Microbiology and Biotechnology Letters (한국미생물·생명공학회지)

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Pan-Genome Analysis Reveals Origin Specific Genome Expansion in Enterococcus mundtii Strains

  • Neeti Pandey (Kalindi College, Department of Zoology, University of Delhi) ;
  • Raman Rajagopal (Gut Biology Lab, Room No 117, Department of Zoology, University of Delhi-07) ;
  • Shubham Dhara (SGTB Khalsa College, University of Delhi-07)
  • Received : 2023.06.15
  • Accepted : 2023.10.16
  • Published : 2024.06.28
Download PDF
⟨ Previous Next ⟩

Abstract

Pan-genome analysis is used to interpret genome heterogeneity and diversification of bacterial species. Here, we present pan-genome analysis of 22 strains of Enterococcus mundtii. The GenBank file of E. mundtii strains that have been isolated from different sources i.e., human fecal matter, soil, leaf, dairy products, and insects was downloaded from National Center for Biotechnology Information (NCBI) database and analyzed using BPGA-1.3.0 (Bacterial Pan Genome Analysis) pipeline. Out of a total, 4503 gene families, 1843 belongs to the core genes whereas 1,762 gene families represent the accessory genes and 898 gene families depict the unique genes among all the selected genomes. Majority of the core genes belongs to the categories of Metabolism (37.83%) and Information storage & processing (29.84%) whereas unique genes belongs to the category of Information storage & processing (48.08%). Further, accessory genes are almost equally present in both functional categories i.e. Information storage & processing and Metabolism (34.34% and 32.27% respectively). Further, subset analysis on the basis of the origin of isolates exhibits presence and absence of exclusive gene families. The observation suggests that even closely related strains of a species show extensive disparity in genome owing to their ability to adapt to a specific environment.

Keywords

Acknowledgement

We thank Dr. Vinod Kumar Gupta (Mayo clinic, Rochester) for his valuable time, suggestions and guidance that improved the manuscript.

References

  1. Holzapfel WH, Wood BJB. 2014. Lactic acid bacteria: Biodiversity and taxonomy. Wiley-Blackwell. 
  2. Thiercelin ME, Jouhaud L. 1903. Reproduction de l'enterocoque; tachescentrales; granulations peripheriques et microblastes. Comptes Rendus desSeances de la Societe de Biologie et de ses Filiales 55: 686-698. 
  3. Andrewes FW, Horder TJ. 1906. A study of the Streptococci pathogenic for man. Lancet 168: 708-713. 
  4. Schleifer KH, Kilpper-Balz R. 1984. Transfer of Streptococcus faecalis and Streptococcus faecium to the genus Enterococcus nom rev. as Enterococcus faecalis comb. nov. and Enterococcus faecium comb. nov. Int. J. Syst. Bacteriol. 34: 31-34. 
  5. Collins MD, Jones D, Farrow JAE, Kilpper-Balz R, Schleifer KH. 1984. Enterococcus avium nom. rev., comb. nov.; E. casseliflavus norn. rev., comb. nov.; E. durans norn. rev., comb. nov.; E. gallinarum comb. nov.; and E. malodoratus sp. nova. Int. J. Syst. Bacteriol. 34: 220-223. 
  6. Naser SM, Vancanneyt M, De Graef E, Devriese LA, Snauwaert C, Lefebvre K, et al. 2005. Enterococcus canintestini sp. nov., from faecal samples of healthydogs. Int. J. Syst. Evol. Microbiol. 55: 2177-2182. 
  7. de Vaux A, Laguerre G, Divies C, Prevost H. 1998. Enterococcus asini sp. nov. isolated from the caecum of donkeys (Equus asinus). Int. J. Syst. Bacteriol. 48 (Pt. (2)): 383-387. 
  8. Lebreton F, Willems RJL, Gilmore MS. 2014. Enterococcus Diversity, Origins in Nature, and Gut Colonization. In: Gilmore, M. S., Clewell, D. B., Ike, Y., Shankar, N. (Eds.), Enterococci: From Commensals to Leading Causes of Drug Resistant Infection. Massachusetts Eye and Ear Infirmary, Boston, pp. 5-63. 
  9. Sistek V, Maheux AF, Boissinot M, Bernard KA, Cantin P, Cleenwerck I, et al. 2012. Enterococcus ureasiticus sp. nov. and Enterococcus quebecensis sp. nov., isolated from water. Int. J. Syst. Evol. Microbiol. 62: 1314-1320. 
  10. Foulquie Moreno MR, Sarantinopoulos P, Tsakalidou E, De Vuyst L. 2006. The role and application of Enterococci in food and health. Int. J. Food Microbiol. 106: 1-24. 
  11. Giraffa G. 2003. Functionality of Enterococci in dairy products. Int. J. Food Microbiol. 88: 215-222. 
  12. Franz CM, Huch M, Abriouel H, Holzapfel W, Galvez A. 2011. Enterococci asprobiotics and their implications in food safety. Int. J. Food Microbiol. 151: 125-140. 
  13. Moellering Jr. RC. 1992. Emergence of Enterococcus as a significant pathogen. Clin. Infect. Dis. 14: 1173-1176. 
  14. O'Driscoll T, Crank CW. 2015. Vancomycin-resistant Enterococcal infections: epidemiology, clinical manifestations, and optimal management. Infect. Drug Resist. 8: 217-230. 
  15. Klein G. 2003. Taxonomy, ecology and antibiotic resistance of enterococci from food and the gastrointestinal tract. Int. J. Food Microbiol. 88: 123-131. 
  16. Collins MD, Farrow JA, Jones D. 1986. Enterococcus mundtii sp. nov. Int. J. Systemat. Evol. Microbiol. 36: 8-12. 
  17. Giraffa G, Carminati D, Neviani E. 1997. Enterococci isolated from dairy products: a review of risks and potential technological use. J. Food Protect. 60: 732-738. 
  18. Espeche MC, Otero MC, Sesma F, Nader-Macias ME. 2009. Screening of surface properties and antagonistic substances production by lactic acid bacteria isolated from the mammary gland of healthy and mastitic cows. Vet. Microbiol. 135: 346-357. 
  19. De Kwaadsteniet M, Todorov SD, Knoetze H, Dicks LM. 2005. Characterization of a 3944 Da bacteriocin, produced by Enterococcus mundtii ST15, with activity against Gram-positive and Gram-negative bacteria. Int. J. Food Microbiol. 105: 433-444. 
  20. Ferreira AE, Canal N, Morales D, Fuentefria DB, Corcao G. 2007. Characterization of enterocins produced by Enterococcus mundtii isolated from humans feces. Brazil. Arch. Biol. Technol. 50: 249-258. 
  21. Settanni L, Valmorri S, Suzzi G, Corsetti A. 2008. The role of environmental factors and medium composition on bacteriocin-like inhibitory substances (BLIS) production by Enterococcus mundtii strains. Food Microbiol. 25: 722-728. 
  22. Giraffa G. 1995. Enterococcal bacteriocins: their potential use as anti-Listeria factors in dairy technology. Food Microbiol. 12: 551-556. 
  23. Franz CMAP, Holzapfel WH, Stiles ME. 1999. Enterococci at the crossroads of food safety? Intern. J. Food Microbiol. 47: 1-24. 
  24. De Vuyst L, Foulquie Moreno M, Revets H. 2002. Screening for enterocins and detection of hemolysin and vancomycin resistance in enterococci of different origins. Intern. J. Food Microbiol. 2635: 1-20. 
  25. Ferreira AE, Canal N, Morales D, Bopp D, Corcao G. 2007. Characterization of enterocins produced by Enterococcus mundtii isolated from humans feces. Braz. Arch. Biol. Technol. 50: 249-258. 
  26. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2014. Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25: 1043-1055. 
  27. Alexey G, Vladislav S, Nikolay V, Glenn Tesler. 2013. QUAST VERSION 5.2: quality assessment tool for genome assemblies. Bioinformatics 29: 1072-1075. 
  28. Chaudhari N, Gupta V, Dutta C. 2016. BPGA-1.3.0- an ultra-fast pan-genome analysis pipeline. Sci. Rep. 6: 24373. 
  29. Rodriguez-R LM, Konstantinidis KT. 2016. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ. 4: e1900v1. 
  30. Morpheus. https://software.broadinstitute.org/morpheus 
  31. Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol. 33: 1870-1874. 
  32. Rice P, Longden I, Bleasby A. 2000. EMBOSS: The european molecular biology open software suite. Trends Gen. 16: 276-277. 
  33. Wang D, Zhang Y, Zhang Z, et al. 2010. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genom. Proteom. Bioinform. 8: 77-80. 
  34. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E, Thompson FL. 2013. Microbial genomic taxonomy. BMC Genomics, doi: 10.1186/1471-2164-14-913. 
  35. Singh NK, Tyagi A. 2017. A detailed analysis of codon usage patterns and influencing factors in Zika virus. Arch. Virol. 162: 1963-1973. 
  36. Chen Y, Shi Y, Deng H, Gu T, Xu J, Ou J, et al. 2014. Characterization of the porcine epidemic diarrhea virus codon usage bias. Infect. Genet. Evol. 28: 95-100. 
  37. Butt AM, Nasrullah I, Qamar R, Tong Y. 2016. Evolution of codon usage in Zika virus genomes is host and vector specific. Emerg. Microbes Infect. 5: e107. 
  38. Singh RK, Pandey SP. 2017. Phylogenetic and evolutionary analysis of plant ARGONAUTES. Methods Mol. Biol. 1640: 267-294. 
  39. Scaria J, Ponnala L, Janvilisri T, Yan W, Mueller LA, Chang YF. 2010. Analysis of ultra low genome conservation in Clostridium difficile. PLoS One 5: e15147. 
  40. Dutta C, Paul S. 2012. Microbial lifestyle and genome signatures. Curr. Genomics 13: 153-162. 
  41. Ochman H, Moran NA. 2001. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292: 1096-1099. 
  42. Toft C, Andersson SG. 2010. Evolutionary microbial genomics: insights into bacterial host adaptation. Nat. Rev. Genet. 11: 465-475. 
  43. Dobrindt U, Hochhut B, Hentschel U, Hacker J. 2004. Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2: 414-424. 
  44. Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304. 
  45. Didelot X, Maiden MC. 2010. Impact of recombination on bacterial evolution. Trends Microbiol. 18: 315-322. 
  46. Lefebure T, Stanhope MJ. 2009. Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res. 19: 1224-1232. 
  47. Liu LX, Li R, Worth JRP, Li X, Li P, Cameron KM, et al. 2017. The complete chloroplast genome of Chinese bayberry (Morella rubra, myricaceae): Implications for understanding the evolution of fagales. Front. Plant Sci. 8. doi: 10.3389/fpls.2017.00968.