Bacteriophages exhibit great diversity and are classically divided into lytic and temperate lifestyles. Commonly, bioinformatics is used to predict the temperate lifestyle. As the nosocomial pathogen Pseudomonas aeruginosa is common in freshwater, this biome represents an ideal location for the discovery of Pseudomonas phages.
Materials and Methods:
We characterized a genetically distinct species of Pseudomonas phage using next-generation sequencing and conventional microbiological methods. We characterized its lifestyle by purifying infected colonies and identifying persistent phage production.
Results:
Genetics revealed a phage of a novel genus. Characterization showed a narrow host range and bioinformatics suggested a lytic lifestyle. Experimental data showed lysogeny and analysis was consistent with an episomal lifestyle instead of the classical model of integration into the host genome.
Conclusions:
We identify and characterize a new Pseudomonas phage, show potential limitations of bioinformatic predictions of lifestyle, and further contribute to the diversity of the phage tree of life.
BreitbartM, RohwerF. Here a virus, there a virus, everywhere the same virus? Trends Microbiol, 2005; 13(6):278–284; doi: 10.1016/j.tim.2005.04.003
2.
KrishnamurthySR, WangD. Origins and challenges of viral dark matter. Virus Res, 2017; 239:136–142; doi: 10.1016/j.virusres.2017.02.002
3.
AbedonST, GarciaP, MullanyP, et al.Editorial: Phage therapy: Past, present and future. Front Microbiol, 2017; 8:981; doi: 10.3389/fmicb.2017.00981
4.
ChanishviliN. Phage therapy–history from Twort and d’Herelle through Soviet experience to current approaches. Adv Virus Res, 2012; 83:3–40; doi: 10.1016/B978-0-12-394438-2.00001-3
5.
ZaczekM, Weber-DabrowskaB, MiedzybrodzkiR, et al.Phage therapy in Poland—A centennial journey to the first ethically approved treatment facility in Europe. Front Microbiol, 2020; 11:1056; doi: 10.3389/fmicb.2020.01056
6.
TerwilligerA, ClarkJ, KarrisM, et al.Phage therapy related microbial succession associated with successful clinical outcome for a recurrent urinary tract infection. Viruses, 2021; 13(10):2049; doi: 10.3390/v13102049
7.
GreenSI, ClarkJR, SantosHH, et al.A retrospective, observational study of 12 cases of expanded-access customized phage therapy: Production, characteristics, and clinical outcomes. Clin Infect Dis, 2023; 77(8):1079–1091; doi: 10.1093/cid/ciad335
8.
AslamS, LampleyE, WootenD, et al.Lessons learned from the first 10 consecutive cases of intravenous bacteriophage therapy to treat multidrug-resistant bacterial infections at a single center in the United States. Open Forum Infect Dis, 2020; 7(9):ofaa389; doi: 10.1093/ofid/ofaa389
9.
HatfullGF, DedrickRM, SchooleyRT. Phage therapy for antibiotic-resistant bacterial infections. Annu Rev Med, 2022; 73:197–211; doi: 10.1146/annurev-med-080219-122208
Morcinek-OrlowskaJ, ZdrojewskaK, WegrzynA. Bacteriophage-encoded DNA polymerases-beyond the traditional view of polymerase activities. Int J Mol Sci, 2022; 23(2); doi: 10.3390/ijms23020635
12.
OfirG, SorekR. Contemporary phage biology: From classic models to new insights. Cell, 2018; 172(6):1260–1270; doi: 10.1016/j.cell.2017.10.045
13.
DedrickRM, Guerrero BustamanteCA, GarlenaRA, et al.Mycobacteriophage ZoeJ: A broad host-range close relative of mycobacteriophage TM4. Tuberculosis (Edinb), 2019; 115:14–23; doi: 10.1016/j.tube.2019.01.002
14.
DedrickRM, Guerrero-BustamanteCA, GarlenaRA, et al.Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus. Nat Med, 2019; 25(5):730–733; doi: 10.1038/s41591-019-0437-z
15.
CasjensSR, HendrixRW. Bacteriophage lambda: Early pioneer and still relevant. Virology, 2015; 479–480:310–330; doi: 10.1016/j.virol.2015.02.010
16.
OtsujiN, SekiguchiM, IijimaT, et al.Induction of phage formation in the lysogenic Escherichia coli K-12 by mitomycin C. Nature, 1959; 184(4692):1079–1080; doi: 10.1038/1841079b0
17.
BarnhartBJ, CoxSH, JettJH. Prophage induction and inactivation by UV light. J Virol, 1976; 18(3):950–955; doi: 10.1128/JVI.18.3.950-955.1976
18.
Engelberg-KulkaH, KumarS. Yet another way that phage lambda manipulates its Escherichia coli host: LambdarexB is involved in the lysogenic-lytic switch. Mol Microbiol, 2015; 96(4):689–693; doi: 10.1111/mmi.12969
19.
CortesMG, LinY, ZengL, et al.From bench to keyboard and back again: A brief history of lambda phage modeling. Annu Rev Biophys, 2021; 50:117–134; doi: 10.1146/annurev-biophys-082020-063558
20.
ShaoQ, TrinhJT, ZengL. High-resolution studies of lysis-lysogeny decision-making in bacteriophage lambda. J Biol Chem, 2019; 294(10):3343–3349; doi: 10.1074/jbc.TM118.003209
21.
McNairK, BaileyBA, EdwardsRA. PHACTS, a computational approach to classifying the lifestyle of phages. Bioinformatics, 2012; 28(5):614–618; doi: 10.1093/bioinformatics/bts014
22.
HockenberryAJ, WilkeCO. BACPHLIP: Predicting bacteriophage lifestyle from conserved protein domains. PeerJ, 2021; 9:e11396; doi: 10.7717/peerj.11396
23.
TyneckiP, GuzińskiA, KazimierczakJ, et al.PhageAI—Bacteriophage life cycle recognition with machine learning and natural language processing. bioRxiv, 2020; doi: 10.1101/2020.07.11.198606
24.
AbedonST. Disambiguating bacteriophage pseudolysogeny: an historical analysis of lysogeny, pseudolysogeny, and the phage carrier state. In: Contemporary Trends in Bacteriophage Research. (AdamsHT. ed.) Nova Science Publishers, Inc.: 2009.
25.
LobockaMB, RoseDJ, PlunkettG3rd, et al.Genome of bacteriophage P1. J Bacteriol, 2004; 186(21):7032–7068; doi: 10.1128/JB.186.21.7032-7068.2004
26.
HamiltonDL, AbremskiK. Site-specific recombination by the bacteriophage P1 lox-Cre system. Cre-mediated synapsis of two lox sites. J Mol Biol, 1984; 178(2):481–486; doi: 10.1016/0022-2836(84)90154-2
27.
YarmolinskyM, HoessR. The legacy of nat sternberg: The Genesis of Cre-lox technology. Annu Rev Virol, 2015; 2(1):25–40; doi: 10.1146/annurev-virology-100114-054930
28.
HoessRH, ZieseM, SternbergN. P1 site-specific recombination: Nucleotide sequence of the recombining sites. Proc Natl Acad Sci U S A, 1982; 79(11):3398–3402; doi: 10.1073/pnas.79.11.3398
29.
AbelesAL, FriedmanSA, AustinSJ. Partition of unit-copy miniplasmids to daughter cells. III. The DNA sequence and functional organization of the P1 partition region. J Mol Biol, 1985; 185(2):261–272; doi: 10.1016/0022-2836(85)90402-4
30.
LehnherrH, MaguinE, JafriS, et al.Plasmid addiction genes of bacteriophage P1: Doc, which causes cell death on curing of prophage, and phd, which prevents host death when prophage is retained. J Mol Biol, 1993; 233(3):414–428; doi: 10.1006/jmbi.1993.1521
31.
NichollsP, ClarkJR, Gu LiuC, et al.Class-driven synergy and antagonism between a pseudomonas phage and antibiotics. Infect Immun, 2023; 91(8):e0006523; doi: 10.1128/iai.00065-23
32.
GreenSI, KaelberJT, MaL, et al.Bacteriophages from ExPEC reservoirs kill pandemic multidrug-resistant strains of Clonal Group ST131 in animal models of bacteremia. Sci Rep, 2017; 7:46151; doi: 10.1038/srep46151
33.
GibsonSB, GreenSI, LiuCG, et al.Constructing and characterizing bacteriophage libraries for phage therapy of human infections. Front Microbiol, 2019; 10:2537; doi: 10.3389/fmicb.2019.02537
34.
MoraruC, VarsaniA, KropinskiAM. VIRIDIC-A novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses, 2020; 12(11):1268; doi: 10.3390/v12111268
35.
NishimuraY, YoshidaT, KuronishiM, et al.ViPTree: The viral proteomic tree server. Bioinformatics, 2017; 33(15):2379–2380; doi: 10.1093/bioinformatics/btx157
36.
AltamiranoFLG, BarrJJ. Screening for lysogen activity in therapeutically relevant bacteriophages. Bio Protoc, 2021; 11(8):e3997; doi: 10.21769/BioProtoc.3997
37.
GlontiT, PirnayJP. In vitro techniques and measurements of phage characteristics that are important for phage therapy success. Viruses, 2022; 14(7):1490; doi: 10.3390/v14071490
38.
LangmeadB, SalzbergSL. Fast gapped-read alignment with Bowtie 2. Nat Methods, 2012; 9(4):357–359; doi: 10.1038/nmeth.1923
39.
GarneauJR, DepardieuF, FortierLC, et al.PhageTerm: A tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data. Sci Rep, 2017; 7(1):8292; doi: 10.1038/s41598-017-07910-5
40.
RohwerF, EdwardsR. The Phage Proteomic Tree: A genome-based taxonomy for phage. J Bacteriol, 2002; 184(16):4529–4535; doi: 10.1128/JB.184.16.4529-4535.2002
41.
HatfullGF, HendrixRW. Bacteriophages and their genomes. Curr Opin Virol, 2011; 1(4):298–303; doi: 10.1016/j.coviro.2011.06.009
42.
ShangJ, PengC, LiaoH, et al.PhaBOX: A web server for identifying and characterizing phage contigs in metagenomic data. Bioinform Adv, 2023; 3(1):vbad101; doi: 10.1093/bioadv/vbad101
43.
BolducB, JangHB, DoulcierG, et al.vConTACT: An iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ, 2017; 5:e3243; doi: 10.7717/peerj.3243
44.
YukgehnaishK, RajandasH, ParimannanS, et al.PhageLeads: Rapid assessment of phage therapeutic suitability using an ensemble machine learning approach. Viruses, 2022; 14(2):342; doi: 10.3390/v14020342
45.
CheongKH, WenT, BenlerS, et al.Alternating lysis and lysogeny is a winning strategy in bacteriophages due to Parrondo’s paradox. Proc Natl Acad Sci U S A, 2022; 119(13):e2115145119; doi: 10.1073/pnas.2115145119
46.
DeutschDR, UtterB, VerrattiKJ, et al.Extra-chromosomal DNA sequencing reveals episomal prophages capable of impacting virulence factor expression in staphylococcus aureus. Front Microbiol, 2018; 9:1406; doi: 10.3389/fmicb.2018.01406
47.
MohammadiT, ElyB. Dolichocephalovirinae phages exist as episomal pseudolysogens across diverse soil bacteria. Microorganisms, 2025; 13(6):1239; doi: 10.3390/microorganisms13061239
48.
CenensW, MebrhatuMT, MakumiA, et al.Expression of a novel P22 ORFan gene reveals the phage carrier state in Salmonella typhimurium. PLoS Genet, 2013; 9(2):e1003269; doi: 10.1371/journal.pgen.1003269
Supplementary Material
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
