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Home / Equine Research Bank / Appl Environ Microbiol / Equine Intestinal O-Seroconverting Temperate Coliphage Hf4s:...
Applied and environmental microbiology2021; 87(21); e0112421; doi: 10.1128/AEM.01124-21

Equine Intestinal O-Seroconverting Temperate Coliphage Hf4s: Genomic and Biological Characterization.

Abstract: Tailed bacteriophages constitute the bulk of the intestinal viromes of vertebrate animals. However, the relationships between lytic and lysogenic lifestyles of phages in these ecosystems are not always clear and may vary between the species or even between the individuals. The human intestinal (fecal) viromes are dominated mostly by temperate phages, while in horse feces virulent phages are more prevalent. To our knowledge, all the previously reported isolates of horse fecal coliphages are virulent. Temperate coliphage Hf4s was isolated from horse feces, from the indigenous equine Escherichia coli 4s strain. It is a podovirus related to the genus (including the well-characterized Salmonella bacteriophage P22). Hf4s recognizes the host O antigen as its primary receptor and possesses a functional O antigen seroconversion cluster that renders the lysogens protected from superinfection by the same bacteriophage and also abolishes the adsorption of some indigenous equine virulent coliphages, such as DT57C, while other phages, such as G7C or phiKT, retain the ability to infect E. coli 4s (Hf4s) lysogens. The relationships between virulent and temperate bacteriophages and their impact on high-density symbiotic microbial ecosystems of animals are not always clear and may vary between species or even between individuals. The horse intestinal virome is dominated by virulent phages, and Hf4s is the first temperate equine intestinal coliphage characterized. It recognizes the host O antigen as its primary receptor and possesses a functional O antigen seroconversion cluster that renders the lysogens protected from superinfection by some indigenous equine virulent coliphages, such as DT57C, while other phages, such as G7C or phiKT, retain the ability to infect E. coli 4s (Hf4s) lysogens. These findings raise questions on the significance of bacteriophage-bacteriophage interactions within the ecology of microbial viruses in mammal intestinal ecosystems.
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Publication Date: 2021-08-18 PubMed ID: 34406832PubMed Central: PMC8516047DOI: 10.1128/AEM.01124-21Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article discusses the genomic and biological characterizations of a temperate bacteriophage isolated from horse feces, known as Hf4s. This phage interacts with some specific types of other phages and has the capacity to alter the receptor of the host, thereby inhibiting certain infections.

Objective of the Research

  • The researchers aim to conduct a comprehensive genomic and biological characterization of an equine intestinal temperate coliphage, identified as Hf4s. This bacteriophage was derived from horse feces and pertains to Escherichia coli 4s strain.

Nature of Tailed Bacteriophages

  • Vertebrate animals are mostly occupied by tailed bacteriophages in their intestinal viromes; however, the relationship and functionality that exist between lytic and lysogenic bacteriophages within these systems remain somewhat unclear. This may vary widely between different species and even between individuals within the same species.

Virulent and Temperate Bacteriophages

  • Previously-reported isolates of horse fecal coliphages have always been virulent. The current study, however, identifies and focuses on the first temperate coliphage isolated from horse feces – Hf4s.
  • The study finds that the human intestinal viromes are generally dominated by temperate phages, while in the horse feces, virulent phages are more prevalent.

Detailed Characterization of Hf4s Phage

  • Hf4s is related to the Podovirus genus, represented by the well-known Salmonella bacteriophage P22. The primary receptor of Hf4s is the host O antigen.
  • Interestingly, Hf4s has an operational O antigen seroconversion cluster. This functionality allows lysogens, the bacterial cells carrying the phage DNA, to be shielded from superinfection by the same bacteriophage.

Implications for Microbial Ecology

  • The study sheds light on the potential bacteriophage-bacteriophage interactions within the microbial virus ecology in mammalian intestinal systems. More specifically, it recognizes and emphasizes the complex ecological roles played by bacteriophages in animal intestinal microbial ecosystems.
  • The Hf4s phage, as demonstrated in the research, can prevent adsorption by some native equine virulent coliphages, such as DT57C, while it does not affect the ability of some other phages, such as G7C or phiKT, to infect the E. coli 4s strain.

Cite This Article

APA
Kulikov EE, Golomidova AK, Efimov AD, Belalov IS, Letarova MA, Zdorovenko EL, Knirel YA, Dmitrenok AS, Letarov AV. (2021). Equine Intestinal O-Seroconverting Temperate Coliphage Hf4s: Genomic and Biological Characterization. Appl Environ Microbiol, 87(21), e0112421. https://doi.org/10.1128/AEM.01124-21

Publication

Applied and environmental microbiology
ISSN: 1098-5336
NlmUniqueID: 7605801
Country: United States
Language: English
Volume: 87
Issue: 21
Pages: e0112421
PII: e01124-21

Researcher Affiliations

Kulikov, Eugene E
  • Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of Sciencesgrid.4886.2, Moscow, Russia.
Golomidova, Alla K
  • Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of Sciencesgrid.4886.2, Moscow, Russia.
Efimov, Alexandr D
  • Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of Sciencesgrid.4886.2, Moscow, Russia.
Belalov, Ilya S
  • Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of Sciencesgrid.4886.2, Moscow, Russia.
Letarova, Maria A
  • Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of Sciencesgrid.4886.2, Moscow, Russia.
Zdorovenko, Evelina L
  • N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciencesgrid.4886.2, Moscow, Russia.
Knirel, Yuriy A
  • N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciencesgrid.4886.2, Moscow, Russia.
Dmitrenok, Andrei S
  • N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciencesgrid.4886.2, Moscow, Russia.
Letarov, Andrey V
  • Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of Sciencesgrid.4886.2, Moscow, Russia.

MeSH Terms

  • Animals
  • Coliphages / genetics
  • Escherichia coli / virology
  • Genomics
  • Horses / virology
  • O Antigens
  • Podoviridae / genetics
  • Superinfection

Grant Funding

  • State assignment / Ministry of Education and Science of the Russian Federation (Minobrnauka)
  • 18-29-13029 / Russian Foundation for Basic Research (u0420u0424u0424u0418)
  • 18-14-00098-P / Russian Science Foundation (RSF)

References

This article includes 58 references
  1. Letarov A, Kulikov E. The bacteriophages in human- and animal body-associated microbial communities.. J Appl Microbiol 2009 Jul;107(1):1-13.
    doi: 10.1111/j.1365-2672.2009.04143.xpubmed: 19239553google scholar: lookup
  2. Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector TD, Bell JT, Youngblut ND, Hewson I, Reyes A, Ley RE. Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins.. Cell Host Microbe 2019 Feb 13;25(2):261-272.e5.
    doi: 10.1016/j.chom.2019.01.019pmc: PMC6411085pubmed: 30763537google scholar: lookup
  3. Seo SU, Kweon MN. Virome-host interactions in intestinal health and disease.. Curr Opin Virol 2019 Aug;37:63-71.
    doi: 10.1016/j.coviro.2019.06.003pubmed: 31295677google scholar: lookup
  4. Shkoporov AN, Hill C. Bacteriophages of the Human Gut: The "Known Unknown" of the Microbiome.. Cell Host Microbe 2019 Feb 13;25(2):195-209.
    doi: 10.1016/j.chom.2019.01.017pubmed: 30763534google scholar: lookup
  5. Sausset R, Petit MA, Gaboriau-Routhiau V, De Paepe M. New insights into intestinal phages.. Mucosal Immunol 2020 Mar;13(2):205-215.
    doi: 10.1038/s41385-019-0250-5pmc: PMC7039812pubmed: 31907364google scholar: lookup
  6. Babenko VV, Millard A, Kulikov EE, Spasskaya NN, Letarova MA, Konanov DN, Belalov IS, Letarov AV. The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses.. Comput Struct Biotechnol J 2020;18:3457-3467.
    doi: 10.1016/j.csbj.2020.10.036pmc: PMC7691681pubmed: 33294140google scholar: lookup
  7. Guerin E, Shkoporov AN, Stockdale SR, Comas JC, Khokhlova EV, Clooney AG, Daly KM, Draper LA, Stephens N, Scholz D, Ross RP, Hill C. Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens.. Microbiome 2021 Apr 12;9(1):89.
    doi: 10.1186/s40168-021-01036-7pmc: PMC8042965pubmed: 33845877google scholar: lookup
  8. Cervantes-Echeverría M, Equihua-Medina E, Cornejo-Granados F, Hernández-Reyna A, Sánchez F, López-Contreras BE, Canizales-Quinteros S, Ochoa-Leyva A. Whole-genome of Mexican-crAssphage isolated from the human gut microbiome.. BMC Res Notes 2018 Dec 17;11(1):902.
    doi: 10.1186/s13104-018-4010-5pmc: PMC6296078pubmed: 30558657google scholar: lookup
  9. Mathieu A, Dion M, Deng L, Tremblay D, Moncaut E, Shah SA, Stokholm J, Krogfelt KA, Schjørring S, Bisgaard H, Nielsen DS, Moineau S, Petit MA. Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages.. Nat Commun 2020 Jan 17;11(1):378.
    doi: 10.1038/s41467-019-14042-zpmc: PMC6969025pubmed: 31953385google scholar: lookup
  10. Babenko V, Golomidova A, Ivanov P, Letarova M, Kulikov E, Manolov A, Prokhorov N, Kostrukova E, Matyushkina D, Prilipov A. Phages associated with horses provide new insights into the dominance of lateral gene transfer in virulent bacteriophages evolution in natural systems. bioRxiv .
    doi: 10.1101/542787google scholar: lookup
  11. Golomidova A, Kulikov E, Isaeva A, Manykin A, Letarov A. The diversity of coliphages and coliforms in horse feces reveals a complex pattern of ecological interactions.. Appl Environ Microbiol 2007 Oct;73(19):5975-81.
    doi: 10.1128/AEM.01145-07pmc: PMC2075005pubmed: 17704275google scholar: lookup
  12. Howard-Varona C, Hargreaves KR, Abedon ST, Sullivan MB. Lysogeny in nature: mechanisms, impact and ecology of temperate phages.. ISME J 2017 Jul;11(7):1511-1520.
    doi: 10.1038/ismej.2017.16pmc: PMC5520141pubmed: 28291233google scholar: lookup
  13. Baxter JC, Waples WG, Funnell BE. Nonspecific DNA binding by P1 ParA determines the distribution of plasmid partition and repressor activities.. J Biol Chem 2020 Dec 11;295(50):17298-17309.
    doi: 10.1074/jbc.RA120.015642pmc: PMC7863886pubmed: 33055234google scholar: lookup
  14. Hammerl JA, Jäckel C, Funk E, Pinnau S, Mache C, Hertwig S. The diverse genetic switch of enterobacterial and marine telomere phages.. Bacteriophage 2016 Apr-Jun;6(2):e1148805.
    doi: 10.1080/21597081.2016.1148805pmc: PMC4951001pubmed: 27607141google scholar: lookup
  15. Vander Byl C, Kropinski AM. Sequence of the genome of Salmonella bacteriophage P22.. J Bacteriol 2000 Nov;182(22):6472-81.
    doi: 10.1128/JB.182.22.6472-6481.2000pmc: PMC94795pubmed: 11053393google scholar: lookup
  16. Samson JE, Magadán AH, Sabri M, Moineau S. Revenge of the phages: defeating bacterial defences.. Nat Rev Microbiol 2013 Oct;11(10):675-87.
    doi: 10.1038/nrmicro3096pubmed: 23979432google scholar: lookup
  17. Taylor VL, Fitzpatrick AD, Islam Z, Maxwell KL. The Diverse Impacts of Phage Morons on Bacterial Fitness and Virulence.. Adv Virus Res 2019;103:1-31.
    doi: 10.1016/bs.aivir.2018.08.001pubmed: 30635074google scholar: lookup
  18. Feiner R, Argov T, Rabinovich L, Sigal N, Borovok I, Herskovits AA. A new perspective on lysogeny: prophages as active regulatory switches of bacteria.. Nat Rev Microbiol 2015 Oct;13(10):641-50.
    doi: 10.1038/nrmicro3527pubmed: 26373372google scholar: lookup
  19. Holt GS, Lodge JK, McCarthy AJ, Graham AK, Young G, Bridge SH, Brown AK, Veses-Garcia M, Lanyon CV, Sails A, Allison HE, Smith DL. Shigatoxin encoding Bacteriophage ϕ24(B) modulates bacterial metabolism to raise antimicrobial tolerance.. Sci Rep 2017 Jan 20;7:40424.
    doi: 10.1038/srep40424pmc: PMC5247750pubmed: 28106081google scholar: lookup
  20. Bobay LM, Touchon M, Rocha EP. Pervasive domestication of defective prophages by bacteria.. Proc Natl Acad Sci U S A 2014 Aug 19;111(33):12127-32.
    doi: 10.1073/pnas.1405336111pmc: PMC4143005pubmed: 25092302google scholar: lookup
  21. Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI. Viruses in the faecal microbiota of monozygotic twins and their mothers.. Nature 2010 Jul 15;466(7304):334-8.
    doi: 10.1038/nature09199pmc: PMC2919852pubmed: 20631792google scholar: lookup
  22. Furuse K, Osawa S, Kawashiro J, Tanaka R, Ozawa A, Sawamura S, Yanagawa Y, Nagao T, Watanabe I. Bacteriophage distribution in human faeces: continuous survey of healthy subjects and patients with internal and leukaemic diseases.. J Gen Virol 1983 Sep;64 (Pt 9):2039-43.
    doi: 10.1099/0022-1317-64-9-2039pubmed: 6886680google scholar: lookup
  23. Chibani-Chennoufi S, Sidoti J, Bruttin A, Dillmann ML, Kutter E, Qadri F, Sarker SA, Brüssow H. Isolation of Escherichia coli bacteriophages from the stool of pediatric diarrhea patients in Bangladesh.. J Bacteriol 2004 Dec;186(24):8287-94.
    doi: 10.1128/JB.186.24.8287-8294.2004pmc: PMC532420pubmed: 15576777google scholar: lookup
  24. Kulikov E, Kropinski AM, Golomidova A, Lingohr E, Govorun V, Serebryakova M, Prokhorov N, Letarova M, Manykin A, Strotskaya A, Letarov A. Isolation and characterization of a novel indigenous intestinal N4-related coliphage vB_EcoP_G7C.. Virology 2012 May 10;426(2):93-9.
    doi: 10.1016/j.virol.2012.01.027pubmed: 22341309google scholar: lookup
  25. Kulikov EE, Golomidova AK, Letarova MA, Kostryukova ES, Zelenin AS, Prokhorov NS, Letarov AV. Genomic sequencing and biological characteristics of a novel Escherichia coli bacteriophage 9g, a putative representative of a new Siphoviridae genus.. Viruses 2014 Dec 19;6(12):5077-92.
    doi: 10.3390/v6125077pmc: PMC4276943pubmed: 25533657google scholar: lookup
  26. Golomidova AK, Kulikov EE, Prokhorov NS, Guerrero-Ferreira RC, Ksenzenko VN, Tarasyan KK, Letarov AV. Complete genome sequences of T5-related Escherichia coli bacteriophages DT57C and DT571/2 isolated from horse feces.. Arch Virol 2015 Dec;160(12):3133-7.
    doi: 10.1007/s00705-015-2582-0pubmed: 26350770google scholar: lookup
  27. Golomidova AK, Kulikov EE, Babenko VV, Kostryukova ES, Letarov AV. Complete Genome Sequence of Bacteriophage St11Ph5, Which Infects Uropathogenic Escherichia coli Strain up11.. Genome Announc 2018 Jan 11;6(2).
    doi: 10.1128/genomeA.01371-17pmc: PMC5764931pubmed: 29326207google scholar: lookup
  28. Zdorovenko EL, Wang Y, Shashkov AS, Chen T, Ovchinnikova OG, Liu B, Golomidova AK, Babenko VV, Letarov AV, Knirel YA. O-Antigens of Escherichia coli Strains O81 and HS3-104 Are Structurally and Genetically Related, Except O-Antigen Glucosylation in E. coli HS3-104.. Biochemistry (Mosc) 2018 May;83(5):534-541.
    doi: 10.1134/S0006297918050061pubmed: 29738687google scholar: lookup
  29. de Siqueira RS, Dodd CE, Rees CE. Evaluation of the natural virucidal activity of teas for use in the phage amplification assay.. Int J Food Microbiol 2006 Oct 1;111(3):259-62.
    doi: 10.1016/j.ijfoodmicro.2006.04.047pubmed: 16920213google scholar: lookup
  30. Juhala RJ, Ford ME, Duda RL, Youlton A, Hatfull GF, Hendrix RW. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages.. J Mol Biol 2000 May 26;299(1):27-51.
    doi: 10.1006/jmbi.2000.3729pubmed: 10860721google scholar: lookup
  31. Meier-Kolthoff JP, Göker M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses.. Bioinformatics 2017 Nov 1;33(21):3396-3404.
    doi: 10.1093/bioinformatics/btx440pmc: PMC5860169pubmed: 29036289google scholar: lookup
  32. Kulikov EE, Golomidova AK, Prokhorov NS, Ivanov PA, Letarov AV. High-throughput LPS profiling as a tool for revealing of bacteriophage infection strategies.. Sci Rep 2019 Feb 27;9(1):2958.
    doi: 10.1038/s41598-019-39590-8pmc: PMC6393563pubmed: 30814597google scholar: lookup
  33. Knirel YA, Prokhorov NS, Shashkov AS, Ovchinnikova OG, Zdorovenko EL, Liu B, Kostryukova ES, Larin AK, Golomidova AK, Letarov AV. Variations in O-antigen biosynthesis and O-acetylation associated with altered phage sensitivity in Escherichia coli 4s.. J Bacteriol 2015 Mar;197(5):905-12.
    doi: 10.1128/JB.02398-14pmc: PMC4325112pubmed: 25512310google scholar: lookup
  34. Sauvageau D, Cooper DG. Two-stage, self-cycling process for the production of bacteriophages.. Microb Cell Fact 2010 Nov 1;9:81.
    doi: 10.1186/1475-2859-9-81pmc: PMC2989940pubmed: 21040541google scholar: lookup
  35. Wang G, Jin S, Ling X, Li Y, Hu Y, Zhang Y, Huang Y, Chen T, Lin J, Ning Z, Meng Y, Li X. Proteomic Profiling of LPS-Induced Macrophage-Derived Exosomes Indicates Their Involvement in Acute Liver Injury.. Proteomics 2019 Feb;19(3):e1800274.
    doi: 10.1002/pmic.201800274pubmed: 30474914google scholar: lookup
  36. Letarov AV, Kulikov EE. Adsorption of Bacteriophages on Bacterial Cells.. Biochemistry (Mosc) 2017 Dec;82(13):1632-1658.
    doi: 10.1134/S0006297917130053pubmed: 29523063google scholar: lookup
  37. Golomidova AK, Kulikov EE, Prokhorov NS, Guerrero-Ferreira RС, Knirel YA, Kostryukova ES, Tarasyan KK, Letarov AV. Branched Lateral Tail Fiber Organization in T5-Like Bacteriophages DT57C and DT571/2 is Revealed by Genetic and Functional Analysis.. Viruses 2016 Jan 21;8(1).
    doi: 10.3390/v8010026pmc: PMC4728585pubmed: 26805872google scholar: lookup
  38. Walter M, Fiedler C, Grassl R, Biebl M, Rachel R, Hermo-Parrado XL, Llamas-Saiz AL, Seckler R, Miller S, van Raaij MJ. Structure of the receptor-binding protein of bacteriophage det7: a podoviral tail spike in a myovirus.. J Virol 2008 Mar;82(5):2265-73.
    doi: 10.1128/JVI.01641-07pmc: PMC2258939pubmed: 18077713google scholar: lookup
  39. Andres D, Baxa U, Hanke C, Seckler R, Barbirz S. Carbohydrate binding of Salmonella phage P22 tailspike protein and its role during host cell infection.. Biochem Soc Trans 2010 Oct;38(5):1386-9.
    doi: 10.1042/BST0381386pubmed: 20863318google scholar: lookup
  40. Prokhorov NS, Riccio C, Zdorovenko EL, Shneider MM, Browning C, Knirel YA, Leiman PG, Letarov AV. Function of bacteriophage G7C esterase tailspike in host cell adsorption.. Mol Microbiol 2017 Aug;105(3):385-398.
    doi: 10.1111/mmi.13710pubmed: 28513100google scholar: lookup
  41. Shashkov AS, Lipkind GM, Knirel YA, Kochetkov NK. Stereochemical factors determining the effects of glycosylation on the 13C chemical shifts in carbohydrates. Magn Reson Chem 26:735–747.
    doi: 10.1002/mrc.1260260904google scholar: lookup
  42. Kapaev RR, Toukach PV. Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software.. J Chem Inf Model 2016 Jun 27;56(6):1100-4.
    doi: 10.1021/acs.jcim.6b00083pubmed: 27227420google scholar: lookup
  43. Golomidova AK, Kulikov EE, Babenko VV, Ivanov PA, Prokhorov NS, Letarov AV. Escherichia coli bacteriophage Gostya9, representing a new species within the genus T5virus.. Arch Virol 2019 Mar;164(3):879-884.
    doi: 10.1007/s00705-018-4113-2pubmed: 30506471google scholar: lookup
  44. Golomidova AK, Kulikov EE, Kudryavtseva AV, Letarov AV. Complete Genome Sequence of Escherichia coli Bacteriophage PGT2.. Genome Announc 2018 Jan 18;6(3).
    doi: 10.1128/genomeA.01370-17pmc: PMC5773715pubmed: 29348330google scholar: lookup
  45. Isaeva AS, Kulikov EE, Tarasyan KK, Letarov AV. A Novel High-Resolving Method for Genomic PCR-Fingerprinting of Enterobacteria.. Acta Naturae 2010 Apr;2(1):82-8.
    doi: 10.32607/20758251-2010-2-1-82-87pmc: PMC3347548pubmed: 22649631google scholar: lookup
  46. Mitarai N, Brown S, Sneppen K. Population Dynamics of Phage and Bacteria in Spatially Structured Habitats Using Phage λ and Escherichia coli.. J Bacteriol 2016 Jun 15;198(12):1783-93.
    doi: 10.1128/JB.00965-15pmc: PMC4886755pubmed: 27068593google scholar: lookup
  47. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.. J Comput Biol 2012 May;19(5):455-77.
    doi: 10.1089/cmb.2012.0021pmc: PMC3342519pubmed: 22506599google scholar: lookup
  48. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications.. BMC Bioinformatics 2009 Dec 15;10:421.
    doi: 10.1186/1471-2105-10-421pmc: PMC2803857pubmed: 20003500google scholar: lookup
  49. Starikova EV, Tikhonova PO, Prianichnikov NA, Rands CM, Zdobnov EM, Ilina EN, Govorun VM. Phigaro: high-throughput prophage sequence annotation.. Bioinformatics 2020 Jun 1;36(12):3882-3884.
    doi: 10.1093/bioinformatics/btaa250pubmed: 32311023google scholar: lookup
  50. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer.. Bioinformatics 2011 Apr 1;27(7):1009-10.
    doi: 10.1093/bioinformatics/btr039pmc: PMC3065679pubmed: 21278367google scholar: lookup
  51. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.. PLoS One 2010 Jun 25;5(6):e11147.
    doi: 10.1371/journal.pone.0011147pmc: PMC2892488pubmed: 20593022google scholar: lookup
  52. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions.. BMC Bioinformatics 2013 Feb 21;14:60.
    doi: 10.1186/1471-2105-14-60pmc: PMC3665452pubmed: 23432962google scholar: lookup
  53. Lefort V, Desper R, Gascuel O. FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program.. Mol Biol Evol 2015 Oct;32(10):2798-800.
    doi: 10.1093/molbev/msv150pmc: PMC4576710pubmed: 26130081google scholar: lookup
  54. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 106:645–668.
    doi: 10.1086/282802google scholar: lookup
  55. Rambaut A. FigTree. Tree figure drawing tool. .
  56. Göker M, García-Blázquez G, Voglmayr H, Tellería MT, Martín MP. Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora.. PLoS One 2009 Jul 29;4(7):e6319.
    doi: 10.1371/journal.pone.0006319pmc: PMC2712678pubmed: 19641601google scholar: lookup
  57. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C, Rohde M, Fartmann B, Goodwin LA, Chertkov O, Reddy T, Pati A, Ivanova NN, Markowitz V, Kyrpides NC, Woyke T, Göker M, Klenk HP. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy.. Stand Genomic Sci 2014;9:2.
    doi: 10.1186/1944-3277-9-2pmc: PMC4334874pubmed: 25780495google scholar: lookup
  58. L'vov VL, Dashunin VM, Ramos EL, Shashkov AS, Dmitriev BA, Kochetkov NK. Somatic antigens of Shigella: the structure of the polysaccharide chain of Shigella boydii type 2 lipopolysaccharide.. Carbohydr Res 1983 Dec 10;124(1):141-9.
    doi: 10.1016/0008-6215(83)88362-1pubmed: 6362879google scholar: lookup

Citations

This article has been cited 2 times.
  1. Letarov AV, Letarova MA. The Burden of Survivors: How Can Phage Infection Impact Non-Infected Bacteria?. Int J Mol Sci 2023 Feb 1;24(3).
    doi: 10.3390/ijms24032733pubmed: 36769055google scholar: lookup
  2. Efimov AD, Golomidova AK, Kulikov EE, Belalov IS, Ivanov PA, Letarov AV. RB49-like Bacteriophages Recognize O Antigens as One of the Alternative Primary Receptors.. Int J Mol Sci 2022 Sep 26;23(19).
    doi: 10.3390/ijms231911329pubmed: 36232640google scholar: lookup
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