Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Papadimitriou, Konstantinos ^a   Anastasiou, Rania ^a   Mavrogonatou, Eleni ^b   Blom, Jochen ^c   Papandreou, Nikos C ^d   Hamodrakas, Stavros J ^d   Ferreira, Stéphanie ^e   Renault, Pierre ^f   Supply, Philip ^e,g,h   Pot, Bruno ^g,h   Tsakalidou, Effie ^a  

^a AGRICULTURAL UNIVERSITY OF ATHENS   (Greece)

^b INSTITUTE OF NANOSCIENCE AND NANOTECHNOLOGY   (Greece)

^c BIELEFELD UNIVERSITY   (Germany)

^d UNIVERSITY OF ATHENS   (Greece)

^e Genoscreen   (France)

^f UMR1319 MICALIS   (France)

^g INSERM U1019   (France)

^h UNIV LILLE   (France)

Author keywords

Adaptation; Gene decay; Genome; Horizontal gene transfer; Milk; Niche; Pathogenicity; Pseudogene; Streptococcus; Virulence factor

Indexed keywords

CARBOHYDRATE; CASEIN; GALACTOSE; LACTOSE; TOXIC SUBSTANCE; VITAMIN;

ARTICLE; AUXOTROPHY; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL SURVIVAL; BACTERIAL VIRULENCE; BACTERIOPHAGE; BACTERIUM ISOLATE; BACTERIUM PILUS; CARBOHYDRATE METABOLISM; CATABOLISM; COMPUTER MODEL; CONTROLLED STUDY; DETOXIFICATION; EXTRACELLULAR MATRIX; GENE CLUSTER; HORIZONTAL GENE TRANSFER; LACTOCOCCUS LACTIS; MILK; MOLECULAR EVOLUTION; NONHUMAN; PROTEIN DEGRADATION; PROTEIN HYDROLYSIS; RUMINANT STOMACH; SEQUENCE HOMOLOGY; STREPTOCOCCUS; STREPTOCOCCUS BOVIS; STREPTOCOCCUS EQUINUS; STREPTOCOCCUS GALLOLYTICUS; STREPTOCOCCUS INFANTARIUS; STREPTOCOCCUS MACEDONICUS; STREPTOCOCCUS PASTEURIANUS; STREPTOCOCCUS THERMOPHILUS;

BACTERIA (MICROORGANISMS); LACTOCOCCUS LACTIS; STREPTOCOCCUS; STREPTOCOCCUS GALLOLYTICUS; STREPTOCOCCUS GALLOLYTICUS SUBSP. GALLOLYTICUS; STREPTOCOCCUS INFANTARIUS; STREPTOCOCCUS MACEDONICUS; STREPTOCOCCUS PASTEURIANUS; STREPTOCOCCUS THERMOPHILUS;

ADAPTATION, BIOLOGICAL; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; DAIRY PRODUCTS; ENERGY METABOLISM; FOOD MICROBIOLOGY; GASTROINTESTINAL TRACT; GENE ORDER; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMIC ISLANDS; GENOMICS; HUMANS; PHYLOGENY; PROTEOLYSIS; STREPTOCOCCUS; STREPTOCOCCUS BOVIS; VIRULENCE FACTORS; VITAMINS;

EID: 84899485943     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-272     Document Type: Article

References (82)

1. Konings WN, Kok J, Kuipers OP, Poolman B. Lactic acid bacteria: the bugs of the new millennium. Curr Opin Microbiol 2000, 3(3):276-282. 10.1016/S1369-5274(00)00089-8, 10851157.
2. Masood MI, Qadir MI, Shirazi JH, Khan IU. Beneficial effects of lactic acid bacteria on human beings. Crit Rev Microbiol 2011, 37(1):91-98. 10.3109/1040841X.2010.536522, 21162695.
3. Donohue DC, Gueimonde M. Some Considerations for the Safety of Novel Probiotic Bacteria. Lactic Acid Bacteria: Microbiological and Functional Aspects 2012, Boca Raton: CRC Press Taylor & Francis Group, Lahtinen S, Salminen S, von Wright A, Ouwehand AC, 4.
4. Woodford N, Livermore DM. Infections caused by Gram-positive bacteria: a review of the global challenge. J Infect 2009, 59(Suppl 1):S4-S16.
5. Facklam R. What happened to the streptococci: overview of taxonomic and nomenclature changes. Clin Microbiol Rev 2002, 15(4):613-630. 10.1128/CMR.15.4.613-630.2002, 126867, 12364372.
6. Nobbs AH, Lamont RJ, Jenkinson HF. Streptococcus adherence and colonization. Microbiol Mol Biol Rev 2009, 73(3):407-450. 10.1128/MMBR.00014-09, 2738137, 19721085.
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. Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol 2004, 22(12):1554-1558. 10.1038/nbt1034, 15543133.
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. New insights in the molecular biology and physiology of Streptococcus thermophilus revealed by comparative genomics. FEMS Microbiol Rev 2005, 29(3):435-463.
9. Jans C, Lacroix C, Meile L. 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 2012, 326(2):144-150. 10.1111/j.1574-6968.2011.02443.x, 22092382.
10. Abdulamir AS, Hafidh RR, Abu Bakar F. The association of Streptococcus bovis/gallolyticus with colorectal tumors: the nature and the underlying mechanisms of its etiological role. J Exp Clin Cancer Res 2011, 30:11. 10.1186/1756-9966-30-11, 3032743, 21247505.
11. Galdy S, Nastasi G. Streptococcus bovis endocarditis and colon cancer: myth or reality? A case report and literature review. BMJ Case Rep 2012, 2012:1-2.
12. Herrera P, Kwon YM, Ricke SC. Ecology and pathogenicity of gastrointestinal Streptococcus bovis. Anaerobe 2009, 15(1-2):44-54.
13. De Vuyst L, Tsakalidou E. Streptococcus macedonicus, a multi-functional and promising species for dairy fermentations. Int Dairy J 2008, 18(5):476-485.
14. Maragkoudakis PA, Papadelli M, Georgalaki M, Panayotopoulou EG, Martinez-Gonzalez B, Mentis AF, Petraki K, Sgouras DN, Tsakalidou E. In vitro and in vivo safety evaluation of the bacteriocin producer Streptococcus macedonicus ACA-DC 198. Int J Food Microbiol 2009, 133(1-2):141-147.
15. Tsakalidou E, Zoidou E, Pot B, Wassill L, Ludwig W, Devriese LA, Kalantzopoulos G, Schleifer KH, Kersters K. Identification of streptococci from Greek Kasseri cheese and description of Streptococcus macedonicus sp. nov. Int J Syst Bacteriol 1998, 48(Pt 2):519-527.
16. Schlegel L, Grimont F, Ageron E, Grimont PA, Bouvet A. 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 2003, 53(Pt 3):631-645.
17. Whiley RA, Kilian M. 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 2003, 53(3):915-917.
18. Danne C, Entenza JM, Mallet A, Briandet R, Debarbouille M, Nato F, Glaser P, Jouvion G, Moreillon P, Trieu-Cuot P, Dramsi S. Molecular characterization of a Streptococcus gallolyticus genomic island encoding a pilus involved in endocarditis. J Infect Dis 2011, 204(12):1960-1970. 10.1093/infdis/jir666, 22043018.
19. Papadimitriou K, Ferreira S, Papandreou NC, Mavrogonatou E, Supply P, Pot B, Tsakalidou E. Complete genome sequence of the dairy isolate Streptococcus macedonicus ACA-DC 198. J Bacteriol 2012, 194(7):1838-1839. 10.1128/JB.06804-11, 3302469, 22408241.
20. Jans C, Follador R, Hochstrasser M, Lacroix C, Meile L, Stevens MJ. Comparative genome analysis of Streptococcus infantarius subsp. infantarius CJ18, an African fermented camel milk isolate with adaptations to dairy environment. BMC Genomics 2013, 14:200. 10.1186/1471-2164-14-200, 3640971, 23521820.
21. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010, 7(6):455-457. 10.1038/nmeth.1457, 20436475.
22. Lin IH, Liu TT, Teng YT, Wu HL, Liu YM, Wu KM, Chang CH, Hsu MT. Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence. PLoS One 2011, 6(5):e20519. 10.1371/journal.pone.0020519, 3102119, 21633709.
23. Blom J, Albaum SP, Doppmeier D, Puhler A, Vorholter FJ, Zakrzewski M, Goesmann A. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinforma 2009, 10:154.
24. Darling AE, Mau B, Perna NT. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010, 5(6):e11147. 10.1371/journal.pone.0011147, 2892488, 20593022.
25. Rusniok C, Couve E, Da Cunha V, El Gana R, Zidane N, Bouchier C, Poyart C, Leclercq R, Trieu-Cuot P, Glaser P. Genome sequence of Streptococcus gallolyticus: insights into its adaptation to the bovine rumen and its ability to cause endocarditis. J Bacteriol 2010, 192(8):2266-2276. 10.1128/JB.01659-09, 2849448, 20139183.
26. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 2014, 42(1):D490-D495. 3965031, 24270786.
27. Crost EH, Tailford LE, Le Gall G, Fons M, Henrissat B, Juge N. Utilisation of mucin glycans by the human gut symbiont Ruminococcus gnavus is strain-dependent. PLoS One 2013, 8(10):e76341. 10.1371/journal.pone.0076341, 3808388, 24204617.
28. Ficko-Blean E, Boraston AB. Insights into the recognition of the human glycome by microbial carbohydrate-binding modules. Curr Opin Struct Biol 2012, 22(5):570-577. 10.1016/j.sbi.2012.07.009, 22858095.
29. Liu M, Bayjanov JR, Renckens B, Nauta A, Siezen RJ. The proteolytic system of lactic acid bacteria revisited: a genomic comparison. BMC Genomics 2010, 11:36. 10.1186/1471-2164-11-36, 2827410, 20078865.
30. Jans C, Gerber A, Bugnard J, Njage PM, Lacroix C, Meile L. Novel Streptococcus infantarius subsp. infantarius variants harboring lactose metabolism genes homologous to Streptococcus thermophilus. Food Microbiol 2012, 31(1):33-42. 10.1016/j.fm.2012.02.001, 22475940.
31. Fernandez-Espla MD, Garault P, Monnet V, Rul F. Streptococcus thermophilus cell wall-anchored proteinase: release, purification, and biochemical and genetic characterization. Appl Environ Microbiol 2000, 66(11):4772-4778. 10.1128/AEM.66.11.4772-4778.2000, 92378, 11055922.
32. Dandoy D, Fremaux C, de Frahan MH, Horvath P, Boyaval P, Hols P, Fontaine L. 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 2011, 10(Suppl 1):S21. 10.1186/1475-2859-10-S1-S21, 3231928, 21995822.
33. Calasso M, Gobbetti M. Lactic Acid Bacteria | Lactobacillus spp.: Other Species. Encyclopedia of Dairy Sciences 2011, 125-131. San Diego: cademic Press, Fuquay JW, 2.
34. El Qaidi S, Yang J, Zhang JR, Metzger DW, Bai G. The vitamin B(6) biosynthesis pathway in Streptococcus pneumoniae is controlled by pyridoxal 5′-phosphate and the transcription factor PdxR and has an impact on ear infection. J Bacteriol 2013, 195(10):2187-2196. 10.1128/JB.00041-13, 3650526, 23475965.
35. LeBlanc JG, Laino JE, del Valle MJ, Vannini V, van Sinderen D, Taranto MP, de Valdez GF, de Giori GS, Sesma F. B-group vitamin production by lactic acid bacteria-current knowledge and potential applications. J Appl Microbiol 2011, 111(6):1297-1309. 10.1111/j.1365-2672.2011.05157.x, 21933312.
36. Dhillon BK, Chiu TA, Laird MR, Langille MG, Brinkman FS. IslandViewer update: improved genomic island discovery and visualization. Nucleic Acids Res 2013, 41(Web Server issue):W129-W132. 3692065, 23677610.
37. Georgalaki M, Papadimitriou K, Anastasiou R, Pot B, Van Driessche G, Devreese B, Tsakalidou E. Macedovicin, the second food-grade lantibiotic produced by Streptococcus macedonicus ACA-DC 198. Food Microbiol 2013, 33(1):124-130. 10.1016/j.fm.2012.09.008, 23122510.
38. Georgalaki MD, Van Den Berghe E, Kritikos D, Devreese B, Van Beeumen J, Kalantzopoulos G, De Vuyst L, Tsakalidou E. Macedocin, a food-grade lantibiotic produced by Streptococcus macedonicus ACA-DC 198. Appl Environ Microbiol 2002, 68(12):5891-5903. 10.1128/AEM.68.12.5891-5903.2002, 134371, 12450808.
39. Georgalaki M, Papadelli M, Chassioti E, Anastasiou R, Aktypis A, De Vuyst L, Van Driessche G, Devreese B, Tsakalidou E. Milk protein fragments induce the biosynthesis of macedocin, the lantibiotic produced by Streptococcus macedonicus ACA-DC 198. Appl Environ Microbiol 2010, 76(4):1143-1151. 10.1128/AEM.00151-09, 2820984, 20023075.
40. O'Sullivan O, O'Callaghan J, Sangrador-Vegas A, McAuliffe O, Slattery L, Kaleta P, Callanan M, Fitzgerald GF, Ross RP, Beresford T. Comparative genomics of lactic acid bacteria reveals a niche-specific gene set. BMC Microbiol 2009, 9:50. 10.1186/1471-2180-9-50, 2660350, 19265535.
41. Szczepankowska AK, Górecki RK, Kołakowski P, Bardowski JK. Lactic Acid Bacteria Resistance to Bacteriophage and Prevention Techniques to Lower Phage Contamination. Dairy Fermentation in R & D for Food, Health and Livestock Purposes 2013, Croatia: InTech, Kongo JM.
42. Marco MB, Moineau S, Quiberoni A. Bacteriophages and dairy fermentations. Bacteriophage 2012, 2(3):149-158. 10.4161/bact.21868, 3530524, 23275866.
43. Solioz M, Mermod M, Abicht HKM, Mancini S. Responses of Lactic Acid Bacteria to Heavy Metal Stress. Stress Responses of Lactic Acid Bacteria 2011, New York: Springer, Tsakalidou E, Papadimitriou K, 1.
44. Liu CQ, Khunajakr N, Chia LG, Deng YM, Charoenchai P, Dunn NW. Genetic analysis of regions involved in replication and cadmium resistance of the plasmid pND302 from Lactococcus lactis. Plasmid 1997, 38(2):79-90. 10.1006/plas.1997.1301, 9339465.
45. Magnani D, Barre O, Gerber SD, Solioz M. Characterization of the CopR regulon of Lactococcus lactis IL1403. J Bacteriol 2008, 190(2):536-545. 10.1128/JB.01481-07, 2223693, 17993525.
46. Schirawski J, Hagens W, Fitzgerald GF, Van Sinderen D. Molecular characterization of cadmium resistance in Streptococcus thermophilus strain 4134: an example of lateral gene transfer. Appl Environ Microbiol 2002, 68(11):5508-5516. 10.1128/AEM.68.11.5508-5516.2002, 129935, 12406744.
47. Siezen RJ, Renckens B, van Swam I, Peters S, van Kranenburg R, Kleerebezem M, de Vos WM. Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment. Appl Environ Microbiol 2005, 71(12):8371-8382. 10.1128/AEM.71.12.8371-8382.2005, 1317451, 16332824.
48. Fallico V, McAuliffe O, Fitzgerald GF, Ross RP. Plasmids of raw milk cheese isolate Lactococcus lactis subsp. lactis biovar diacetylactis DPC3901 suggest a plant-based origin for the strain. Appl Environ Microbiol 2011, 77(18):6451-6462. 10.1128/AEM.00661-11, 3187126, 21803914.
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. 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 2009, 191(21):6643-6653. 10.1128/JB.00909-09, 2795296, 19717590.
50. Boleij A, Muytjens CM, Bukhari SI, Cayet N, Glaser P, Hermans PW, Swinkels DW, Bolhuis A, Tjalsma H. Novel clues on the specific association of Streptococcus gallolyticus subsp gallolyticus with colorectal cancer. J Infect Dis 2011, 203(8):1101-1109. 10.1093/infdis/jiq169, 21451000.
51. Boleij A, Schaeps RM, de Kleijn S, Hermans PW, Glaser P, Pancholi V, Swinkels DW, Tjalsma H. Surface-exposed histone-like protein a modulates adherence of Streptococcus gallolyticus to colon adenocarcinoma cells. Infect Immun 2009, 77(12):5519-5527. 10.1128/IAI.00384-09, 2786452, 19752027.
52. Jung CJ, Zheng QH, Shieh YH, Lin CS, Chia JS. Streptococcus mutans autolysin AtlA is a fibronectin-binding protein and contributes to bacterial survival in the bloodstream and virulence for infective endocarditis. Mol Microbiol 2009, 74(4):888-902. 10.1111/j.1365-2958.2009.06903.x, 19818020.
53. Garcia B, Latasa C, Solano C, Garcia-del Portillo F, Gamazo C, Lasa I. Role of the GGDEF protein family in Salmonella cellulose biosynthesis and biofilm formation. Mol Microbiol 2004, 54(1):264-277. 10.1111/j.1365-2958.2004.04269.x, 15458421.
54. Hinse D, Vollmer T, Ruckert C, Blom J, Kalinowski J, Knabbe C, Dreier J. Complete genome and comparative analysis of Streptococcus gallolyticus subsp. gallolyticus, an emerging pathogen of infective endocarditis. BMC Genomics 2011, 12:400. 10.1186/1471-2164-12-400, 3173452, 21824414.
55. Chen L, Xiong Z, Sun L, Yang J, Jin Q. VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 2012, 40(Database issue):D641-D645. 3245122, 22067448.
56. VFDB Comparison of pathogenomic composition of Streptococcus. [http://www.mgc.ac.cn/cgi-bin/VFs/compvfs.cgi?Genus=Streptococcus], VFDB.
57. Demuth DR, Lammey MS, Huck M, Lally ET, Malamud D. Comparison of Streptococcus mutans and Streptococcus sanguis receptors for human salivary agglutinin. Microb Pathog 1990, 9(3):199-211. 10.1016/0882-4010(90)90022-I, 1708078.
58. Courtney HS, Li Y, Dale JB, Hasty DL. Cloning, sequencing, and expression of a fibronectin/fibrinogen-binding protein from group A streptococci. Infect Immun 1994, 62(9):3937-3946. 303051, 8063411.
59. Holmes AR, McNab R, Millsap KW, Rohde M, Hammerschmidt S, Mawdsley JL, Jenkinson HF. The pavA gene of Streptococcus pneumoniae encodes a fibronectin-binding protein that is essential for virulence. Mol Microbiol 2001, 41(6):1395-1408. 10.1046/j.1365-2958.2001.02610.x, 11580843.
60. Hermans PW, Adrian PV, Albert C, Estevao S, Hoogenboezem T, Luijendijk IH, Kamphausen T, Hammerschmidt S. The streptococcal lipoprotein rotamase A (SlrA) is a functional peptidyl-prolyl isomerase involved in pneumococcal colonization. J Biol Chem 2006, 281(2):968-976. 10.1074/jbc.M510014200, 16260779.
61. Terao Y, Yamaguchi M, Hamada S, Kawabata S. Multifunctional glyceraldehyde-3-phosphate dehydrogenase of Streptococcus pyogenes is essential for evasion from neutrophils. J Biol Chem 2006, 281(20):14215-14223. 10.1074/jbc.M513408200, 16565520.
62. Winram SB, Lottenberg R. The plasmin-binding protein Plr of group a streptococci is identified as glyceraldehyde-3-phosphate dehydrogenase. Microbiology 1996, 142(Pt 8):2311-2320.
63. Pancholi V, Fischetti VA. alpha-enolase, a novel strong plasmin(ogen) binding protein on the surface of pathogenic streptococci. J Biol Chem 1998, 273(23):14503-14515. 10.1074/jbc.273.23.14503, 9603964.
64. Tseng HJ, McEwan AG, Paton JC, Jennings MP. Virulence of Streptococcus pneumoniae: PsaA mutants are hypersensitive to oxidative stress. Infect Immun 2002, 70(3):1635-1639. 10.1128/IAI.70.3.1635-1639.2002, 127802, 11854257.
65. Angel CS, Ruzek M, Hostetter MK. Degradation of C3 by Streptococcus pneumoniae. J Infect Dis 1994, 170(3):600-608. 10.1093/infdis/170.3.600, 8077717.
66. Ibrahim YM, Kerr AR, McCluskey J, Mitchell TJ. Role of HtrA in the virulence and competence of Streptococcus pneumoniae. Infect Immun 2004, 72(6):3584-3591. 10.1128/IAI.72.6.3584-3591.2004, 415679, 15155668.
67. Lyon WR, Caparon MG. Trigger factor-mediated prolyl isomerization influences maturation of the Streptococcus pyogenes cysteine protease. J Bacteriol 2003, 185(12):3661-3667. 10.1128/JB.185.12.3661-3667.2003, 156213, 12775704.
68. Kadioglu A, Taylor S, Iannelli F, Pozzi G, Mitchell TJ, Andrew PW. Upper and lower respiratory tract infection by Streptococcus pneumoniae is affected by pneumolysin deficiency and differences in capsule type. Infect Immun 2002, 70(6):2886-2890. 10.1128/IAI.70.6.2886-2890.2002, 128015, 12010976.
69. Herrero IA, Rouse MS, Piper KE, Alyaseen SA, Steckelberg JM, Patel R. Reevaluation of Streptococcus bovis endocarditis cases from 1975 to 1985 by 16S ribosomal DNA sequence analysis. J Clin Microbiol 2002, 40(10):3848-3850. 10.1128/JCM.40.10.3848-3850.2002, 130892, 12354897.
70. Malkin J, Kimmitt PT, Ou HY, Bhasker PS, Khare M, Deng Z, Stephenson I, Sosnowski AW, Perera N, Rajakumar K. 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 2008, 17(5):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. Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis. BMC Microbiol 2013, 13:141. 10.1186/1471-2180-13-141, 3716944, 23782707.
72. Romero B, Morosini MI, Loza E, Rodriguez-Banos M, Navas E, Canton R, Campo RD. Reidentification of Streptococcus bovis isolates causing bacteremia according to the new taxonomy criteria: still an issue?. J Clin Microbiol 2011, 49(9):3228-3233. 10.1128/JCM.00524-11, 3165630, 21752968.
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. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008, 9:75. 10.1186/1471-2164-9-75, 2265698, 18261238.
74. Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS. BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res 2005, 33(Web Server issue):W455-W459. 1160269, 15980511.
75. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009, 25(1):119-120. 10.1093/bioinformatics/btn578, 2612626,2612626, 18990721.
76. Chen H, Boutros PC. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinforma 2011, 12:35.
77. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
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. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res 2013, 41(Database issue):D348-D352. 3531192, 23197659.
79. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011, 27(7):1009-1010. 10.1093/bioinformatics/btr039, 3065679, 21278367.
80. Shao Y, He X, Harrison EM, Tai C, Ou HY, Rajakumar K, Deng Z. mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes. Nucleic Acids Res 2010, 38(Web Server issue):W194-W200. 2896100, 20435682.
81. Grissa I, Vergnaud G, Pourcel C. CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2008, 36(Web Server issue):W145-W148. 2447796, 18442988.
82. Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 2010, 38(Database issue):D234-D236. 2808884, 19846593.