The Experts below are selected from a list of 2004 Experts worldwide ranked by ideXlab platform
Andrew M. Kropinski - One of the best experts on this subject based on the ideXlab platform.
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A Roadmap for Genome-Based Phage Taxonomy
MDPI AG, 2021Co-Authors: Dann Turner, Andrew M. Kropinski, Evelien M. AdriaenssensAbstract:Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae. Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy.
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a suggested new bacteriophage genus kp34likevirus within the autographivirinae subfamily of Podoviridae
Viruses, 2015Co-Authors: Harald Eriksson, Andrew M. Kropinski, Barbara Maciejewska, Agnieszka Latka, Grazyna Majkowskaskrobek, Marios Hellstrand, Ojar Melefors, Jintown Wang, Zuzanna Druliskawa, Anders S NilssonAbstract:Klebsiella pneumoniae phages vB_KpnP_SU503 (SU503) and vB_KpnP_SU552A (SU552A) are virulent viruses belonging to theAutographivirinae subfamily of Podoviridae that infect and kill multi-resistant K ...
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complete genome sequence of bacteriophage vb_yenp_ap5 which infects yersinia enterocolitica of serotype o 3
Virology Journal, 2014Co-Authors: Carlos G Leonvelarde, Andrew M. Kropinski, Shu Chen, Arash Abbasifar, Mansel W Griffiths, Joseph OdumeruAbstract:Background: Bacteriophage vB_YenP_AP5 is a lytic bacteriophage capable of infecting Yersinia enterocolitica strains of serotype O:3, an epidemiologically significant serotype within this bacterial species that causes yersiniosis in humans. This work describes the complete genome sequence of this phage. Results: The genome consists of linear double-stranded DNA of 38,646 bp, with direct terminal repeats of 235 bp in length, and a GC content of 50.7%. There are 45 open reading frames which occupy 89.9% of the genome. Most of the proteins encoded by this virus exhibit sequence similarity to Yersinia phage φYeO3-12 and Salmonella phage φSG-JL2 proteins. Conclusions: Genomic and morphological analyses place the bacteriophage vB_YenP_AP5 in the T7likevirus genus of the subfamily Autographivirinae within the family Podoviridae.
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classification of myoviridae bacteriophages using protein sequence similarity
BMC Microbiology, 2009Co-Authors: Rob Lavigne, Hans-w. Ackermann, Andrew M. Kropinski, Paul Darius, Elizabeth J Summer, Donald Seto, Padmanabhan Mahadevan, Anders S NilssonAbstract:Background We advocate unifying classical and genomic classification of bacteriophages by integration of proteomic data and physicochemical parameters. Our previous application of this approach to the entirely sequenced members of the Podoviridae fully supported the current phage classification of the International Committee on Taxonomy of Viruses (ICTV). It appears that horizontal gene transfer generally does not totally obliterate evolutionary relationships between phages.
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unifying classical and molecular taxonomic classification analysis of the Podoviridae using blastp based tools
Research in Microbiology, 2008Co-Authors: Rob Lavigne, Hans-w. Ackermann, Andrew M. Kropinski, Donald Seto, Padmanabhan MahadevanAbstract:We defined phage genera by measuring genome relationships by the numbers of shared homologous/orthologous proteins. We used BLAST-based tools (CoreExtractor.vbs and CoreGenes) to analyze 55 fully sequenced bacteriophage genomes from the NCBI and EBI databases. This approach was first applied to the T7-related phages. Using a cut-off score of 40% homologous proteins, we identified three genera within the T7-related phages, redefined the φ29-related phages, and introduced five novel genera. The T7- and φ29-related phages were given subfamily status and named “Autographivirinae” and “Picovirinae”, respectively. Our results confirm and refine the ICTV phage classification, enable elimination of errors in public databases, and provide a straightforward tool for the molecular classification of new phage genomes.
Wen Huang - One of the best experts on this subject based on the ideXlab platform.
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complete genomic sequence of the vibrio alginolyticus bacteriophage vp670 and characterization of the lysis related genes cwlq and hola
BMC Genomics, 2018Co-Authors: Peng Luo, Long Yun, Yushun Tian, Qiuting Liu, Wen HuangAbstract:Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically important farmed marine animals. To date, few V. alginolyticus phages have been successfully isolated, and only three complete genome sequences of them have been released. The limited available phage resources and poor genomic data hamper research on V. alginolyticus phages and their applications for the biocontrol of V. alginolyticus. We isolated a phage, Vp670, against the V. alginolyticus strain E06333 and obtained its full genomic sequence. It contains 43,121 nucleotides with a GC content of 43.4%, and codes for 49 predicted open reading frames. Observation by electron microscope combined with phylogenetic analysis of DNA polymerase indicates that Vp670 belongs to the subfamily Autographivirinae in the family Podoviridae. orf3 (designated holA) and orf8 (designated cwlQ) are predicted to encode a holin (HolA) and an endolysin (CwlQ), respectively. Expression of holA alone or coexpression of holA and cwlQ from within arrested the growth of Escherichia coli and V. alginolyticus while the expression of cwlQ alone had no effect on the growth of them. Further observation by transmission electron microscopy revealed that the expression of holA vanished the outer membrane and caused the release of cellular contents of V. alginolyticus and the coexpression of holA and cwlQ directly burst the cells and caused a more drastic release of cellular contents. Expression of cwlQ alone in V. alginolyticus did not cause cytomorphological changes. Phage Vp670 is a V. alginolyticus phage belonging to the family of Podoviridae. The genome of Vp670 contains a two-component lysis module, which is comprised of holA and cwlQ. holA is predicted to encode for the holin protein, HolA, and cwlQ is predicted to encode for the endolysin protein, CwlQ. Both holA and cwlQ likely play important roles during the release of phage progeny.
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Complete genomic sequence of the Vibrio alginolyticus bacteriophage Vp670 and characterization of the lysis-related genes, cwlQ and holA
BMC, 2018Co-Authors: Peng Luo, Long Yun, Yushun Tian, Qiuting Liu, Wen HuangAbstract:Abstract Background Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically important farmed marine animals. To date, few V. alginolyticus phages have been successfully isolated, and only three complete genome sequences of them have been released. The limited available phage resources and poor genomic data hamper research on V. alginolyticus phages and their applications for the biocontrol of V. alginolyticus. Results We isolated a phage, Vp670, against the V. alginolyticus strain E06333 and obtained its full genomic sequence. It contains 43,121 nucleotides with a GC content of 43.4%, and codes for 49 predicted open reading frames. Observation by electron microscope combined with phylogenetic analysis of DNA polymerase indicates that Vp670 belongs to the subfamily Autographivirinae in the family Podoviridae. orf3 (designated holA) and orf8 (designated cwlQ) are predicted to encode a holin (HolA) and an endolysin (CwlQ), respectively. Expression of holA alone or coexpression of holA and cwlQ from within arrested the growth of Escherichia coli and V. alginolyticus while the expression of cwlQ alone had no effect on the growth of them. Further observation by transmission electron microscopy revealed that the expression of holA vanished the outer membrane and caused the release of cellular contents of V. alginolyticus and the coexpression of holA and cwlQ directly burst the cells and caused a more drastic release of cellular contents. Expression of cwlQ alone in V. alginolyticus did not cause cytomorphological changes. Conclusions Phage Vp670 is a V. alginolyticus phage belonging to the family of Podoviridae. The genome of Vp670 contains a two-component lysis module, which is comprised of holA and cwlQ. holA is predicted to encode for the holin protein, HolA, and cwlQ is predicted to encode for the endolysin protein, CwlQ. Both holA and cwlQ likely play important roles during the release of phage progeny
Hans-w. Ackermann - One of the best experts on this subject based on the ideXlab platform.
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morphology and genome sequence of phage ϕ1402 a dwarf myovirus of the predatory bacterium bdellovibrio bacteriovorus
Bacteriophage, 2011Co-Authors: Hans-w. Ackermann, Henry M Krisch, Andre M ComeauAbstract:Phages are among the simplest biological entities known and simultaneously the most numerous and ubiquitous members of the biosphere. Among the three families of tailed dsDNA phages, the Myoviridae have the most structurally sophisticated tails which are capable of contraction, unlike the simpler tails of the Podoviridae and Siphoviridae. Such “nanomachines” tails are involved in both efficient phage adsorption and genome injection. Their structural complexity probably necessitates multistep morphogenetic pathways, involving non-structural components, to correctly assemble the structural constituents. For reasons probably related, at least in part, to such morphological intricacy, myoviruses tend to have larger genomes than simpler phages. As a consequence, there are no well-characterized myoviruses with a size of less than 40 kb. Here we report on the characterization and sequencing of the 23,931 bp genome of the dwarf myovirus ϕ1402 of Bdellovibrio bacteriovorus. Our genomic analysis shows that ϕ1402 di...
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classification of myoviridae bacteriophages using protein sequence similarity
BMC Microbiology, 2009Co-Authors: Rob Lavigne, Hans-w. Ackermann, Andrew M. Kropinski, Paul Darius, Elizabeth J Summer, Donald Seto, Padmanabhan Mahadevan, Anders S NilssonAbstract:Background We advocate unifying classical and genomic classification of bacteriophages by integration of proteomic data and physicochemical parameters. Our previous application of this approach to the entirely sequenced members of the Podoviridae fully supported the current phage classification of the International Committee on Taxonomy of Viruses (ICTV). It appears that horizontal gene transfer generally does not totally obliterate evolutionary relationships between phages.
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unifying classical and molecular taxonomic classification analysis of the Podoviridae using blastp based tools
Research in Microbiology, 2008Co-Authors: Rob Lavigne, Hans-w. Ackermann, Andrew M. Kropinski, Donald Seto, Padmanabhan MahadevanAbstract:We defined phage genera by measuring genome relationships by the numbers of shared homologous/orthologous proteins. We used BLAST-based tools (CoreExtractor.vbs and CoreGenes) to analyze 55 fully sequenced bacteriophage genomes from the NCBI and EBI databases. This approach was first applied to the T7-related phages. Using a cut-off score of 40% homologous proteins, we identified three genera within the T7-related phages, redefined the φ29-related phages, and introduced five novel genera. The T7- and φ29-related phages were given subfamily status and named “Autographivirinae” and “Picovirinae”, respectively. Our results confirm and refine the ICTV phage classification, enable elimination of errors in public databases, and provide a straightforward tool for the molecular classification of new phage genomes.
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taxonomy of bacterial viruses establishment of tailed virus genera and the order caudovirales
Archives of Virology, 1998Co-Authors: Jack Maniloff, Hans-w. AckermannAbstract:Bacterial viruses have been classified into 13 families and 1 unassigned genus. A new order, Caudovirales, has now been established, comprising the three families of tailed bacterial viruses, based on similarities in tailed virus morphology, replication, and assembly. In addition, genera have been established for some species in each tailed virus family, based on properties involving viral DNA replication and packaging, and on some features specific to particular genera (e.g., DNA-termini linked proteins, virus-encoded polymerases, and ability to establish temperate infections). At present, there are six genera in the family Myoviridae (viruses with contractile tails), six in the family Siphoviridae (viruses with long, noncontractile tails), and three in the family Podoviridae (viruses with short noncontractile tails). In recognition that the definitions of tailed virus genera represent a “work in progress” and to keep the nomenclature flexible, tailed virus genera have been assigned vernacular names based on their type species.
George P C Salmond - One of the best experts on this subject based on the ideXlab platform.
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jumbo bacteriophages are represented within an increasing diversity of environmental viruses infecting the emerging phytopathogen dickeya solani
Frontiers in Microbiology, 2018Co-Authors: George P C SalmondAbstract:\textit{Dickeya} species are economically important phytopathogens widespread in mainland Europe that can reduce crop yields by 25$\%$. There are no effective environmentally-acceptable chemical systems available for diseases caused by \textit{Dickeya}. Bacteriophages have been suggested for use in biocontrol of these pathogens in the field, and limited field trials have been conducted. To date the majority of bacteriophages capable of infecting \textit{Dickeya solani}, one of the more aggressive species, are from the same family, the \textit{Ackermannviridae}, many representatives of which have been shown to be unsuitable for use in the field due to their capacity for generalised transduction. Members of this family are also only capable of forming individual plaques on \textit{Dickeya solani}. Here we describe novel bacteriophages from environmental sources isolated on \textit{Dickeya solani}, including members of two other viral families; \textit{Myoviridae} and \textit{Podoviridae}, most of which are capable of forming plaques on multiple \textit{Dickeya} species. Full genomic sequencing revealed that the \textit{Myoviridae} family members form two novel clusters of jumbo bacteriophages with genomes over 250 kbp, with one cluster containing phages of another phytopathogen \textit{Erwinia amylovora}. Transduction experiments showed that the majority of the new environmental bacteriophages are also capable of facilitating efficient horizontal gene transfer, however the single \textit{Podoviridae} family member is not. This particular phage therefore has potential for use as a biocontrol agent against multiple species of \textit{Dickeya}.
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Jumbo Bacteriophages Are Represented Within an Increasing Diversity of Environmental Viruses Infecting the Emerging Phytopathogen, Dickeya solani
'Frontiers Media SA', 2018Co-Authors: Andrew Day, Jiyoon Ahn, George P C SalmondAbstract:Dickeya species are economically important phytopathogens widespread in mainland Europe that can reduce crop yields by 25%. There are no effective environmentally-acceptable chemical systems available for diseases caused by Dickeya. Bacteriophages have been suggested for use in biocontrol of these pathogens in the field, and limited field trials have been conducted. To date the majority of bacteriophages capable of infecting Dickeya solani, one of the more aggressive species, are from the same family, the Ackermannviridae, many representatives of which have been shown to be unsuitable for use in the field due to their capacity for generalized transduction. Members of this family are also only capable of forming individual plaques on D. solani. Here we describe novel bacteriophages from environmental sources isolated on D. solani, including members of two other viral families; Myoviridae and Podoviridae, most of which are capable of forming plaques on multiple Dickeya species. Full genomic sequencing revealed that the Myoviridae family members form two novel clusters of jumbo bacteriophages with genomes over 250 kbp, with one cluster containing phages of another phytopathogen Erwinia amylovora. Transduction experiments showed that the majority of the new environmental bacteriophages are also capable of facilitating efficient horizontal gene transfer, however the single Podoviridae family member is not. This particular phage therefore has potential for use as a biocontrol agent against multiple species of Dickeya
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Data_Sheet_1_Jumbo Bacteriophages Are Represented Within an Increasing Diversity of Environmental Viruses Infecting the Emerging Phytopathogen, Dickeya solani.PDF
2018Co-Authors: Andrew Day, Jiyoon Ahn, George P C SalmondAbstract:Dickeya species are economically important phytopathogens widespread in mainland Europe that can reduce crop yields by 25%. There are no effective environmentally-acceptable chemical systems available for diseases caused by Dickeya. Bacteriophages have been suggested for use in biocontrol of these pathogens in the field, and limited field trials have been conducted. To date the majority of bacteriophages capable of infecting Dickeya solani, one of the more aggressive species, are from the same family, the Ackermannviridae, many representatives of which have been shown to be unsuitable for use in the field due to their capacity for generalized transduction. Members of this family are also only capable of forming individual plaques on D. solani. Here we describe novel bacteriophages from environmental sources isolated on D. solani, including members of two other viral families; Myoviridae and Podoviridae, most of which are capable of forming plaques on multiple Dickeya species. Full genomic sequencing revealed that the Myoviridae family members form two novel clusters of jumbo bacteriophages with genomes over 250 kbp, with one cluster containing phages of another phytopathogen Erwinia amylovora. Transduction experiments showed that the majority of the new environmental bacteriophages are also capable of facilitating efficient horizontal gene transfer, however the single Podoviridae family member is not. This particular phage therefore has potential for use as a biocontrol agent against multiple species of Dickeya.
Peng Luo - One of the best experts on this subject based on the ideXlab platform.
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complete genomic sequence of the vibrio alginolyticus bacteriophage vp670 and characterization of the lysis related genes cwlq and hola
BMC Genomics, 2018Co-Authors: Peng Luo, Long Yun, Yushun Tian, Qiuting Liu, Wen HuangAbstract:Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically important farmed marine animals. To date, few V. alginolyticus phages have been successfully isolated, and only three complete genome sequences of them have been released. The limited available phage resources and poor genomic data hamper research on V. alginolyticus phages and their applications for the biocontrol of V. alginolyticus. We isolated a phage, Vp670, against the V. alginolyticus strain E06333 and obtained its full genomic sequence. It contains 43,121 nucleotides with a GC content of 43.4%, and codes for 49 predicted open reading frames. Observation by electron microscope combined with phylogenetic analysis of DNA polymerase indicates that Vp670 belongs to the subfamily Autographivirinae in the family Podoviridae. orf3 (designated holA) and orf8 (designated cwlQ) are predicted to encode a holin (HolA) and an endolysin (CwlQ), respectively. Expression of holA alone or coexpression of holA and cwlQ from within arrested the growth of Escherichia coli and V. alginolyticus while the expression of cwlQ alone had no effect on the growth of them. Further observation by transmission electron microscopy revealed that the expression of holA vanished the outer membrane and caused the release of cellular contents of V. alginolyticus and the coexpression of holA and cwlQ directly burst the cells and caused a more drastic release of cellular contents. Expression of cwlQ alone in V. alginolyticus did not cause cytomorphological changes. Phage Vp670 is a V. alginolyticus phage belonging to the family of Podoviridae. The genome of Vp670 contains a two-component lysis module, which is comprised of holA and cwlQ. holA is predicted to encode for the holin protein, HolA, and cwlQ is predicted to encode for the endolysin protein, CwlQ. Both holA and cwlQ likely play important roles during the release of phage progeny.
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Complete genomic sequence of the Vibrio alginolyticus bacteriophage Vp670 and characterization of the lysis-related genes, cwlQ and holA
BMC, 2018Co-Authors: Peng Luo, Long Yun, Yushun Tian, Qiuting Liu, Wen HuangAbstract:Abstract Background Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically important farmed marine animals. To date, few V. alginolyticus phages have been successfully isolated, and only three complete genome sequences of them have been released. The limited available phage resources and poor genomic data hamper research on V. alginolyticus phages and their applications for the biocontrol of V. alginolyticus. Results We isolated a phage, Vp670, against the V. alginolyticus strain E06333 and obtained its full genomic sequence. It contains 43,121 nucleotides with a GC content of 43.4%, and codes for 49 predicted open reading frames. Observation by electron microscope combined with phylogenetic analysis of DNA polymerase indicates that Vp670 belongs to the subfamily Autographivirinae in the family Podoviridae. orf3 (designated holA) and orf8 (designated cwlQ) are predicted to encode a holin (HolA) and an endolysin (CwlQ), respectively. Expression of holA alone or coexpression of holA and cwlQ from within arrested the growth of Escherichia coli and V. alginolyticus while the expression of cwlQ alone had no effect on the growth of them. Further observation by transmission electron microscopy revealed that the expression of holA vanished the outer membrane and caused the release of cellular contents of V. alginolyticus and the coexpression of holA and cwlQ directly burst the cells and caused a more drastic release of cellular contents. Expression of cwlQ alone in V. alginolyticus did not cause cytomorphological changes. Conclusions Phage Vp670 is a V. alginolyticus phage belonging to the family of Podoviridae. The genome of Vp670 contains a two-component lysis module, which is comprised of holA and cwlQ. holA is predicted to encode for the holin protein, HolA, and cwlQ is predicted to encode for the endolysin protein, CwlQ. Both holA and cwlQ likely play important roles during the release of phage progeny
