Bacteriophage Genomics

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Systems Microbiology".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 42035

Special Issue Editor

Leading Researcher, Department of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk State University, Novosibirsk, Russia
Interests: virus evolution; human bocavirus; complete genome
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Special Issue Information

Dear Colleagues,

Bacteriophages (or phages) are viruses of prokaryotes and are the most abundant biological entities known so far. The approximate size of the global phage population is more than 1031 phage particles, and recent studies have shown that bacteriophages play an important role in the biosphere. The natural genetic diversity of bacteriophage genomes is enormous, and their genome architectures are typically mosaic. This genetic diversity is first of all driven by the recombination between bacteriophage genomes and horizontal gene transfer from the host genomes. The evolution of bacteriophages is different for that of temperate and lytic phages and depends on the host and genetic structure of phages. Thus, the taxonomic classification of bacteriophages is a complex problem. At present, according to the International Committee on Taxonomy of Viruses (ICTV) and Bacterial and Archaeal Subcommittee (BAVS) within the ICTV, bacteriophages are classified by the type of nucleic acid, the structure of the virus capsid, etc. The number of bacteriophage families is constantly increasing as new objects are studied. Today, bacteriophages are classified into 3 orders (Petitvirales, Tubulavirales and Caudovirales) and 22 families. The vast majority of sequenced bacteriophage genomes belong to double-stranded DNA phages. The diversity of bacteriophage genomes is very large: Genome sizes range from 4 to almost 700 kb.

This Special Issue of Microorganisms will be dedicated to the topic of Bacteriophage Genomics. This includes but is not limited to the following themes: bacteriophage comparative genomics and proteomics, phage genome evolution, phage rates of mutation and recombination, isolation and characterization of new phages, genomics approach for identifying host-range determinants in bacteriophages, bacteriophage taxonomy, approaches to the artificial phage host range management, bacteriophage-mediated gene transfers, as well as other aspects of bacteriophage molecular biology.

Dr. Igor V. Babkin
Guest Editor

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Keywords

  • bacteriophage
  • comparative genomics
  • recombination
  • phylogeny
  • horizontal gene transfer

Published Papers (14 papers)

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13 pages, 17562 KiB  
Article
Isolation, Characterization, and Genomic Analysis of Three Novel E. coli Bacteriophages That Effectively Infect E. coli O18
by Fatma Abdelrahman, Nouran Rezk, Mohamed S. Fayez, Mohamed Abdelmoteleb, Reham Atteya, Mohamed Elhadidy and Ayman El-Shibiny
Microorganisms 2022, 10(3), 589; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10030589 - 09 Mar 2022
Cited by 16 | Viewed by 4649
Abstract
Escherichia coli (E. coli) is one of the most common pathogenic bacteria worldwide. Avian pathogenic E. coli (APEC) causes severe systemic disease in poultry (Colibacillosis), and accordingly, has an extreme risk to the poultry industry and public health worldwide. Due to [...] Read more.
Escherichia coli (E. coli) is one of the most common pathogenic bacteria worldwide. Avian pathogenic E. coli (APEC) causes severe systemic disease in poultry (Colibacillosis), and accordingly, has an extreme risk to the poultry industry and public health worldwide. Due to the increased rate of multi-drug resistance among these bacteria, it is necessary to find an alternative therapy to antibiotics to treat such infections. Bacteriophages are considered one of the best solutions. This study aimed to isolate, characterize, and evaluate the potential use of isolated bacteriophages to control E. coli infections in poultry. Three novel phages against E. coli O18 were isolated from sewage water and characterized in vitro. The genome size of the three phages was estimated to be 44,776 bp, and the electron microscopic analysis showed that they belonged to the Siphoviridae family, in the order Caudovirales. Phages showed good tolerance to a broad range of pH and temperature. The complete genomes of three phages were sequenced and deposited into the GenBank database. The closely related published genomes of Escherichia phages were identified using BLASTn alignment and phylogenetic trees. The prediction of the open reading frames (ORFs) identified protein-coding genes that are responsible for functions that have been assigned such as cell lysis proteins, DNA packaging proteins, structural proteins, and DNA replication/transcription/repair proteins. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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17 pages, 3097 KiB  
Article
Cryptic Prophages Contribution for Campylobacter jejuni and Campylobacter coli Introgression
by Luís Tanoeiro, Mónica Oleastro, Alexandra Nunes, Andreia T. Marques, Sílvia Vaz Duarte, João Paulo Gomes, António Pedro Alves Matos, Jorge M. B. Vítor and Filipa F. Vale
Microorganisms 2022, 10(3), 516; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10030516 - 26 Feb 2022
Cited by 5 | Viewed by 2070
Abstract
Campylobacter coli and C. jejuni, the causing agents of campylobacteriosis, are described to be undergoing introgression events, i.e., the transference of genetic material between different species, with some isolates sharing almost a quarter of its genome. The participation of phages in introgression [...] Read more.
Campylobacter coli and C. jejuni, the causing agents of campylobacteriosis, are described to be undergoing introgression events, i.e., the transference of genetic material between different species, with some isolates sharing almost a quarter of its genome. The participation of phages in introgression events and consequent impact on host ecology and evolution remain elusive. Three distinct prophages, named C. jejuni integrated elements 1, 2, and 4 (CJIE1, CJIE2, and CJIE4), are described in C. jejuni. Here, we identified two unreported prophages, Campylobacter coli integrated elements 1 and 2 (CCIE1 and CCIE2 prophages), which are C. coli homologues of CJIE1 and CJIE2, respectively. No induction was achieved for both prophages. Conversely, induction assays on CJIE1 and CJIE2 point towards the inducibility of these prophages. CCIE2-, CJIE1-, and CJIE4-like prophages were identified in a Campylobacter spp. population of 840 genomes, and phylogenetic analysis revealed clustering in three major groups: CJIE1-CCIE1, CJIE2-CCIE2, and CJIE4, clearly segregating prophages from C. jejuni and C. coli, but not from human- and nonhuman-derived isolates, corroborating the flowing between animals and humans in the agricultural context. Punctual bacteriophage host-jumps were observed in the context of C. jejuni and C. coli, and although random chance cannot be fully discarded, these observations seem to implicate prophages in evolutionary introgression events that are modulating the hybridization of C. jejuni and C. coli species. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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19 pages, 3191 KiB  
Article
Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing
by Katharina Willenbücher, Daniel Wibberg, Liren Huang, Marius Conrady, Patrice Ramm, Julia Gätcke, Tobias Busche, Christian Brandt, Ulrich Szewzyk, Andreas Schlüter, Jimena Barrero Canosa and Irena Maus
Microorganisms 2022, 10(2), 368; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020368 - 04 Feb 2022
Cited by 7 | Viewed by 3681
Abstract
The microbial biogas network is complex and intertwined, and therefore relatively stable in its overall functionality. However, if key functional groups of microorganisms are affected by biotic or abiotic factors, the entire efficacy may be impaired. Bacteriophages are hypothesized to alter the steering [...] Read more.
The microbial biogas network is complex and intertwined, and therefore relatively stable in its overall functionality. However, if key functional groups of microorganisms are affected by biotic or abiotic factors, the entire efficacy may be impaired. Bacteriophages are hypothesized to alter the steering process of the microbial network. In this study, an enriched fraction of virus-like particles was extracted from a mesophilic biogas reactor and sequenced on the Illumina MiSeq and Nanopore GridION sequencing platforms. Metagenome data analysis resulted in identifying 375 metagenome-assembled viral genomes (MAVGs). Two-thirds of the classified sequences were only assigned to the superkingdom Viruses and the remaining third to the family Siphoviridae, followed by Myoviridae, Podoviridae, Tectiviridae, and Inoviridae. The metavirome showed a close relationship to the phage genomes that infect members of the classes Clostridia and Bacilli. Using publicly available biogas metagenomic data, a fragment recruitment approach showed the widespread distribution of the MAVGs studied in other biogas microbiomes. In particular, phage sequences from mesophilic microbiomes were highly similar to the phage sequences of this study. Accordingly, the virus particle enrichment approach and metavirome sequencing provided additional genome sequence information for novel virome members, thus expanding the current knowledge of viral genetic diversity in biogas reactors. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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20 pages, 2922 KiB  
Article
In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health
by Anna-Ursula Happel, Brian R. Kullin, Hoyam Gamieldien, Heather B. Jaspan, Arvind Varsani, Darren Martin, Jo-Ann S. Passmore and Rémy Froissart
Microorganisms 2022, 10(2), 214; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020214 - 20 Jan 2022
Cited by 3 | Viewed by 2667
Abstract
While live biotherapeutics offer a promising approach to optimizing vaginal microbiota, the presence of functional prophages within introduced Lactobacillaceae strains could impact their safety and efficacy. We evaluated the presence of prophages in 895 publicly available Lactobacillaceae genomes using Phaster, Phigaro, Phispy, Prophet [...] Read more.
While live biotherapeutics offer a promising approach to optimizing vaginal microbiota, the presence of functional prophages within introduced Lactobacillaceae strains could impact their safety and efficacy. We evaluated the presence of prophages in 895 publicly available Lactobacillaceae genomes using Phaster, Phigaro, Phispy, Prophet and Virsorter. Prophages were identified according to stringent (detected by ≥4 methods) or lenient criteria (detected by ≥2 methods), both with >80% reciprocal sequence overlap. The stringent approach identified 448 prophages within 359 genomes, with 40.1% genomes harbouring at least one prophage, while the lenient approach identified 1671 prophages within 83.7% of the genomes. To confirm our in silico estimates in vitro, we tested for inducible prophages in 57 vaginally-derived and commercial Lactobacillaceae isolates and found inducible prophages in 61.4% of the isolates. We characterised the in silico predicted prophages based on weighted gene repertoire relatedness and found that most belonged to the Siphoviridae or Myoviridae families. ResFam and eggNOG identified four potential antimicrobial resistance genes within the predicted prophages. Our results suggest that while Lactobacillaceae prophages seldomly carry clinically concerning genes and thus unlikely a pose a direct risk to human vaginal microbiomes, their high prevalence warrants the characterisation of Lactobacillaceae prophages in live biotherapeutics. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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21 pages, 3341 KiB  
Article
Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates
by Andreia T. Marques, Luís Tanoeiro, Aida Duarte, Luisa Gonçalves, Jorge M. B. Vítor and Filipa F. Vale
Microorganisms 2021, 9(11), 2252; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112252 - 28 Oct 2021
Cited by 14 | Viewed by 3169
Abstract
Klebsiella pneumoniae is an increasing threat to public health and represents one of the most concerning pathogens involved in life-threatening infections. The resistant and virulence determinants are coded by mobile genetic elements which can easily spread between bacteria populations and co-evolve with its [...] Read more.
Klebsiella pneumoniae is an increasing threat to public health and represents one of the most concerning pathogens involved in life-threatening infections. The resistant and virulence determinants are coded by mobile genetic elements which can easily spread between bacteria populations and co-evolve with its genomic host. In this study, we present the full genomic sequences, insertion sites and phylogenetic analysis of 150 prophages found in 40 K. pneumoniae clinical isolates obtained from an outbreak in a Portuguese hospital. All strains harbored at least one prophage and we identified 104 intact prophages (69.3%). The prophage size ranges from 29.7 to 50.6 kbp, coding between 32 and 78 putative genes. The prophage GC content is 51.2%, lower than the average GC content of 57.1% in K. pneumoniae. Complete prophages were classified into three families in the order Caudolovirales: Myoviridae (59.6%), Siphoviridae (38.5%) and Podoviridae (1.9%). In addition, an alignment and phylogenetic analysis revealed nine distinct clusters. Evidence of recombination was detected within the genome of some prophages but, in most cases, proteins involved in viral structure, transcription, replication and regulation (lysogenic/lysis) were maintained. These results support the knowledge that prophages are diverse and widely disseminated in K. pneumoniae genomes, contributing to the evolution of this species and conferring additional phenotypes. Moreover, we identified K. pneumoniae prophages in a set of endolysin genes, which were found to code for proteins with lysozyme activity, cleaving the β-1,4 linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in the peptidoglycan network and thus representing genes with the potential for lysin phage therapy. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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16 pages, 4657 KiB  
Article
Genomic Characterization of a Prophage, Smhb1, That Infects Salinivibrio kushneri BNH Isolated from a Namib Desert Saline Spring
by Israel Olonade, Leonardo Joaquim van Zyl and Marla Trindade
Microorganisms 2021, 9(10), 2043; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9102043 - 28 Sep 2021
Cited by 5 | Viewed by 1881
Abstract
Recent years have seen the classification and reclassification of many viruses related to the model enterobacterial phage P2. Here, we report the identification of a prophage (Smhb1) that infects Salinivibrio kushneri BNH isolated from a Namib Desert salt pan (playa). Analysis of the [...] Read more.
Recent years have seen the classification and reclassification of many viruses related to the model enterobacterial phage P2. Here, we report the identification of a prophage (Smhb1) that infects Salinivibrio kushneri BNH isolated from a Namib Desert salt pan (playa). Analysis of the genome revealed that it showed the greatest similarity to P2-like phages that infect Vibrio species and showed no relation to any of the previously described Salinivibrio-infecting phages. Despite being distantly related to these Vibrio infecting phages and sharing the same modular gene arrangement as seen in most P2-like viruses, the nucleotide identity to its closest relatives suggest that, for now, Smhb1 is the lone member of the Peduovirus genus Playavirus. Although host range testing was not extensive and no secondary host could be identified for Smhb1, genomic evidence suggests that the phage is capable of infecting other Salinivibrio species, including Salinivibrio proteolyticus DV isolated from the same playa. Taken together, the analysis presented here demonstrates how adaptable the P2 phage model can be. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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10 pages, 3168 KiB  
Article
The Characterization of a Novel Phage, pPa_SNUABM_DT01, Infecting Pseudomonas aeruginosa
by Jun Kwon, Sang Wha Kim, Sang Guen Kim, Jeong Woo Kang, Won Joon Jung, Sung Bin Lee, Young Min Lee, Sib Sankar Giri, Cheng Chi and Se Chang Park
Microorganisms 2021, 9(10), 2040; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9102040 - 27 Sep 2021
Cited by 7 | Viewed by 2304
Abstract
The bacterial genus Pseudomonas is a common causative agent of infections in veterinary medicine. In this study, we focused on Pseudomonas aeruginosa canine otitis externa isolates. Due to prolonged antibiotic treatment of otitis externa, antibiotic resistance is common and has become a major [...] Read more.
The bacterial genus Pseudomonas is a common causative agent of infections in veterinary medicine. In this study, we focused on Pseudomonas aeruginosa canine otitis externa isolates. Due to prolonged antibiotic treatment of otitis externa, antibiotic resistance is common and has become a major complication. Many alternatives to antibiotics have been studied, with bacteriophages emerging as the most promising alternatives. Here, we isolated and characterized a novel phage, pPa_SNUABM_DT01, by investigating its morphology, growth, lysis kinetics, and genomic characteristics. Phages have a vigorous capacity to eliminate bacterial cells through bacterial lysis. This capacity is dependent on the multiplicity of infection (MOI), but even at low MOIs, the phage successfully inhibited bacterial regrowth. The phage genome was 265,520 bp in size and comprised 312 putative open reading frames (ORFs). Comparative genome analysis demonstrated that the phage is a novel species in Myoviridae. The nucleotide similarity was moderately high compared with the Pseudomonas virus, Noxifer. However, a phylogenetic analysis and a dot plot indicated that pPa_SNUABM_DT01 is not closely related to the Phikzvirus or Noxifervirus genus but, instead, belongs to a novel one. The genome comparisons also indicate that the phage, pPa_SNUABM_DT01, could be a novel genus. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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13 pages, 2436 KiB  
Article
Diverse Bacteriophages Infecting the Bacterial Striped Catfish Pathogen Edwardsiella ictaluri
by Tan-Trung Nguyen, Tran T. T. Xuan, To H. Ngoc, Le T. My Duyen, Tu Q. Vinh, Pham D. T. My, Hoang A. Hoang and Le P. Nga
Microorganisms 2021, 9(9), 1830; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091830 - 28 Aug 2021
Cited by 4 | Viewed by 2495
Abstract
Bacteriophages infecting Edwardsiella ictaluri have been less investigated, although the host bacterium is one of the most important fish pathogens causing enteric septicemia of catfish (ESC). We present here two distinctly novel bacteriophages vB_EiM_PVN06 and vB_EiA_PVN09 infecting Edwardsiella ictaluri E1, with their geographical [...] Read more.
Bacteriophages infecting Edwardsiella ictaluri have been less investigated, although the host bacterium is one of the most important fish pathogens causing enteric septicemia of catfish (ESC). We present here two distinctly novel bacteriophages vB_EiM_PVN06 and vB_EiA_PVN09 infecting Edwardsiella ictaluri E1, with their geographical origins from the Mekong Delta, Vietnam. Bacteriophage vB_EiM_PVN06 native to a mud sample reveals complete differences of biological properties with the phage vB_EiA_PVN09 originated from a viscus of a healthy catfish (Pangasianodon hypophthalmus) cultured in the same area. Morphological analyses combined with genomic data indicate that phage vB_EiM_PVN06 is classified to Myoviridae family and shares high similarity with E. ictaluri phage PEi21 genome, while vB_EiA_PVN09 is a member of Teseptimavirus genus, Autographiviridae family, and mostly closes to phage vB_EcoP_IME390. The vB_EiA_PVN09 is a T7-like bacteriophage, which has been firstly found infecting to E. ictaluri, and host range analysis also evidences for the cross-infection of this phage to Escherichia coli K12 and Escherichia coli DH5α. Together, our research highlights the diversity of bacteriophages infecting the pathogen E. ictaluri and suggests further explorations of lytic phages in environmental niches, to be exploited in feasible strategies of phage therapy in ESC disease control. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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11 pages, 2183 KiB  
Article
Complete Genome Sequence of vB_EcoP_SU7, a Podoviridae Coliphage with the Rare C3 Morphotype
by Shazeeda Koonjan, Callum J. Cooper and Anders S. Nilsson
Microorganisms 2021, 9(8), 1576; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081576 - 24 Jul 2021
Cited by 6 | Viewed by 2329
Abstract
Enterotoxigenic Escherichia coli (ETEC) strains are an important cause of bacterial diarrheal illness in humans and animals. Infections arising from ETEC could potentially be treated through the use of bacteriophage (phage) therapy, as phages encode for enzymes capable of bacterial cell lysis. vB_EcoP_SU7 [...] Read more.
Enterotoxigenic Escherichia coli (ETEC) strains are an important cause of bacterial diarrheal illness in humans and animals. Infections arising from ETEC could potentially be treated through the use of bacteriophage (phage) therapy, as phages encode for enzymes capable of bacterial cell lysis. vB_EcoP_SU7 was isolated from the Käppala wastewater treatment plant in Stockholm, Sweden, and propagated on an ETEC strain exhibiting the O:139 serovar. Transmission electron microscopy confirmed that vB_EcoP_SU7 belongs to the Podoviridae family and has the rare C3 morphotype of an elongated head. Bioinformatic analyses showed that the genome was 76,626 base pairs long and contained 35 genes with predicted functions. A total of 81 open reading frames encoding proteins with hypothetical function and two encoding proteins of no significant similarity were also found. A putative tRNA gene, which may aid in vB_EcoP_SU7’s translation, was also identified. Phylogenetic analyses showed that compared to other Podoviridae, vB_EcoP_SU7 is a rare Kuravirus and is closely related to E. coli phages with the uncommon C3 morphotype, such as ECBP2, EK010, vB_EcoP_EcoN5, and vB_EcoP_SU10. Phage vB_EcoP_SU7 has a narrow host range, infecting 11 out of the 137 E. coli strains tested, a latency period of 30 min, a burst size of 12 PFU/cell, and an adsorption rate of 8.78 × 10−9 mL/min five minutes post infection. With a limited host range and poor infection kinetics, it is unlikely that SU7 can be a standalone phage used for therapeutic purposes; rather, it must be used in combination with other phages for broad-spectrum therapeutic success. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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20 pages, 3784 KiB  
Article
Genome Characterization of Nocturne116, Novel Lactococcus lactis-Infecting Phage Isolated from Moth
by Nikita Zrelovs, Andris Dislers and Andris Kazaks
Microorganisms 2021, 9(7), 1540; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071540 - 20 Jul 2021
Cited by 5 | Viewed by 3447
Abstract
While looking for novel insect-associated phages, a unique siphophage, Nocturne116, was isolated from a deceased local moth specimen along with its host, which was identified by 16S rRNA gene sequencing as a strain of Lactococcus lactis. Next-generation sequencing and the subsequent genome [...] Read more.
While looking for novel insect-associated phages, a unique siphophage, Nocturne116, was isolated from a deceased local moth specimen along with its host, which was identified by 16S rRNA gene sequencing as a strain of Lactococcus lactis. Next-generation sequencing and the subsequent genome annotation elaborated on herein revealed that the genome of Nocturne116 is a 25,554 bp long dsDNA molecule with 10 bp long 3′ cos overhangs and a GC content of 37.99%, comprising 52 predicted open reading frames. The complete nucleotide sequence of phage Nocturne116 genome is dissimilar to any of the already sequenced phages, save for a distant link with Lactococcus phage Q54. Functions for only 15/52 of Nocturne116 gene products could be reliably predicted using contemporary comparative genomics approaches, while 22 of its gene products do not yet have any homologous entries in the public biological sequence repositories. Despite the public availability of nearly 350 elucidated Lactococcus phage complete genomes as of now, Nocturne116 firmly stands out as a sole representative of novel phage genus. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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16 pages, 4121 KiB  
Article
Characterization of Two New Shiga Toxin-Producing Escherichia coli O103-Infecting Phages Isolated from an Organic Farm
by Yujie Zhang, Yen-Te Liao, Alexandra Salvador, Valerie M. Lavenburg and Vivian C. H. Wu
Microorganisms 2021, 9(7), 1527; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071527 - 17 Jul 2021
Cited by 10 | Viewed by 2905
Abstract
Shiga toxin-producing Escherichia coli (STEC) O103 strains have been recently attributed to various foodborne outbreaks in the United States. Due to the emergence of antibiotic-resistant strains, lytic phages are considered as alternative biocontrol agents. This study was to biologically and genomically characterize two [...] Read more.
Shiga toxin-producing Escherichia coli (STEC) O103 strains have been recently attributed to various foodborne outbreaks in the United States. Due to the emergence of antibiotic-resistant strains, lytic phages are considered as alternative biocontrol agents. This study was to biologically and genomically characterize two STEC O103-infecting bacteriophages, vB_EcoP-Ro103C3lw (or Ro103C3lw) and vB_EcoM-Pr103Blw (or Pr103Blw), isolated from an organic farm. Based on genomic and morphological analyses, phages Ro103C3lw and Pr103Blw belonged to Autographiviridae and Myoviridae families, respectively. Ro103C3lw contained a 39,389-bp double-stranded DNA and encoded a unique tail fiber with depolymerase activity, resulting in huge plaques. Pr103Blw had an 88,421-bp double-stranded DNA with 26 predicted tRNAs associated with the enhancement of the phage fitness. Within each phage genome, no virulence, antibiotic-resistant, and lysogenic genes were detected. Additionally, Ro103C3lw had a short latent period (2 min) and a narrow host range, infecting only STEC O103 strains. By contrast, Pr103Blw had a large burst size (152 PFU/CFU) and a broad host range against STEC O103, O26, O111, O157:H7, and Salmonella Javiana strains. Furthermore, both phages showed strong antimicrobial activities against STEC O103:H2 strains. The findings provide valuable insight into these two phages’ genomic features with the potential antimicrobial activities against STEC O103. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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15 pages, 2379 KiB  
Communication
Comparative Genomics of Prophages Sato and Sole Expands the Genetic Diversity Found in the Genus Betatectivirus
by Annika Gillis, Louise Hock and Jacques Mahillon
Microorganisms 2021, 9(6), 1335; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061335 - 19 Jun 2021
Cited by 1 | Viewed by 2672
Abstract
Tectiviruses infecting the Bacillus cereus group represent part of the bacterial “plasmid repertoire” as they behave as linear plasmids during their lysogenic cycle. Several novel tectiviruses have been recently found infecting diverse strains belonging the B. cereus lineage. Here, we report and analyze [...] Read more.
Tectiviruses infecting the Bacillus cereus group represent part of the bacterial “plasmid repertoire” as they behave as linear plasmids during their lysogenic cycle. Several novel tectiviruses have been recently found infecting diverse strains belonging the B. cereus lineage. Here, we report and analyze the complete genome sequences of phages Sato and Sole. The linear dsDNA genome of Sato spans 14,852 bp with 32 coding DNA sequences (CDSs), whereas the one of Sole has 14,444 bp comprising 30 CDSs. Both phage genomes contain inverted terminal repeats and no tRNAs. Genomic comparisons and phylogenetic analyses placed these two phages within the genus Betatectivirus in the family Tectiviridae. Additional comparative genomic analyses indicated that the “gene regulation-genome replication” module of phages Sato and Sole is more diverse than previously observed among other fully sequenced betatectiviruses, displaying very low sequence similarities and containing some ORFans. Interestingly, the ssDNA binding protein encoded in this genomic module in phages Sato and Sole has very little amino acid similarity with those of reference betatectiviruses. Phylogenetic analyses showed that both Sato and Sole represent novel tectivirus species, thus we propose to include them as two novel species in the genus Betatectivirus. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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11 pages, 3179 KiB  
Article
Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes
by Katelyn McNair, Carol L. Ecale Zhou, Brian Souza, Stephanie Malfatti and Robert A. Edwards
Microorganisms 2021, 9(1), 129; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010129 - 08 Jan 2021
Cited by 5 | Viewed by 2203
Abstract
One of the main steps in gene-finding in prokaryotes is determining which open reading frames encode for a protein, and which occur by chance alone. There are many different methods to differentiate the two; the most prevalent approach is using shared homology with [...] Read more.
One of the main steps in gene-finding in prokaryotes is determining which open reading frames encode for a protein, and which occur by chance alone. There are many different methods to differentiate the two; the most prevalent approach is using shared homology with a database of known genes. This method presents many pitfalls, most notably the catch that you only find genes that you have seen before. The four most popular prokaryotic gene-prediction programs (GeneMark, Glimmer, Prodigal, Phanotate) all use a protein-coding training model to predict protein-coding genes, with the latter three allowing for the training model to be created ab initio from the input genome. Different methods are available for creating the training model, and to increase the accuracy of such tools, we present here GOODORFS, a method for identifying protein-coding genes within a set of all possible open reading frames (ORFS). Our workflow begins with taking the amino acid frequencies of each ORF, calculating an entropy density profile (EDP), using KMeans to cluster the EDPs, and then selecting the cluster with the lowest variation as the coding ORFs. To test the efficacy of our method, we ran GOODORFS on 14,179 annotated phage genomes, and compared our results to the initial training-set creation step of four other similar methods (Glimmer, MED2, PHANOTATE, Prodigal). We found that GOODORFS was the most accurate (0.94) and had the best F1-score (0.85), while Glimmer had the highest precision (0.92) and PHANOTATE had the highest recall (0.96). Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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Review
Computational Prediction of Bacteriophage Host Ranges
by Cyril J. Versoza and Susanne P. Pfeifer
Microorganisms 2022, 10(1), 149; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010149 - 12 Jan 2022
Cited by 16 | Viewed by 3027
Abstract
Increased antibiotic resistance has prompted the development of bacteriophage agents for a multitude of applications in agriculture, biotechnology, and medicine. A key factor in the choice of agents for these applications is the host range of a bacteriophage, i.e., the bacterial genera, species, [...] Read more.
Increased antibiotic resistance has prompted the development of bacteriophage agents for a multitude of applications in agriculture, biotechnology, and medicine. A key factor in the choice of agents for these applications is the host range of a bacteriophage, i.e., the bacterial genera, species, and strains a bacteriophage is able to infect. Although experimental explorations of host ranges remain the gold standard, such investigations are inherently limited to a small number of viruses and bacteria amendable to cultivation. Here, we review recently developed bioinformatic tools that offer a promising and high-throughput alternative by computationally predicting the putative host ranges of bacteriophages, including those challenging to grow in laboratory environments. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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