Access the full text.
Sign up today, get DeepDyve free for 14 days.
David Arndt, J. Grant, A. Marcu, Tanvir Sajed, Allison Pon, Yongjie Liang, D. Wishart (2016)
PHASTER: a better, faster version of the PHAST phage search toolNucleic Acids Research, 44
A. Cisek, I. Dąbrowska, K. Gregorczyk, Z. Wyżewski (2016)
Phage Therapy in Bacterial Infections Treatment: One Hundred Years After the Discovery of BacteriophagesCurrent Microbiology, 74
G. Tetz, V. Tetz (2018)
Bacteriophages as New Human Viral PathogensMicroorganisms, 6
C. Suttle (2007)
Marine viruses — major players in the global ecosystemNature Reviews Microbiology, 5
L. Fernández, D. Gutiérrez, Ana Rodríguez, P. García (2018)
Application of Bacteriophages in the Agro-Food Sector: A Long Way Toward ApprovalFrontiers in Cellular and Infection Microbiology, 8
H. Brüssow, R. Hendrix (2002)
Phage Genomics Small Is BeautifulCell, 108
S. Joseph, K. Hanley, L. Chao, C. Burch (2008)
Coinfection rates in Φ6 bacteriophage are enhanced by virus-induced changes in host cellsEvolutionary Applications, 2
Robert Shereda, A. Kozlov, T. Lohman, M. Cox, J. Keck, D. Kozlov, Alexander Lohman, Timothy Cox, Michael Keck, James L
Please Scroll down for Article Critical Reviews in Biochemistry and Molecular Biology Ssb as an Organizer/mobilizer of Genome Maintenance Complexes
Katelyn McNair, C. Zhou, E. Dinsdale, B. Souza, R. Edwards (2019)
PHANOTATE: a novel approach to gene identification in phage genomesBioinformatics, 35
I. Auzat, A. Dröge, F. Weise, R. Lurz, P. Tavares (2008)
Origin and function of the two major tail proteins of bacteriophage SPP1Molecular Microbiology, 70
Seung-Joo Lee, B. Zhu, S. Hamdan, C. Richardson (2010)
Mechanism of sequence-specific template binding by the DNA primase of bacteriophage T7Nucleic Acids Research, 38
D. Refardt (2011)
Within-host competition determines reproductive success of temperate bacteriophagesThe ISME Journal, 5
M. Worobey, E. Holmes (1999)
Evolutionary aspects of recombination in RNA viruses.The Journal of general virology, 80 ( Pt 10)
Ekaterine Gabashvili, Mariam Osepashvili, S. Koulouris, L. Ujmajuridze, Zurab Tskhitishvili, M. Kotetishvili (2019)
Phage Transduction is Involved in the Intergeneric Spread of Antibiotic Resistance-Associated blaCTX-M, mel, and tetM Loci in Natural Populations of Some Human and Animal Bacterial PathogensCurrent Microbiology, 77
R. Hendrix, Margaret Smith, R. Burns, M. Ford, G. Hatfull (1999)
Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage.Proceedings of the National Academy of Sciences of the United States of America, 96 5
Samuel Muñoz (2016)
Viral coinfection is shaped by host ecology and virus–virus interactions across diverse microbial taxa and environmentsVirus Evolution, 3
Yannick Born, Leandra Knecht, Mirjam Eigenmann, M. Bolliger, J. Klumpp, L. Fieseler (2019)
A major-capsid-protein-based multiplex PCR assay for rapid identification of selected virulent bacteriophage typesArchives of Virology, 164
E. Gaasbeek, J. Wagenaar, M. Guilhabert, M. Wösten, J. Putten, L. Bloois, C. Parker, F. Wal (2009)
A DNase Encoded by Integrated Element CJIE1 Inhibits Natural Transformation of Campylobacter jejuniJournal of Bacteriology, 191
A. Costa, Rodrigo Monteiro, J. Azeredo (2018)
Genomic analysis of Acinetobacter baumannii prophages reveals remarkable diversity and suggests profound impact on bacterial virulence and fitnessScientific Reports, 8
S. Sarker, S. McCallin, C. Barretto, B. Berger, A. Pittet, S. Sultana, L. Krause, Sayeda Huq, R. Bibiloni, A. Bruttin, G. Reuteler, H. Brüssow (2012)
Oral T4-like phage cocktail application to healthy adult volunteers from Bangladesh.Virology, 434 2
Zelin Cui, Xiaokui Guo, K. Dong, Yan Zhang, Qingtian Li, Yongzhang Zhu, L. Zeng, R. Tang, Li Li (2017)
Safety assessment of Staphylococcus phages of the family Myoviridae based on complete genome sequencesScientific Reports, 7
H. Sandmeier, Shigeru Iida, Werner Arber (1992)
DNA inversion regions Min of plasmid p15B and Cin of bacteriophage P1: evolution of bacteriophage tail fiber genesJournal of Bacteriology, 174
S. Altschul, W. Gish, W. Miller, E. Myers, D. Lipman (1990)
Basic local alignment search tool.Journal of molecular biology, 215 3
John Smith (1992)
Analyzing the mosaic structure of genesJournal of Molecular Evolution, 34
A. Seper, V. Fengler, Sandro Roier, H. Wolinski, S. Kohlwein, Anne Bishop, A. Camilli, J. Reidl, S. Schild (2011)
Extracellular nucleases and extracellular DNA play important roles in Vibrio cholerae biofilm formationMolecular Microbiology, 82
E. Hambly, C. Suttle (2005)
The viriosphere, diversity, and genetic exchange within phage communities.Current opinion in microbiology, 8 4
E. Haggård-Ljungquist, C. Halling, R. Calendar (1992)
DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophagesJournal of Bacteriology, 174
S. Nilsson, G. Magnusson (1982)
Sealing of gaps in duplex DNA by T4 DNA ligase.Nucleic acids research, 10 5
E. Jensen, Holly Schrader, Brenda Rieland, T. Thompson, Kit Lee, K. Nickerson, T. Kokjohn (1998)
Prevalence of Broad-Host-Range Lytic Bacteriophages of Sphaerotilus natans, Escherichia coli, andPseudomonas aeruginosaApplied and Environmental Microbiology, 64
Zheng Zhang, C. Tian, Jiangtao Zhao, Xiao Chen, Xiao Wei, Huan Li, Weishi Lin, R. Feng, Aimin Jiang, Wenhui Yang, Jing Yuan, Xiangna Zhao (2018)
Characterization of Tail Sheath Protein of N4-Like Phage phiAxp-3Frontiers in Microbiology, 9
D. Martin, E. Rybicki (2000)
RDP: detection of recombination amongst aligned sequencesBioinformatics, 16 6
Anne Lopes, P. Tavares, M. Petit, Raphaël Guérois, Sophie Zinn-Justin (2014)
Automated classification of tailed bacteriophages according to their neck organizationBMC Genomics, 15
R. Czajkowski, Zofia Ozymko, Szymon Żwirowski, E. Lojkowska (2014)
Complete genome sequence of a broad-host-range lytic Dickeya spp. bacteriophage ϕD5Archives of Virology, 159
M. Sullivan, J. Waterbury, S. Chisholm (2003)
Cyanophages infecting the oceanic cyanobacterium ProchlorococcusNature, 424
P. Bollyky, P. Secor (2019)
The Innate Sense of Bacteriophages.Cell host & microbe, 25 2
Yan Zhang, Xiao-juan Tan, A. Cui, N. Mao, Song-tao Xu, Zhen Zhu, Jian-hui Zhou, Jing Shi, Yueping Zhao, Xianjun Wang, Xueyong Huang, Shuang-li Zhu, Yong Zhang, Wei-Feng Tang, H. Ling, Wenbo Xu (2013)
Complete Genome Analysis of the C4 Subgenotype Strains of Enterovirus 71: Predominant Recombination C4 Viruses Persistently Circulating in China for 14 YearsPLoS ONE, 8
L. Bobay, M. Touchon, E. Rocha (2013)
Manipulating or Superseding Host Recombination Functions: A Dilemma That Shapes Phage EvolvabilityPLoS Genetics, 9
C. Suttle (2005)
Viruses in the seaNature, 437
Daniel White, D. Bryant, N. Gemmell (2013)
How Good Are Indirect Tests at Detecting Recombination in Human mtDNA?G3: Genes|Genomes|Genetics, 3
K. Wommack, R. Colwell (2000)
Virioplankton: Viruses in Aquatic EcosystemsMicrobiology and Molecular Biology Reviews, 64
J. Norman, S. Handley, Megan Baldridge, L. Droit, Catherine Liu, B. Keller, Amal Kambal, Cynthia Monaco, Guoyan Zhao, P. Fleshner, T. Stappenbeck, D. McGovern, A. Keshavarzian, E. Mutlu, J. Sauk, D. Gevers, R. Xavier, David Wang, M. Parkes, H. Virgin (2015)
Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel DiseaseCell, 160
Evelien Adriaenssens, D. Cowan (2014)
Using Signature Genes as Tools To Assess Environmental Viral Ecology and DiversityApplied and Environmental Microbiology, 80
M. Paepe, Geoffrey Hutinet, O. Son, Jihane Amarir-Bouhram, Sophie Schbath, M. Petit (2014)
Temperate Phages Acquire DNA from Defective Prophages by Relaxed Homologous Recombination: The Role of Rad52-Like RecombinasesPLoS Genetics, 10
Rachid Menouni, Geoffrey Hutinet, M. Petit, M. Ansaldi (2015)
Bacterial genome remodeling through bacteriophage recombination.FEMS microbiology letters, 362 1
G. Tetz, V. Tetz (2016)
Bacteriophage infections of microbiota can lead to leaky gut in an experimental rodent modelGut Pathogens, 8
A. Wichels, S. Biel, H. Gelderblom, T. Brinkhoff, G. Muyzer, C. Schütt (1998)
Bacteriophage Diversity in the North SeaApplied and Environmental Microbiology, 64
Jati Adiputra, S. Jarugula, R. Naidu (2019)
Intra-species recombination among strains of the ampelovirus Grapevine leafroll-associated virus 4Virology Journal, 16
M. Boni, D. Posada, M. Feldman (2007)
An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence TripletsGenetics, 176
R. Rossi, A. Montecucco, G. Ciarrocchi, G. Biamonti (1997)
Functional characterization of the T4 DNA ligase: a new insight into the mechanism of action.Nucleic acids research, 25 11
J. Sousa, E. Pfeifer, M. Touchon, E. Rocha (2020)
Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial TaxaMolecular Biology and Evolution, 38
Ella Bedford, S. Tabor, C. Richardson (1997)
The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I.Proceedings of the National Academy of Sciences of the United States of America, 94 2
Charles Jones, T. Mueser, K. Dudas, K. Kreuzer, N. Nossal (2001)
Bacteriophage T4 gene 41 helicase and gene 59 helicase-loading protein: A versatile couple with roles in replication and recombinationProceedings of the National Academy of Sciences of the United States of America, 98
E. Durmaz, T. Klaenhammer (2000)
Genetic Analysis of Chromosomal Regions ofLactococcus lactis Acquired by Recombinant Lytic PhagesApplied and Environmental Microbiology, 66
Darius Kazlauskas, M. Krupovic, Č. Venclovas (2016)
The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomesNucleic Acids Research, 44
Pilar Manrique, M. Dills, M. Young (2017)
The Human Gut Phage Community and Its Implications for Health and DiseaseViruses, 9
César Flores, Justin Meyer, S. Valverde, Lauren Farr, J. Weitz (2011)
Statistical structure of host–phage interactionsProceedings of the National Academy of Sciences, 108
Wei-Lin Wang, Shao-Yan Xu, Z. Ren, Liang Tao, Jianwen Jiang, Shusen Zheng (2015)
Application of metagenomics in the human gut microbiome.World journal of gastroenterology, 21 3
S. Chaturongakul, P. Ounjai (2014)
Phage–host interplay: examples from tailed phages and Gram-negative bacterial pathogensFrontiers in Microbiology, 5
Jong-Bong Lee, R. Hite, S. Hamdan, X. Xie, C. Richardson, A. Oijen (2006)
DNA primase acts as a molecular brake in DNA replicationNature, 439
Lasha Gogokhia, Lasha Gogokhia, K. Buhrke, Rickesha Bell, B. Hoffman, D. Brown, Christin Hanke-Gogokhia, N. Ajami, M. Wong, A. Ghazaryan, J. Valentine, Nathan Porter, E. Martens, Ryan O’Connell, Vinita Jacob, E. Scherl, C. Crawford, W. Stephens, S. Casjens, R. Longman, J. Round (2019)
Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis.Cell host & microbe, 25 2
D. Pride, J. Salzman, Matthew Haynes, F. Rohwer, Clara Davis-Long, Richard White, P. Loomer, G. Armitage, D. Relman (2011)
Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary viromeThe ISME Journal, 6
Nichole Cumby, K. Reimer, D. Mengin-Lecreulx, A. Davidson, K. Maxwell (2015)
The phage tail tape measure protein, an inner membrane protein and a periplasmic chaperone play connected roles in the genome injection process of E. coli phage HK97Molecular Microbiology, 96
S. Roux, Alyse Hawley, Monica Beltran, M. Scofield, P. Schwientek, R. Stepanauskas, T. Woyke, S. Hallam, M. Sullivan (2014)
Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomicseLife, 3
Mark Larkin, G. Blackshields, N. Brown, R. Chenna, P. McGettigan, Hamish McWilliam, F. Valentin, Iain Wallace, A. Wilm, R. Lopez, J. Thompson, T. Gibson, D. Higgins (2007)
Clustal W and Clustal X version 2.0Bioinformatics, 23 21
M. Weinbauer (2004)
Ecology of prokaryotic viruses.FEMS microbiology reviews, 28 2
D. Posada, K. Crandall (2001)
Evaluation of methods for detecting recombination from DNA sequences: Computer simulationsProceedings of the National Academy of Sciences of the United States of America, 98
Y. Fujio, And, S. Mizushima (1982)
Roles of lipopolysaccharide and outer membrane protein OmpC of Escherichia coli K-12 in the receptor function for bacteriophage T4Journal of Bacteriology, 151
L. Bobay, H. Ochman (2017)
Impact of Recombination on the Base Composition of Bacteriaand ArchaeaMolecular Biology and Evolution, 34
L. Kurochkina, P. Semenyuk, N. Sykilinda, K. Miroshnikov (2018)
The unique two-component tail sheath of giant Pseudomonas phage PaBG.Virology, 515
E. Boyd (2012)
Bacteriophage-encoded bacterial virulence factors and phage-pathogenicity island interactions.Advances in virus research, 82
You Zhou, Yongjie Liang, K. Lynch, J. Dennis, D. Wishart (2011)
PHAST: A Fast Phage Search ToolNucleic Acids Research, 39
Xiaodong Shen, Ming Li, Yijun Zeng, Xiaomei Hu, Yinling Tan, X. Rao, Xiaoling Jin, Shu Li, Junmin Zhu, Kebin Zhang, F. Hu (2012)
Functional identification of the DNA packaging terminase from Pseudomonas aeruginosa phage PaP3Archives of Virology, 157
B. Duerkop, M. Kleiner, David Páez-Espino, Wenhan Zhu, Brian Bushnell, Brian Hassell, S. Winter, N. Kyrpides, L. Hooper (2018)
Murine colitis reveals a disease-associated bacteriophage communityNature microbiology, 3
Zachary Moye, Joelle Woolston, A. Sulakvelidze (2018)
Bacteriophage Applications for Food Production and ProcessingViruses, 10
Masato Kato, Takuhiro Ito, G. Wagner, T. Ellenberger (2004)
A Molecular Handoff between Bacteriophage T7 DNA Primase and T7 DNA Polymerase Initiates DNA Synthesis*Journal of Biological Chemistry, 279
L. Čičin-Šain, J. Podlech, M. Messerle, M. Reddehase, U. Koszinowski (2005)
Frequent Coinfection of Cells Explains Functional In Vivo Complementation between Cytomegalovirus Variants in the Multiply Infected HostJournal of Virology, 79
Julie Bouchard, Sylvain Moineau (2000)
Homologous recombination between a lactococcal bacteriophage and the chromosome of its host strain.Virology, 270 1
A. Cherepanov, Eseng¨l Yildirim, S. Vries (2001)
Joining of short DNA oligonucleotides with base pair mismatches by T4 DNA ligase.Journal of biochemistry, 129 1
A. Kupczok, H. Neve, Kun Huang, M. Hoeppner, K. Heller, C. Franz, Tal Dagan (2018)
Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three DecadesMolecular Biology and Evolution, 35
Junshu Wang, Fapeng Liu, Tianyuan Su, Yizhao Chang, Qi Guo, Qian Wang, Quanfeng Liang, Q. Qi (2019)
The phage T4 DNA ligase in vivo improves the survival-coupled bacterial mutagenesisMicrobial Cell Factories, 18
T. Hollis, James Stattel, D. Walther, C. Richardson, T. Ellenberger (2001)
Structure of the gene 2.5 protein, a single-stranded DNA binding protein encoded by bacteriophage T7Proceedings of the National Academy of Sciences of the United States of America, 98
Katelyn McNair, Barbara Bailey, R. Edwards (2012)
PHACTS, a computational approach to classifying the lifestyle of phagesBioinformatics, 28
G. Ciarrocchi, M. Lestingi, G. Wright, A. Montecucco (1993)
Bacteriophage T4 and human type I DNA ligases relax DNA under joining conditions.Nucleic acids research, 21 25
D. Montag, H. Schwarz, U. Henning (1989)
A component of the side tail fiber of Escherichia coli bacteriophage lambda can functionally replace the receptor-recognizing part of a long tail fiber protein of the unrelated bacteriophage T4Journal of Bacteriology, 171
D. Martin, D. Posada, K. Crandall, C. Williamson (2005)
A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints.AIDS research and human retroviruses, 21 1
G. Tetz, Kelly Ruggles, Hua Zhou, A. Heguy, A. Tsirigos, V. Tetz (2017)
Bacteriophages as potential new mammalian pathogensScientific Reports, 7
S. Ahamed, Banibrata Roy, Utpal Basu, S. Dutta, A. Ghosh, B. Bandyopadhyay, Nabanita Giri (2019)
Genomic and Proteomic Characterizations of Sfin-1, a Novel Lytic Phage Infecting Multidrug-Resistant Shigella spp. and Escherichia coli CFrontiers in Microbiology, 10
Jinxia Wang, Xinglou Yang, Haizhou Liu, Li Wang, Ji-hua Zhou, Xi Han, Yancai Zhu, Wei-hong Yang, Hong Pan, Yunzhi Zhang, Z. Shí (2019)
Prevalence of Wēnzhōu virus in small mammals in Yunnan Province, ChinaPLoS Neglected Tropical Diseases, 13
P. Miernikiewicz, A. Klopot, Ryszard Soluch, Piotr Szkuta, W. Kęska, K. Hodyra-Stefaniak, Agnieszka Konopka, M. Nowak, Dorota Lecion, Z. Kaźmierczak, J. Majewska, M. Harhala, A. Górski, K. Dąbrowska (2016)
T4 Phage Tail Adhesin Gp12 Counteracts LPS-Induced Inflammation In VivoFrontiers in Microbiology, 7
E. Kutter, D. Vos, G. Gvasalia, Z. Alavidze, Lasha Gogokhia, Sarah Kuhl, S. Abedon (2010)
Phage therapy in clinical practice: treatment of human infections.Current pharmaceutical biotechnology, 11 1
Melanie Blokesch, G. Schoolnik (2008)
The Extracellular Nuclease Dns and Its Role in Natural Transformation of Vibrio choleraeJournal of Bacteriology, 190
D. Paraskevis, E. Kostaki, G. Magiorkinis, G. Panayiotakopoulos, G. Sourvinos, S. Tsiodras (2020)
Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination eventInfection, Genetics and Evolution, 79
H. Wong, Tzu-Yun Wang, Chu-Wen Yang, Chung-Tao Tang, C. Ying, Chun-Hsiung Wang, Wei-Hau Chang (2019)
Characterization of a lytic vibriophage VP06 of Vibrio parahaemolyticus.Research in microbiology, 170 1
Lin Yuan, Zelin Cui, Yanchun Wang, Xiaokui Guo, Yong Zhao (2014)
Complete genome sequence of virulent bacteriophage SHOU24, which infects foodborne pathogenic Vibrio parahaemolyticusArchives of Virology, 159
T. Bruen, H. Philippe, D. Bryant (2006)
A Simple and Robust Statistical Test for Detecting the Presence of RecombinationGenetics, 172
M. Dunne, M. Loessner (2019)
Modified Bacteriophage Tail Fiber Proteins for Labeling, Immobilization, Capture, and Detection of Bacteria.Methods in molecular biology, 1918
J. Mahony, M. Alqarni, S. Stockdale, S. Spinelli, Marine Feyereisen, C. Cambillau, D. Sinderen (2016)
Functional and structural dissection of the tape measure protein of lactococcal phage TP901-1Scientific Reports, 6
T. Brettin, James Davis, T. Disz, R. Edwards, S. Gerdes, G. Olsen, R. Olson, R. Overbeek, B. Parrello, G. Pusch, Maulik Shukla, Jim Thomason, Rick Stevens, V. Vonstein, A. Wattam, Fangfang Xia (2015)
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomesScientific Reports, 5
D. Huson, D. Bryant (2006)
Application of phylogenetic networks in evolutionary studies.Molecular biology and evolution, 23 2
S. Roux, S. Hallam, T. Woyke, M. Sullivan (2015)
Viral dark matter and virus–host interactions resolved from publicly available microbial genomeseLife, 4
M. Akmal, Aryan Rahimi-Midani, M. Hafeez-ur-Rehman, A. Hussain, T. Choi (2020)
Isolation, Characterization, and Application of a Bacteriophage Infecting the Fish Pathogen Aeromonas hydrophilaPathogens, 9
M. Bailly-Bechet, M. Vergassola, E. Rocha (2007)
Causes for the intriguing presence of tRNAs in phages.Genome research, 17 10
C. Manaia (2017)
Assessing the Risk of Antibiotic Resistance Transmission from the Environment to Humans: Non-Direct Proportionality between Abundance and Risk.Trends in microbiology, 25 3
L. Bielke, S. Higgins, A. Donoghue, D. Donoghue, B. Hargis (2007)
Salmonella host range of bacteriophages that infect multiple genera.Poultry science, 86 12
T. Abuladze, Manrong Li, M. Menetrez, T. Dean, A. Senecal, A. Sulakvelidze (2008)
Bacteriophages Reduce Experimental Contamination of Hard Surfaces, Tomato, Spinach, Broccoli, and Ground Beef by Escherichia coli O157:H7Applied and Environmental Microbiology, 74
S. Roux, M. Krupovic, Axel Poulet, D. Debroas, François Enault (2012)
Evolution and Diversity of the Microviridae Viral Family through a Collection of 81 New Complete Genomes Assembled from Virome ReadsPLoS ONE, 7
Kyle Smith, E. Castro-Nallar, Joshua Fisher, D. Breakwell, J. Grose, S. Burnett (2013)
Phage cluster relationships identified through single gene analysisBMC Genomics, 14
S. Wilhelm, W. Jeffrey, C. Suttle, D. Mitchell (2002)
Estimation of Biologically Damaging UV Levels in Marine Surface Waters with DNA and Viral Dosimeters¶, 76
Maryury Brown-Jaque, William Calero-Cáceres, M. Muniesa (2015)
Transfer of antibiotic-resistance genes via phage-related mobile elements.Plasmid, 79
A. Aksyuk, P. Leiman, L. Kurochkina, M. Shneider, V. Kostyuchenko, V. Mesyanzhinov, M. Rossmann (2009)
The tail sheath structure of bacteriophage T4: a molecular machine for infecting bacteriaThe EMBO Journal, 28
L. Bobay, E. Rocha, M. Touchon (2012)
The Adaptation of Temperate Bacteriophages to Their Host GenomesMolecular Biology and Evolution, 30
A. Reyes, Matthew Haynes, N. Hanson, Florent Angly, A. Heath, F. Rohwer, J. Gordon (2010)
Viruses in the fecal microbiota of monozygotic twins and their mothersNature, 466
D. Martin, B. Murrell, Michael Golden, Arjun Khoosal, B. Muhire (2015)
RDP4: Detection and analysis of recombination patterns in virus genomesVirus Evolution, 1
P. Gauss, K. Park, T. Spencer, K. Hacker (1994)
DNA helicase requirements for DNA replication during bacteriophage T4 infectionJournal of Bacteriology, 176
A. Gigante, R. Atterbury (2019)
Veterinary use of bacteriophage therapy in intensively-reared livestockVirology Journal, 16
Yiqin Deng, Haidong Xu, Youlu Su, Songlin Liu, Li-wen Xu, Zhixun Guo, Jinjun Wu, Changhong Cheng, Juan Feng (2019)
Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysisBMC Genomics, 20
J. Martinsohn, M. Radman, M. Petit (2008)
The λ Red Proteins Promote Efficient Recombination between Diverged Sequences: Implications for Bacteriophage Genome MosaicismPLoS Genetics, 4
E. Cernooka, J. Rūmnieks, K. Tārs, A. Kazaks (2017)
Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34Scientific Reports, 7
Travis Mavrich, G. Hatfull (2017)
Bacteriophage evolution differs by host, lifestyle and genomeNature microbiology, 2
Chaowen Yuan, Wenxin Liu, Yingbo Wang, Jinlong Hou, Liguo Zhang, Guoqing Wang (2017)
Homologous recombination is a force in the evolution of canine distemper virusPLoS ONE, 12
Lisa Rezende, S. Willcox, J. Griffith, C. Richardson (2003)
A Single-stranded DNA-binding Protein of Bacteriophage T7 Defective in DNA Annealing*Journal of Biological Chemistry, 278
S. Casjens, P. Thuman-Commike (2011)
Evolution of mosaically related tailed bacteriophage genomes seen through the lens of phage P22 virion assembly.Virology, 411 2
T. Mueser, J. Hinerman, J. Devos, R. Boyer, K. Williams (2010)
Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relativesVirology Journal, 7
F. Cruz, J. Davies (2000)
Horizontal gene transfer and the origin of species: lessons from bacteria.Trends in microbiology, 8 3
K. Lole, R. Bollinger, R. Paranjape, D. Gadkari, S. Kulkarni, Nicole Novak, Roxann Ingersoll, H. Sheppard, S. Ray (1999)
Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype RecombinationJournal of Virology, 73
C. Loc-Carrillo, S. Abedon (2011)
Pros and cons of phage therapyBacteriophage, 1
N. Cangi, J. Gordon, L. Bournez, V. Pinarello, R. Aprelon, K. Huber, T. Lefrançois, L. Neves, D. Meyer, N. Vachiéry (2016)
Recombination Is a Major Driving Force of Genetic Diversity in the Anaplasmataceae Ehrlichia ruminantiumFrontiers in Cellular and Infection Microbiology, 6
M. Padidam, S. Sawyer, C. Fauquet (1999)
Possible emergence of new geminiviruses by frequent recombination.Virology, 265 2
Lorraine Endersen, J. O'Mahony, C. Hill, R. Ross, O. McAuliffe, A. Coffey (2014)
Phage therapy in the food industry.Annual review of food science and technology, 5
S. Casjens (2005)
Comparative genomics and evolution of the tailed-bacteriophages.Current opinion in microbiology, 8 4
M. Gibbs, J. Armstrong, A. Gibbs (2000)
Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequencesBioinformatics, 16 7
Joshua Maurer, Bonnie Oh, C. Moyer, R. Duda (2020)
Capsids and portals influence each other's conformation during assembly and maturation.Journal of molecular biology
P. Lepage, J. Colombet, P. Marteau, T. Sime-Ngando, J. Doré, M. Leclerc (2008)
Dysbiosis in inflammatory bowel disease: a role for bacteriophages?Gut, 57
H. Bandelt, A. Dress (1992)
Split decomposition: a new and useful approach to phylogenetic analysis of distance data.Molecular phylogenetics and evolution, 1 3
R. Hendrix (2002)
Bacteriophages: evolution of the majority.Theoretical population biology, 61 4
F. Rohwer, K. Barott (2012)
Viral informationBiology & Philosophy, 28
H. Jia, Wenyang Dong, Lvfeng Yuan, Jiale Ma, Qinqin Bai, Z. Pan, Chengping Lu, Huochun Yao (2015)
Characterization and complete genome sequence analysis of Staphylococcus aureus bacteriophage JS01Virus Genes, 50
N. Principi, Ettore Silvestri, S. Esposito (2019)
Advantages and Limitations of Bacteriophages for the Treatment of Bacterial InfectionsFrontiers in Pharmacology, 10
A. Henein (2013)
What are the limitations on the wider therapeutic use of phage?Bacteriophage, 3
J. Grose, S. Casjens (2014)
Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae.Virology, 468-470
Que Dang, Jianbo Chen, D. Unutmaz, J. Coffin, V. Pathak, D. Powell, V. KewalRamani, F. Maldarelli, Wei-Shau Hu (2004)
Nonrandom HIV-1 infection and double infection via direct and cell-mediated pathways.Proceedings of the National Academy of Sciences of the United States of America, 101 2
Karin Holmfeldt, M. Middelboe, O. Nybroe, L. Riemann (2007)
Large Variabilities in Host Strain Susceptibility and Phage Host Range Govern Interactions between Lytic Marine Phages and Their Flavobacterium HostsApplied and Environmental Microbiology, 73
J. Villarroel, K. Kleinheinz, V. Jurtz, Henrike Zschach, O. Lund, M. Nielsen, M. Larsen (2016)
HostPhinder: A Phage Host Prediction ToolViruses, 8
A. Beceiro, M. Tomás, G. Bou (2013)
Antimicrobial Resistance and Virulence: a Successful or Deleterious Association in the Bacterial World?Clinical Microbiology Reviews, 26
A. Wright, C. Hawkins, E. Änggård, D. Harper (2009)
A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic‐resistant Pseudomonas aeruginosa; a preliminary report of efficacyClinical Otolaryngology, 34
R. Hendrix, G. Hatfull, Margaret Smith (2003)
Bacteriophages with tails: chasing their origins and evolution.Research in microbiology, 154 4
S. Minot, R. Sinha, Jun Chen, Hongzhe Li, S. Keilbaugh, Gary Wu, J. Lewis, F. Bushman (2011)
The human gut virome: inter-individual variation and dynamic response to diet.Genome research, 21 10
Chongli Yuan, X. Lou, E. Rhoades, Huimin Chen, L. Archer (2007)
T4 DNA ligase is more than an effective trap of cyclized dsDNANucleic Acids Research, 35
J. Filée, P. Forterre, Sen-Lin Tang, J. Laurent (2002)
Evolution of DNA Polymerase Families: Evidences for Multiple Gene Exchange Between Cellular and Viral ProteinsJournal of Molecular Evolution, 54
S. Moineau, S. Pandian, T. Klaenhammer (1994)
Evolution of a Lytic Bacteriophage via DNA Acquisition from the Lactococcus lactis ChromosomeApplied and Environmental Microbiology, 60
Unraveling the trends of phage-host versus phage-phage coevolution is critical for avoiding possible undesirable outcomes from the use of phage preparations intended for therapeutic, food safety or environmental safety purposes. We aimed to investigate a phenomenon of intergeneric recombination and its trajectories across the natural populations of phages predominantly linked to foodborne pathogens. The results from the recombination analyses, using a large array of the recombination detection algorithms imbedded in SplitsTree, RDP4, and Simplot software packages, provided strong evidence (fit: 100; P ≤ 0.014) for both bi- and multi-directional intergeneric recombination of the genetic loci involved collectively in phage morphogenesis, host specificity, virulence, replication, and persistence. Intergeneric recombination was determined to occur not only among conspecifics of the virulent versus temperate phages but also between the phages with these different lifestyles. The recombining polyvalent phages were suggested to interact with fairly large host species networks, including sometimes genetically very distinct species, such as e.g., Salmonella enterica and/or Escherichia coli versus Staphylococcus aureus or Yersinia pestis. Further studies are needed to understand whether phage-driven intergeneric recombination can lead to undesirable changes of intestinal and other microbiota in humans and animals.
Food and Environmental Virology – Springer Journals
Published: Jan 23, 2021
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.