(s):  
Yellow Sea ◽  
Coastal Sediments ◽  
The Yellow Sea
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