Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex
详细信息 查看全文
- 作者：Konstantinos Papadimitriou (49)
Rania Anastasiou (49)
Eleni Mavrogonatou (50)
Jochen Blom (51)
Nikos C Papandreou (52)
Stavros J Hamodrakas (52)
St茅phanie Ferreira (53)
Pierre Renault (54) (55)
Philip Supply (53) (56) (57) (58) (59)
Bruno Pot (56) (57) (58) (59)
Effie Tsakalidou (49)
49. Laboratory of Dairy Research ; Department of Food Science and Human Nutrition ; Agricultural University of Athens ; Iera Odos 75 ; Athens ; 118 55 ; Greece
50. Laboratory of Cell Proliferation and Ageing ; Institute of Biosciences and Applications ; National Centre for Scientific Research 鈥淒emokritos鈥? Athens ; 153 10 ; Greece
51. Computational Genomics ; Center for Biotechnology ; Bielefeld University ; Bielefeld ; Germany
52. Department of Cell Biology and Biophysics ; Faculty of Biology ; University of Athens ; Panepistimiopolis ; Athens ; 157 01 ; Greece
53. Genoscreen ; Genomic Platform and R&D ; Campus de l鈥橧nstitut Pasteur ; 1 rue du Professeur Calmette ; Lille ; 59000 ; France
54. INRA ; UMR1319 Micalis ; Jouy-en-Josas ; F-78352 ; France
55. AgroParisTech ; UMR Micalis ; Jouy-en-Josas ; F-78352 ; France
56. Institut Pasteur de Lille ; Center for Infection and Immunity of Lille (CIIL) ; Lille ; F-59019 ; France
57. Inserm U1019 ; F-59019 ; Lille ; France
58. CNRS UMR8204 ; Lille ; F-59021 ; France
59. Univ Lille de Nord France ; Lille ; F-59000 ; France - 关键词：Streptococcus ; Genome ; Adaptation ; Gene decay ; Pseudogene ; Horizontal gene transfer ; Pathogenicity ; Virulence factor ; Milk ; Niche
- 刊名：BMC Genomics
- 出版年：2014
- 出版时间：December 2014
- 年：2014
- 卷：15
- 期：1
- 全文大小：797 KB
- 参考文献：1. Konings, WN, Kok, J, Kuipers, OP, Poolman, B (2000) Lactic acid bacteria: the bugs of the new millennium. Curr Opin Microbiol 3: pp. 276-282 CrossRef
2. Masood, MI, Qadir, MI, Shirazi, JH, Khan, IU (2011) Beneficial effects of lactic acid bacteria on human beings. Crit Rev Microbiol 37: pp. 91-98 CrossRef
3. Donohue, DC, Gueimonde, M Some Considerations for the Safety of Novel Probiotic Bacteria. In: Lahtinen, S, Salminen, S, von Wright, A, Ouwehand, AC eds. (2012) Lactic Acid Bacteria: Microbiological and Functional Aspects. CRC Press Taylor & Francis Group, Boca Raton
4. Woodford, N, Livermore, DM (2009) Infections caused by Gram-positive bacteria: a review of the global challenge. J Infect 59: pp. S4-S16 CrossRef
5. Facklam, R (2002) What happened to the streptococci: overview of taxonomic and nomenclature changes. Clin Microbiol Rev 15: pp. 613-630 CrossRef
6. Nobbs, AH, Lamont, RJ, Jenkinson, HF (2009) Streptococcus adherence and colonization. Microbiol Mol Biol Rev 73: pp. 407-450 CrossRef
7. Bolotin, A, Quinquis, B, Renault, P, Sorokin, A, Ehrlich, SD, Kulakauskas, S, Lapidus, A, Goltsman, E, Mazur, M, Pusch, GD, Fonstein, M, Overbeek, R, Kyprides, N, Purnelle, B, Prozzi, D, Ngui, K, Masuy, D, Hancy, F, Burteau, S, Boutry, M, Delcour, J, Goffeau, A, Hols, P (2004) Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol 22: pp. 1554-1558 CrossRef
8. Hols, P, Hancy, F, Fontaine, L, Grossiord, B, Prozzi, D, Leblond-Bourget, N, Decaris, B, Bolotin, A, Delorme, C, Dusko Ehrlich, S, Guedon, E, Monnet, V, Renault, P, Kleerebezem, M (2005) New insights in the molecular biology and physiology of Streptococcus thermophilus revealed by comparative genomics. FEMS Microbiol Rev 29: pp. 435-463
9. Jans, C, Lacroix, C, Meile, L (2012) A novel multiplex PCR/RFLP assay for the identification of Streptococcus bovis/Streptococcus equinus complex members from dairy microbial communities based on the 16S rRNA gene. FEMS Microbiol Lett 326: pp. 144-150 CrossRef
10. Abdulamir, AS, Hafidh, RR, Abu Bakar, F (2011) The association of Streptococcus bovis/gallolyticus with colorectal tumors: the nature and the underlying mechanisms of its etiological role. J Exp Clin Cancer Res 30: pp. 11 CrossRef
11. Galdy, S, Nastasi, G (2012) Streptococcus bovis endocarditis and colon cancer: myth or reality? A case report and literature review. BMJ Case Rep 2012: pp. 1-2
12. Herrera, P, Kwon, YM, Ricke, SC (2009) Ecology and pathogenicity of gastrointestinal Streptococcus bovis. Anaerobe 15: pp. 44-54 CrossRef
13. De Vuyst, L, Tsakalidou, E (2008) Streptococcus macedonicus, a multi-functional and promising species for dairy fermentations. Int Dairy J 18: pp. 476-485 CrossRef
14. Maragkoudakis, PA, Papadelli, M, Georgalaki, M, Panayotopoulou, EG, Martinez-Gonzalez, B, Mentis, AF, Petraki, K, Sgouras, DN, Tsakalidou, E (2009) In vitro and in vivo safety evaluation of the bacteriocin producer Streptococcus macedonicus ACA-DC 198.. Int J Food Microbiol 133: pp. 141-147 CrossRef
15. Tsakalidou, E, Zoidou, E, Pot, B, Wassill, L, Ludwig, W, Devriese, LA, Kalantzopoulos, G, Schleifer, KH, Kersters, K (1998) Identification of streptococci from Greek Kasseri cheese and description of Streptococcus macedonicus sp. nov. Int J Syst Bacteriol 48: pp. 519-527 CrossRef
16. Schlegel, L, Grimont, F, Ageron, E, Grimont, PA, Bouvet, A (2003) Reappraisal of the taxonomy of the Streptococcus bovis/Streptococcus equinus complex and related species: description of Streptococcus gallolyticus subsp. gallolyticus subsp. nov., S. gallolyticus subsp. macedonicus subsp. nov. and S. gallolyticus subsp. pasteurianus subsp. nov. Int J Syst Evol Microbiol 53: pp. 631-645 CrossRef
17. Whiley, RA, Kilian, M (2003) International committee on systematics of prokaryotes subcommittee on the taxonomy of staphylococci and streptococci: minutes of the closed meeting, 31 July 2002, paris France. Int J Syst Evol Microbiol 53: pp. 915-917 CrossRef
18. Danne, C, Entenza, JM, Mallet, A, Briandet, R, Debarbouille, M, Nato, F, Glaser, P, Jouvion, G, Moreillon, P, Trieu-Cuot, P, Dramsi, S (2011) Molecular characterization of a Streptococcus gallolyticus genomic island encoding a pilus involved in endocarditis. J Infect Dis 204: pp. 1960-1970 CrossRef
19. Papadimitriou, K, Ferreira, S, Papandreou, NC, Mavrogonatou, E, Supply, P, Pot, B, Tsakalidou, E (2012) Complete genome sequence of the dairy isolate Streptococcus macedonicus ACA-DC 198. J Bacteriol 194: pp. 1838-1839 CrossRef
20. Jans, C, Follador, R, Hochstrasser, M, Lacroix, C, Meile, L, Stevens, MJ (2013) Comparative genome analysis of Streptococcus infantarius subsp.infantarius CJ18, an African fermented camel milk isolate with adaptations to dairy environment.. BMC Genomics 14: pp. 200 CrossRef
21. Pati, A, Ivanova, NN, Mikhailova, N, Ovchinnikova, G, Hooper, SD, Lykidis, A, Kyrpides, NC (2010) GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 7: pp. 455-457 CrossRef
22. Lin, IH, Liu, TT, Teng, YT, Wu, HL, Liu, YM, Wu, KM, Chang, CH, Hsu, MT (2011) Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence. PLoS One 6: pp. e20519 CrossRef
23. Blom, J, Albaum, SP, Doppmeier, D, Puhler, A, Vorholter, FJ, Zakrzewski, M, Goesmann, A (2009) EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinforma 10: pp. 154 CrossRef
24. Darling, AE, Mau, B, Perna, NT (2010) ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5: pp. e11147 CrossRef
25. Rusniok, C, Couve, E, Da Cunha, V, El Gana, R, Zidane, N, Bouchier, C, Poyart, C, Leclercq, R, Trieu-Cuot, P, Glaser, P (2010) Genome sequence of Streptococcus gallolyticus: insights into its adaptation to the bovine rumen and its ability to cause endocarditis. J Bacteriol 192: pp. 2266-2276 CrossRef
26. Lombard, V, Golaconda Ramulu, H, Drula, E, Coutinho, PM, Henrissat, B (2014) The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42: pp. D490-D495 CrossRef
27. Crost, EH, Tailford, LE, Le Gall, G, Fons, M, Henrissat, B, Juge, N (2013) Utilisation of mucin glycans by the human gut symbiont Ruminococcus gnavus is strain-dependent. PLoS One 8: pp. e76341 CrossRef
28. Ficko-Blean, E, Boraston, AB (2012) Insights into the recognition of the human glycome by microbial carbohydrate-binding modules. Curr Opin Struct Biol 22: pp. 570-577 CrossRef
29. Liu, M, Bayjanov, JR, Renckens, B, Nauta, A, Siezen, RJ (2010) The proteolytic system of lactic acid bacteria revisited: a genomic comparison. BMC Genomics 11: pp. 36 CrossRef
30. Jans, C, Gerber, A, Bugnard, J, Njage, PM, Lacroix, C, Meile, L (2012) Novel Streptococcus infantarius subsp. infantarius variants harboring lactose metabolism genes homologous to Streptococcus thermophilus.. Food Microbiol 31: pp. 33-42 CrossRef
31. Fernandez-Espla, MD, Garault, P, Monnet, V, Rul, F (2000) Streptococcus thermophilus cell wall-anchored proteinase: release, purification, and biochemical and genetic characterization. Appl Environ Microbiol 66: pp. 4772-4778 CrossRef
32. Dandoy, D, Fremaux, C, de Frahan, MH, Horvath, P, Boyaval, P, Hols, P, Fontaine, L (2011) The fast milk acidifying phenotype of Streptococcus thermophilus can be acquired by natural transformation of the genomic island encoding the cell-envelope proteinase PrtS. Microb Cell Fact 10: pp. S21 CrossRef
33. Calasso, M, Gobbetti, M Lactic Acid Bacteria | Lactobacillus spp.: Other Species. In: Fuquay, JW eds. (2011) Encyclopedia of Dairy Sciences. cademic Press, San Diego, pp. 125-131 CrossRef
34. El Qaidi, S, Yang, J, Zhang, JR, Metzger, DW, Bai, G (2013) The vitamin B(6) biosynthesis pathway in Streptococcus pneumoniae is controlled by pyridoxal 5鈥?phosphate and the transcription factor PdxR and has an impact on ear infection. J Bacteriol 195: pp. 2187-2196 CrossRef
35. LeBlanc, JG, Laino, JE, del Valle, MJ, Vannini, V, van Sinderen, D, Taranto, MP, de Valdez, GF, de Giori, GS, Sesma, F (2011) B-group vitamin production by lactic acid bacteria鈥揷urrent knowledge and potential applications. J Appl Microbiol 111: pp. 1297-1309 CrossRef
36. Dhillon, BK, Chiu, TA, Laird, MR, Langille, MG, Brinkman, FS (2013) IslandViewer update: improved genomic island discovery and visualization. Nucleic Acids Res 41: pp. W129-W132 CrossRef
37. Georgalaki, M, Papadimitriou, K, Anastasiou, R, Pot, B, Van Driessche, G, Devreese, B, Tsakalidou, E (2013) Macedovicin, the second food-grade lantibiotic produced by Streptococcus macedonicus ACA-DC 198. Food Microbiol 33: pp. 124-130 CrossRef
38. Georgalaki, MD, Van Den Berghe, E, Kritikos, D, Devreese, B, Van Beeumen, J, Kalantzopoulos, G, De Vuyst, L, Tsakalidou, E (2002) Macedocin, a food-grade lantibiotic produced by Streptococcus macedonicus ACA-DC 198. Appl Environ Microbiol 68: pp. 5891-5903 CrossRef
39. Georgalaki, M, Papadelli, M, Chassioti, E, Anastasiou, R, Aktypis, A, De Vuyst, L, Van Driessche, G, Devreese, B, Tsakalidou, E (2010) Milk protein fragments induce the biosynthesis of macedocin, the lantibiotic produced by Streptococcus macedonicus ACA-DC 198. Appl Environ Microbiol 76: pp. 1143-1151 CrossRef
40. O鈥橲ullivan, O, O鈥機allaghan, J, Sangrador-Vegas, A, McAuliffe, O, Slattery, L, Kaleta, P, Callanan, M, Fitzgerald, GF, Ross, RP, Beresford, T (2009) Comparative genomics of lactic acid bacteria reveals a niche-specific gene set. BMC Microbiol 9: pp. 50 CrossRef
41. Szczepankowska, AK, G贸recki, RK, Ko艂akowski, P, Bardowski, JK Lactic Acid Bacteria Resistance to Bacteriophage and Prevention Techniques to Lower Phage Contamination. In: Kongo, JM eds. (2013) Dairy Fermentation in R & D for Food, Health and Livestock Purposes. InTech, Croatia
42. Marco, MB, Moineau, S, Quiberoni, A (2012) Bacteriophages and dairy fermentations. Bacteriophage 2: pp. 149-158 CrossRef
43. Solioz, M, Mermod, M, Abicht, HKM, Mancini, S Responses of Lactic Acid Bacteria to Heavy Metal Stress. In: Tsakalidou, E, Papadimitriou, K eds. (2011) Stress Responses of Lactic Acid Bacteria. Springer, New York
44. Liu, CQ, Khunajakr, N, Chia, LG, Deng, YM, Charoenchai, P, Dunn, NW (1997) Genetic analysis of regions involved in replication and cadmium resistance of the plasmid pND302 from Lactococcus lactis. Plasmid 38: pp. 79-90 CrossRef
45. Magnani, D, Barre, O, Gerber, SD, Solioz, M (2008) Characterization of the CopR regulon of Lactococcus lactis IL1403. J Bacteriol 190: pp. 536-545 CrossRef
46. Schirawski, J, Hagens, W, Fitzgerald, GF, Van Sinderen, D (2002) Molecular characterization of cadmium resistance in Streptococcus thermophilus strain 4134: an example of lateral gene transfer. Appl Environ Microbiol 68: pp. 5508-5516 CrossRef
47. Siezen, RJ, Renckens, B, van Swam, I, Peters, S, van Kranenburg, R, Kleerebezem, M, de Vos, WM (2005) Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment. Appl Environ Microbiol 71: pp. 8371-8382 CrossRef
48. Fallico, V, McAuliffe, O, Fitzgerald, GF, Ross, RP (2011) Plasmids of raw milk cheese isolate Lactococcus lactis subsp. lactis biovar diacetylactis DPC3901 suggest a plant-based origin for the strain.. Appl Environ Microbiol 77: pp. 6451-6462 CrossRef
49. Sillanpaa, J, Nallapareddy, SR, Qin, X, Singh, KV, Muzny, DM, Kovar, CL, Nazareth, LV, Gibbs, RA, Ferraro, MJ, Steckelberg, JM, Weinstock, GM, Murray, BE (2009) A collagen-binding adhesin, Acb, and ten other putative MSCRAMM and pilus family proteins of Streptococcus gallolyticus subsp. gallolyticus (Streptococcus bovis Group, biotype I). J Bacteriol 191: pp. 6643-6653 CrossRef
50. Boleij, A, Muytjens, CM, Bukhari, SI, Cayet, N, Glaser, P, Hermans, PW, Swinkels, DW, Bolhuis, A, Tjalsma, H (2011) Novel clues on the specific association of Streptococcus gallolyticus subsp gallolyticus with colorectal cancer. J Infect Dis 203: pp. 1101-1109 CrossRef
51. Boleij, A, Schaeps, RM, de Kleijn, S, Hermans, PW, Glaser, P, Pancholi, V, Swinkels, DW, Tjalsma, H (2009) Surface-exposed histone-like protein a modulates adherence of Streptococcus gallolyticus to colon adenocarcinoma cells. Infect Immun 77: pp. 5519-5527 CrossRef
52. Jung, CJ, Zheng, QH, Shieh, YH, Lin, CS, Chia, JS (2009) Streptococcus mutans autolysin AtlA is a fibronectin-binding protein and contributes to bacterial survival in the bloodstream and virulence for infective endocarditis. Mol Microbiol 74: pp. 888-902 CrossRef
53. Garcia, B, Latasa, C, Solano, C, Garcia-del Portillo, F, Gamazo, C, Lasa, I (2004) Role of the GGDEF protein family in Salmonella cellulose biosynthesis and biofilm formation. Mol Microbiol 54: pp. 264-277 CrossRef
54. Hinse, D, Vollmer, T, Ruckert, C, Blom, J, Kalinowski, J, Knabbe, C, Dreier, J (2011) Complete genome and comparative analysis of Streptococcus gallolyticus subsp. gallolyticus, an emerging pathogen of infective endocarditis.. BMC Genomics 12: pp. 400 CrossRef
55. Chen, L, Xiong, Z, Sun, L, Yang, J, Jin, Q (2012) VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 40: pp. D641-D645 CrossRef
56. VFDB: Comparison of pathogenomic composition of Streptococcus . [ http://www.mgc.ac.cn/cgi-bin/VFs/compvfs.cgi?Genus=Streptococcus]
57. Demuth, DR, Lammey, MS, Huck, M, Lally, ET, Malamud, D (1990) Comparison of Streptococcus mutans and Streptococcus sanguis receptors for human salivary agglutinin. Microb Pathog 9: pp. 199-211 CrossRef
58. Courtney, HS, Li, Y, Dale, JB, Hasty, DL (1994) Cloning, sequencing, and expression of a fibronectin/fibrinogen-binding protein from group A streptococci. Infect Immun 62: pp. 3937-3946
59. Holmes, AR, McNab, R, Millsap, KW, Rohde, M, Hammerschmidt, S, Mawdsley, JL, Jenkinson, HF (2001) The pavA gene of Streptococcus pneumoniae encodes a fibronectin-binding protein that is essential for virulence. Mol Microbiol 41: pp. 1395-1408 CrossRef
60. Hermans, PW, Adrian, PV, Albert, C, Estevao, S, Hoogenboezem, T, Luijendijk, IH, Kamphausen, T, Hammerschmidt, S (2006) The streptococcal lipoprotein rotamase A (SlrA) is a functional peptidyl-prolyl isomerase involved in pneumococcal colonization. J Biol Chem 281: pp. 968-976 CrossRef
61. Terao, Y, Yamaguchi, M, Hamada, S, Kawabata, S (2006) Multifunctional glyceraldehyde-3-phosphate dehydrogenase of Streptococcus pyogenes is essential for evasion from neutrophils. J Biol Chem 281: pp. 14215-14223 CrossRef
62. Winram, SB, Lottenberg, R (1996) The plasmin-binding protein Plr of group a streptococci is identified as glyceraldehyde-3-phosphate dehydrogenase. Microbiology 142: pp. 2311-2320 CrossRef
63. Pancholi, V, Fischetti, VA (1998) alpha-enolase, a novel strong plasmin(ogen) binding protein on the surface of pathogenic streptococci. J Biol Chem 273: pp. 14503-14515 CrossRef
64. Tseng, HJ, McEwan, AG, Paton, JC, Jennings, MP (2002) Virulence of Streptococcus pneumoniae: PsaA mutants are hypersensitive to oxidative stress. Infect Immun 70: pp. 1635-1639 CrossRef
65. Angel, CS, Ruzek, M, Hostetter, MK (1994) Degradation of C3 by Streptococcus pneumoniae. J Infect Dis 170: pp. 600-608 CrossRef
66. Ibrahim, YM, Kerr, AR, McCluskey, J, Mitchell, TJ (2004) Role of HtrA in the virulence and competence of Streptococcus pneumoniae. Infect Immun 72: pp. 3584-3591 CrossRef
67. Lyon, WR, Caparon, MG (2003) Trigger factor-mediated prolyl isomerization influences maturation of the Streptococcus pyogenes cysteine protease. J Bacteriol 185: pp. 3661-3667 CrossRef
68. Kadioglu, A, Taylor, S, Iannelli, F, Pozzi, G, Mitchell, TJ, Andrew, PW (2002) Upper and lower respiratory tract infection by Streptococcus pneumoniae is affected by pneumolysin deficiency and differences in capsule type. Infect Immun 70: pp. 2886-2890 CrossRef
69. Herrero, IA, Rouse, MS, Piper, KE, Alyaseen, SA, Steckelberg, JM, Patel, R (2002) Reevaluation of Streptococcus bovis endocarditis cases from 1975 to 1985 by 16S ribosomal DNA sequence analysis. J Clin Microbiol 40: pp. 3848-3850 CrossRef
70. Malkin, J, Kimmitt, PT, Ou, HY, Bhasker, PS, Khare, M, Deng, Z, Stephenson, I, Sosnowski, AW, Perera, N, Rajakumar, K (2008) Identification of Streptococcus gallolyticus subsp. macedonicus as the etiological agent in a case of culture-negative multivalve infective endocarditis by 16S rDNA PCR analysis of resected valvular tissue. J Heart Valve Dis 17: pp. 589-592
71. Jin, D, Chen, C, Li, L, Lu, S, Li, Z, Zhou, Z, Jing, H, Xu, Y, Du, P, Wang, H, Xiong, Y, Zheng, H, Bai, X, Sun, H, Wang, L, Ye, C, Gottschalk, M, Xu, J (2013) Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis. BMC Microbiol 13: pp. 141 CrossRef
72. Romero, B, Morosini, MI, Loza, E, Rodriguez-Banos, M, Navas, E, Canton, R, Campo, RD (2011) Reidentification of Streptococcus bovis isolates causing bacteremia according to the new taxonomy criteria: still an issue?. J Clin Microbiol 49: pp. 3228-3233 CrossRef
73. Aziz, RK, Bartels, D, Best, AA, DeJongh, M, Disz, T, Edwards, RA, Formsma, K, Gerdes, S, Glass, EM, Kubal, M, Meyer, F, Olsen, GJ, Olson, R, Osterman, AL, Overbeek, RA, McNeil, LK, Paarmann, D, Paczian, T, Parrello, B, Pusch, GD, Reich, C, Stevens, R, Vassieva, O, Vonstein, V, Wilke, A, Zagnitko, O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: pp. 75 CrossRef
74. Van Domselaar, GH, Stothard, P, Shrivastava, S, Cruz, JA, Guo, A, Dong, X, Lu, P, Szafron, D, Greiner, R, Wishart, DS (2005) BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res 33: pp. W455-W459 CrossRef
75. Carver, T, Thomson, N, Bleasby, A, Berriman, M, Parkhill, J (2009) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25: pp. 119-120 CrossRef
76. Chen, H, Boutros, PC (2011) VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinforma 12: pp. 35 CrossRef
77. Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ (1990) Basic local alignment search tool. J Mol Biol 215: pp. 403-410 CrossRef
78. Marchler-Bauer, A, Zheng, C, Chitsaz, F, Derbyshire, MK, Geer, LY, Geer, RC, Gonzales, NR, Gwadz, M, Hurwitz, DI, Lanczycki, CJ, Lu, F, Lu, S, Marchler, GH, Song, JS, Thanki, N, Yamashita, RA, Zhang, D, Bryant, SH (2013) CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res 41: pp. D348-D352 CrossRef
79. Sullivan, MJ, Petty, NK, Beatson, SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics 27: pp. 1009-1010 CrossRef
80. Shao, Y, He, X, Harrison, EM, Tai, C, Ou, HY, Rajakumar, K, Deng, Z (2010) mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes.. Nucleic Acids Res 38: pp. W194-W200 CrossRef
81. Grissa, I, Vergnaud, G, Pourcel, C (2008) CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 36: pp. W145-W148 CrossRef
82. Roberts, RJ, Vincze, T, Posfai, J, Macelis, D (2010) REBASE鈥揳 database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 38: pp. D234-D236 CrossRef - 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
- 出版者：BioMed Central
- ISSN：1471-2164
文摘
Background Within the genus Streptococcus, only Streptococcus thermophilus is used as a starter culture in food fermentations. Streptococcus macedonicus though, which belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC), is also frequently isolated from fermented foods mainly of dairy origin. Members of the SBSEC have been implicated in human endocarditis and colon cancer. Here we compare the genome sequence of the dairy isolate S. macedonicus ACA-DC 198 to the other SBSEC genomes in order to assess in silico its potential adaptation to milk and its pathogenicity status. Results Despite the fact that the SBSEC species were found tightly related based on whole genome phylogeny of streptococci, two distinct patterns of evolution were identified among them. Streptococcus macedonicus, Streptococcus infantarius CJ18 and Streptococcus pasteurianus ATCC 43144 seem to have undergone reductive evolution resulting in significantly diminished genome sizes and increased percentages of potential pseudogenes when compared to Streptococcus gallolyticus subsp. gallolyticus. In addition, the three species seem to have lost genes for catabolizing complex plant carbohydrates and for detoxifying toxic substances previously linked to the ability of S. gallolyticus to survive in the rumen. Analysis of the S. macedonicus genome revealed features that could support adaptation to milk, including an extra gene cluster for lactose and galactose metabolism, a proteolytic system for casein hydrolysis, auxotrophy for several vitamins, an increased ability to resist bacteriophages and horizontal gene transfer events with the dairy Lactococcus lactis and S. thermophilus as potential donors. In addition, S. macedonicus lacks several pathogenicity-related genes found in S. gallolyticus. For example, S. macedonicus has retained only one (i.e. the pil3) of the three pilus gene clusters which may mediate the binding of S. gallolyticus to the extracellular matrix. Unexpectedly, similar findings were obtained not only for the dairy S. infantarius CJ18, but also for the blood isolate S. pasteurianus ATCC 43144. Conclusions Our whole genome analyses suggest traits of adaptation of S. macedonicus to the nutrient-rich dairy environment. During this process the bacterium gained genes presumably important for this new ecological niche. Finally, S. macedonicus carries a reduced number of putative SBSEC virulence factors, which suggests a diminished pathogenic potential.