REFERENCES

1. Fitz-Gibbon S, Tomida S, Chiu BH, et al. Propionibacterium acnes strain populations in the human skin microbiome associated with acne. J Invest Dermatol 2013;133:2152-60.

2. Li H. The human skin microbiome in health and skin diseases. In: Nelson K, editor. Metagenomics of the human body. New York: Springer. 2011. pp. 145-63.

3. Marinelli LJ, Fitz-Gibbon S, Hayes C, et al. Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates. mBio 2012;3:e00279-12.

4. Perry A, Lambert P. Propionibacterium acnes: infection beyond the skin. Expert Rev Anti Infect Ther 2011;9:1149-56.

5. Leheste JR, Ruvolo KE, Chrostowski JE, et al. P. acnes-driven disease pathology: current knowledge and future directions. Front Cell Infect Microbiol 2017;7:81.

6. Brüggemann H, Lood R. Bacteriophages infecting Propionibacterium acnes. Biomed Res Int 2013;2013:705741.

7. Jończyk-Matysiak E, Weber-Dąbrowska B, Żaczek M, et al. Prospects of phage application in the treatment of acne caused by Propionibacterium acnes. Front Microbiol 2017;8:164.

8. Coenye T, Peeters E, Nelis HJ. Biofilm formation by Propionibacterium acnes is associated with increased resistance to antimicrobial agents and increased production of putative virulence factors. Res Microbiol 2007;158:386-92.

9. Holmberg A, Lood R, Mörgelin M, et al. Biofilm formation by Propionibacterium acnes is a characteristic of invasive isolates. Clin Microbiol Infect 2009;15:787-95.

10. Brüggemann H, Lomholt HB, Kilian M. The flexible gene pool of Propionibacterium acnes. Mob Genet Elements 2012;2:145-8.

11. Liu J, Yan R, Zhong Q, et al. The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin. ISME J 2015;9:2078-93.

12. Labrie SJ, Samson JE, Moineau S. Bacteriophage resistance mechanisms. Nature Rev Microbiol 2010;8:317-27.

13. Sun X, Göhler A, Heller KJ, Neve H. The ltp gene of temperate Streptococcus thermophilus phage TP-J34 confers superinfection exclusion to Streptococcus thermophilus and Lactococcus lactis. Virology 2006;350:146-57.

14. Seed KD. Battling phages: how bacteria defend against viral attack. PLoS Pathog 2015;11:e1004847.

15. McAllister WT, Barrett CL. Superinfection exclusion by bacteriophage T7. J Virol 1977;24:709-11.

16. Hofer B, Ruge M, Dreiseikelmann B. The superinfection exclusion gene (sieA) of bacteriophage P22: identification and overexpression of the gene and localization of the gene product. J Bacteriol 1995;177:3080-6.

17. Mahony J, McGrath S, Fitzgerald GF, van Sinderen D. Identification and characterization of lactococcal-prophage-carried superinfection exclusion genes. Appl Environ Microbiol 2008;74:6206-15.

18. van den Berg B, Silale A, Baslé A, Brandner AF, Mader SL, Khalid S. Structural basis for host recognition and superinfection exclusion by bacteriophage T5. Proc Natl Acad Sci U S A 2022;119:e2211672119.

19. Leavitt JC, Woodbury BM, Gilcrease EB, Bridges CM, Teschke CM, Casjens SR. Bacteriophage P22 SieA mediated superinfection exclusion. mBio 2024;15:e02169-23.

20. Hasan M, Ahn J. Evolutionary dynamics between phages and bacteria as a possible approach for designing effective phage therapies against antibiotic-resistant bacteria. Antibiotics 2022;11:915.

21. Ruiz-Cruz S, Parlindungan E, Erazo Garzon A, et al. Lysogenization of a lactococcal host with three distinct temperate phages provides homologous and heterologous phage resistance. Microorganisms 2020;8:1685.

22. Bebeacua C, Lorenzo Fajardo JC, Blangy S, et al. X-ray structure of a superinfection exclusion lipoprotein from phage TP-J34 and identification of the tape measure protein as its target. Mol Microbiol 2013;89:152-65.

23. Ali Y, Koberg S, Heßner S, et al. Temperate Streptococcus thermophilus phages expressing superinfection exclusion proteins of the Ltp type. Front Microbiol 2014;5:98.

24. Lood R, Collin M. Characterization and genome sequencing of two Propionibacterium acnes phages displaying pseudolysogeny. BMC Genomics 2011;12:198.

25. Cieślik M, Bagińska N, Jończyk-Matysiak E, Węgrzyn A, Węgrzyn G, Górski A. Temperate bacteriophages - the powerful indirect modulators of eukaryotic cells and immune functions. Viruses 2021;13:1013.

26. Shapiro C, Moberg-Parker J, Toma S, et al. Comparing the impact of course-based and apprentice-based research experiences in a life science laboratory curriculum. J Microbiol Biol Educ 2015;16:186-97.

27. Webster GF, Cummins CS. Use of bacteriophage typing to distinguish Propionibacterium acne types I and II. J Clin Microbiol 1978;7:84-90.

28. Neve H, Freudenberg W, Diestel-Feddersen F, Ehlert R, Heller KJ. Biology of the temperate Streptococcus thermophilus bacteriophage TP-J34 and physical characterization of the phage genome. Virology 2003;315:184-94.

29. Russell DA. Sequencing, assembling, and finishing complete bacteriophage genomes. In: Clokie M, Kropinski A, Lavigne R, editors. Bacteriophages: methods in molecular biology. New York: Humana Press. 2018. pp. 109-25.

30. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007;23:673-9.

31. Besemer J, Borodovsky M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 2005;33:W451-4.

32. Lawrence JG. DNA Master. 2007. Available from: http://cobamide2.bio.pitt.edu/computer.htm. [Last accessed on 16 Apr 2024].

33. Jordan TC, Burnett SH, Carson S, et al. A broadly implementable research course in phage discovery and genomics for first-year undergraduate students. mBio 2014;5:e01051-13.

34. Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 2011;12:395.

35. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-10.

36. Söding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005;33:W244-8.

37. Marchler-Bauer A, Derbyshire MK, Gonzales NR, et al. CDD: NCBI’s conserved domain database. Nucleic Acids Res 2015;43:D222-6.

38. Russell DA, Hatfull GF. PhagesDB: the actinobacteriophage database. Bioinformatics 2017;33:784-6.

39. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60.

40. Meier-Kolthoff JP, Göker M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics 2017;33:3396-404.

41. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015;32:2798-800.

42. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972;106:645-68. Available from: http://www.jstor.org/stable/2459725. [Last accessed on 16 Apr 2024]

43. Letunic I, Bork P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021;49:W293-6.

44. Mitchell A, Chang HY, Daugherty L, et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res 2015;43:D213-21.

45. Bailey TJ, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994;2:28-36.

46. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870-4.

47. Källberg M, Wang H, Wang S, et al. Template-based protein structure modeling using the RaptorX web server. Nature Protoc 2012;7:1511-22.

48. Jumper J, Evans R, Pritzel A, et al. Highly accurate protein structure prediction with AlphaFold. Nature 2021;596:583-9.

49. Holm L, Laiho A, Törönen P, Salgado M. DALI shines a light on remote homologs: one hundred discoveries. Protein Sci 2023;32:e4519.

50. Jurrus E, Engel D, Star K, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 2018;27:112-28.

51. Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005;33:2302-9.

52. ImageJ. Image processing and analysis in Java. Available from: https://imagej.nih.gov/ij/. [Last accessed on 16 Apr 2024]

53. Hewetson A, Khan NH, Dominguez MJ, et al. Maturation of the functional mouse CRES amyloid from globular form. Proc Natl Acad Sci U S A 2020;117:16363-72.

54. Whelly S, Johnson S, Powell J, Borchardt C, Hastert MC, Cornwall GA. Nonpathological extracellular amyloid is present during normal epididymal sperm maturation. PLoS One 2012;7:e36394.

55. Wu X, Zhao Y, Sun L, et al. Crystal structure of CagV, the Helicobacter pylori homologue of the T4SS protein VirB8. FEBS J 2019;286:4294-309.

56. Singer ZS, Ambrose PM, Danino T, Rice CM. Quantitative measurements of early alphaviral replication dynamics in single cells reveals the basis for superinfection exclusion. Cell Syst 2021;12:210-9.e3.

57. Biggs KRH, Bailes CL, Scott L, Wichman HA, Schwartz EJ. Ecological approach to understanding superinfection inhibition in bacteriophage. Viruses 2021;13:1389.

58. Carvalho C, Ren R, Han J, Qu F. Natural selection, intracellular bottlenecks of virus populations, and viral superinfection exclusion. Annu Rev Virol 2022;9:121-37.

59. Redman M, King A, Watson C, King D. What is CRISPR/Cas9? Arch Dis Child Educ Pract Ed 2016;101:213-5.

60. Cobian N, Garlet A, Hidalgo-Cantabrana C, Barrangou R. Comparative genomic analyses and CRISPR-Cas characterization of Cutibacterium acnes provide insights into genetic diversity and typing applications. Front Microbiol 2021;12:758749.

61. Kermani AA. A guide to membrane protein X-ray crystallography. FEBS J 2021;288:5788-804.

62. Marinelli LJ, Hatfull GF, Piuri M. Recombineering: a powerful tool for modification of bacteriophage genomes. Bacteriophage 2012;2:5-14.

63. Knödlseder N, Nevot G, Fábrega MJ, et al. Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting. PLoS Pathog 2022;18:e1010420.

Microbiome Research Reports
ISSN 2771-5965 (Online)

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/