Computational Tools for the Analysis of Uncultivated Phage Genomes

Andrade-Martínez, Juan S.; Valera, Laura Carolina Camelo; Cárdenas, Luis Alberto Chica; Forero-Junco, Laura; López-Leal, Gamaliel; Moreno-Gallego, Jaime Leonardo; Rangel-Piñeros, Guillermo; Reyes, Alejandro

doi:10.1128/mmbr.00004-21

Cited by 21 publications

(15 citation statements)

References 159 publications

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“…The BLAST tool of GenBank was used to identify phage species with comparable gene sequences. A phylogenetic tree was constructed for each phage BLAST result against the top 10 similar sequences identified in the NCBI database and the relative similarities among the isolated virus and other viruses identified in the BLAST result were determined [ 29 ].…”

Section: Methodsmentioning

confidence: 99%

Fully Characterized Effective Bacteriophages Specific against Antibiotic-Resistant Enterococcus faecalis, the Causative Agent of Dental Abscess

Ramadan,

Abdel-Monem,

El-Dougdoug

et al. 2024

Medicina

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Background and Objectives: Enterococcus faecalis (E. faecalis) is a primary pathogen responsible for dental abscesses, which cause inflammation and pain when trapped between the crown and soft tissues of an erupted tooth. Therefore, this study aims to use specific phages as an alternative method instead of classical treatments based on antibiotics to destroy multidrug-resistant E. faecalis bacteria for treating dental issues. Materials and Methods: In the current study, twenty-five bacterial isolates were obtained from infected dental specimens; only five had the ability to grow on bile esculin agar, and among these five, only two were described to be extensive multidrug-resistant isolates. Results: Two bacterial isolates, Enterococcus faecalis A.R.A.01 [ON797462.1] and Enterococcus faecalis A.R.A.02, were identified biochemically and through 16S rDNA, which were used as hosts for isolating specific phages. Two isolated phages were characterized through TEM imaging, which indicated that E. faecalis_phage-01 had a long and flexible tail, belonging to the family Siphoviridae, while E. faecalis_phage-02 had a contractile tail, belonging to the family Myoviridae. Genetically, two phages were identified through the PCR amplification and sequencing of the RNA ligase of Enterococcus phage vB_EfaS_HEf13, through which our phages shared 97.2% similarity with Enterococcus phage vB-EfaS-HEf13 based on BLAST analysis. Furthermore, through in silico analysis and annotations of the two phages’ genomes, it was determined that a total of 69 open reading frames (ORFs) were found to be involved in various functions related to integration excision, replication recombination, repair, stability, and defense. In phage optimization, the two isolated phages exhibited a high specific host range with Enterococcus faecalis among six different bacterial hosts, where E. faecalis_phage-01 had a latent period of 30 min with 115.76 PFU/mL, while E. faecalis_phage-02 had a latent period of 25 min with 80.6 PFU/mL. They were also characterized with stability at wide ranges of pH (4–11) and temperature (10–60 °C), with a low cytotoxic effect on the oral epithelial cell line at different concentrations (1000–31.25 PFU/mL). Conclusions: The findings highlight the promise of phage therapy in dental medicine, offering a novel approach to combating antibiotic resistance and enhancing patient outcomes. Further research and clinical trials will be essential to fully understand the therapeutic potential and safety profile of these bacteriophages in human populations.

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Section: Methodsmentioning

confidence: 99%

Fully Characterized Effective Bacteriophages Specific against Antibiotic-Resistant Enterococcus faecalis, the Causative Agent of Dental Abscess

Ramadan,

Abdel-Monem,

El-Dougdoug

et al. 2024

Medicina

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“…Phages, as single entities, as cocktails, genetically engineered or as purified components, also play a role as alternatives or supplements to antimicrobial treatment to restrict infection by human and plant pathogens since almost a century (Parfitt, 2005; Lin et al ., 2017; Farooq et al ., 2022). Established phages are characterized in more detail and novel phages with unique characteristics are urgently sought with large uncultivated phage populations as a pool (Dion et al ., 2020; Kortright et al ., 2020; Andrade‐Martinez et al ., 2022; Busby et al ., 2022).…”

Section: Figmentioning

confidence: 99%

The power of unbiased phenotypic screens – cellulose as a first receptor for the Schitoviridae phage S6 of Erwinia amylovora

Römling

2022

Environmental Microbiology

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Summary Bacteriophages, host‐dependent replicative non‐cellular entities which significantly shape the microbial genomes and consequently physiological and ecological properties of the microbial populations are exploited to restrict plant, animal and human pathogens. Unravelling of phage characteristics aids the understanding of the basic molecular mechanisms of phage infections which can subsequently lead to the development of rationalized strategies to combat microbial pathogens. In an unbiased screen to investigate the molecular basis of infectivity of the fire blight pathogen Erwinia amylovora by the lytic Schitoviridae phage S6, the biofilm extracellular matrix component cellulose has been identified as a cyclic di‐GMP dependent first receptor required for infection with the phage to possess beta‐1,4‐glucosidases to degrade the exopolysaccharide. This absolute receptor dependency allows maintenance of a phage‐microbe equilibrium with a low bacterial density.

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“…In the past, identifying prophage regions was a computational challenge due to the limited knowledge on phage sequence diversity. However, in recent years, the development of powerful computational tools, the growth of viral databases, and the combination of different tools have enabled efficient identification of prophage regions ( 19 ). As a result, the unveiling and characterization of phage and prophage populations is now possible ( 20 ).…”

Section: Introductionmentioning

confidence: 99%

Campylobacter prophage diversity reveals pervasive recombination between prophages from different Campylobacter species

Piña-González,

Castelán-Sánchez,

Hurtado-Ramírez

et al. 2024

Microbiol Spectr

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Prophages, bacteriophages integrated into bacterial genomes, play a critical role in the genetic diversity and evolution of bacterial species. In this study, we investigated the prophage population harbored in Campylobacter species. A total of 446 high-quality and complete genomes of Campylobacter isolated from different sources revealed 431 prophages. We analyzed the phylogenomic relationships between 490 phages and prophages, unveiling a wide diversity of undescribed prophages. Bacteriophage pangenomes revealed shared genetic repertoires among different phage genera. In addition, we found recombination events between prophages from different phage genera, mainly in prophages infecting Campylobacter jejuni and Campylobacter coli , showing distinct evolutionary histories in specific regions of the prophage genomes. Specifically, these regions showed variations in gene content, enrichment in structural genes and others in hypothetical proteins, genes involved in transcription, DNA-associated factors, and genes associated with lysis. Finally, Campylobacter prophages alter the host genetic repertoire by carrying virulence factors and antibiotic-resistance genes. IMPORTANCE Prophages play an important role in shaping the genetic diversity and evolution of their hosts. Acquisition or loss of prophages can lead to genomic variations, including changes in the bacterial phenotype promoted by recombination events, genetic repertoire exchanges and dissemination of virulence factors, and antibiotic resistance. By studying prophages in Campylobacter species, scientists can gain insights into the evolutionary patterns, pathogenicity mechanisms, epidemiology, and population dynamics of these species. This has implications for public health, antibiotic resistance surveillance, and the development of targeted therapeutic approaches.

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Computational Tools for the Analysis of Uncultivated Phage Genomes

Cited by 21 publications

References 159 publications

Fully Characterized Effective Bacteriophages Specific against Antibiotic-Resistant Enterococcus faecalis, the Causative Agent of Dental Abscess

Fully Characterized Effective Bacteriophages Specific against Antibiotic-Resistant Enterococcus faecalis, the Causative Agent of Dental Abscess

The power of unbiased phenotypic screens – cellulose as a first receptor for the Schitoviridae phage S6 of Erwinia amylovora

Campylobacter prophage diversity reveals pervasive recombination between prophages from different Campylobacter species

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