Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Håfström, Therese ^a   Jansson, Désirée S ^a,b   Segerman, Bo ^a  

^a NATIONAL VETERINARY INSTITUTE   (Sweden)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

AT GC skew; Bacteriophages; Brachyspira intermedia; Genome comparison; Horizontal gene transfer

Indexed keywords

BACTERIAL PROTEIN;

ARTICLE; BACTERIAL COLONIZATION; BACTERIAL GENOME; BACTERIOPHAGE; BRACHYSPIRA; BRACHYSPIRA HYODYSENTERIAE; BRACHYSPIRA INTERMEDIA; BRACHYSPIRA MURDOCHII; BRACHYSPIRA PILOSICOLI; CODON; CONTROLLED STUDY; EVOLUTION; GENE EXPRESSION; GENE FUNCTION; GENE SEQUENCE; GENE TRANSLOCATION; GENETIC ANALYSIS; GENOME ANALYSIS; HORIZONTAL GENE TRANSFER; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; SPECIES DIFFERENTIATION;

AVES; BRACHYSPIRA; BRACHYSPIRA HYODYSENTERIAE; BRACHYSPIRA INTERMEDIA; BRACHYSPIRA MURDOCHII; BRACHYSPIRA PILOSICOLI; GALLUS GALLUS; MAMMALIA;

EID: 79961114327     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-395     Document Type: Article

References (39)

1. Paster BJ, Dewhirst FE. Phylogenetic foundation of spirochetes. J Mol Microbiol Biotechnol 2000, 2(4):341-344.
2. Tsinganou E, Gebbers JO. Human intestinal spirochetosis--a review. Ger Med Sci 2010, 8(7):Doc01. 2830567, 20200654.
3. Backhans A, Johansson KE, Fellström C. Phenotypic and molecular characterization of Brachyspira spp. isolated from wild rodents. Environmental Microbiology Reports 2010, 2:720-727.
4. Stanton TB, Fournie-Amazouz E, Postic D, Trott DJ, Grimont PA, Baranton G, Hampson DJ, Saint Girons I. Recognition of two new species of intestinal spirochetes: Serpulina intermedia sp. nov. and Serpulina murdochii sp. nov. Int J Syst Bacteriol 1997, 47(4):1007-1012. 10.1099/00207713-47-4-1007, 9336899.
5. Hampson DJ, La T. Reclassification of Serpulina intermedia and Serpulina murdochii in the genus Brachyspira as Brachyspira intermedia comb. nov. and Brachyspira murdochii comb. nov. Int J Syst Evol Microbiol 2006, 56(Pt 5):1009-1012.
6. Binek M, Szynkiewicz ZM. Physiological properties and classification of strains of Treponema sp. isolated from pigs in Poland. Comp Immunol Microbiol Infect Dis 1984, 7(3-4):141-148. 10.1016/0147-9571(84)90019-5, 6532648.
7. Fellstrom C, Gunnarsson A. Phenotypical characterisation of intestinal spirochaetes isolated from pigs. Res Vet Sci 1995, 59(1):1-4. 10.1016/0034-5288(95)90021-7, 8525077.
8. Komarek V, Maderner A, Spergser J, Weissenbock H. Infections with weakly haemolytic Brachyspira species in pigs with miscellaneous chronic diseases. Vet Microbiol 2009, 134(3-4):311-317. 10.1016/j.vetmic.2008.08.017, 18823725.
9. Hudson MJ, Alexander TJ, Lysons RJ. Diagnosis of swine dysentery: spirochaetes which may be confused with Treponema hyodysenteriae. Vet Rec 1976, 99(25-26):498-500. 10.1136/vr.99.25-26.498, 1014306.
10. Jensen TK, Moller K, Boye M, Leser TD, Jorsal SE. Scanning electron microscopy and fluorescent in situ hybridization of experimental Brachyspira (Serpulina) pilosicoli infection in growing pigs. Vet Pathol 2000, 37(1):22-32. 10.1354/vp.37-1-22, 10643977.
11. Neef NA, Lysons RJ, Trott DJ, Hampson DJ, Jones PW, Morgan JH. Pathogenicity of porcine intestinal spirochetes in gnotobiotic pigs. Infect Immun 1994, 62(6):2395-2403. 186524, 8188364.
12. Dwars RM, Davelaar FG, Smit HF. Infection of broiler parent hens with avian intestinal spirochaetes: effects on egg production and chick quality. Avian Pathol 1993, 22(4):693-701. 10.1080/03079459308418957, 18671054.
13. Dwars RM, Smit HF, Davelaar FG. Influence of infection with avian intestinal spirochaetes on the faeces of laying hens. Avian Pathol 1992, 21(3):513-515. 10.1080/03079459208418870, 18670967.
14. Trott DJ, Hampson DJ. Evaluation of day-old specific pathogen-free chicks as an experimental model for pathogenicity testing of intestinal spirochaete species. J Comp Pathol 1998, 118(4):365-381. 10.1016/S0021-9975(07)80012-0, 9651813.
15. Rasback T, Jansson DS, Johansson KE, Fellstrom C. A novel enteropathogenic, strongly haemolytic spirochaete isolated from pig and mallard, provisionally designated 'Brachyspira suanatina' sp. nov. Environ Microbiol 2007, 9(4):983-991. 10.1111/j.1462-2920.2006.01220.x, 17359270.
16. Pettersson B, Fellstrom C, Andersson A, Uhlen M, Gunnarsson A, Johansson KE. The phylogeny of intestinal porcine spirochetes (Serpulina species) based on sequence analysis of the 16S rRNA gene. J Bacteriol 1996, 178(14):4189-4199. 178177, 8763948.
17. Fellstrom C, Rasback T, Johansson KE, Olofsson T, Aspan A. Identification and genetic fingerprinting of Brachyspira species. J Microbiol Methods 2008, 72(2):133-140. 10.1016/j.mimet.2007.11.015, 18096259.
18. Phillips ND, La T, Adams PJ, Harland BL, Fenwick SG, Hampson DJ. Detection of Brachyspira hyodysenteriae, Lawsonia intracellularis and Brachyspira pilosicoli in feral pigs. Vet Microbiol 2009, 134(3-4):294-299. 10.1016/j.vetmic.2008.08.006, 18818030.
19. Bellgard MI, Wanchanthuek P, La T, Ryan K, Moolhuijzen P, Albertyn Z, Shaban B, Motro Y, Dunn DS, Schibeci D, et al. Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine. PLoS One 2009, 4(3):e4641. 10.1371/journal.pone.0004641, 2650404, 19262690.
20. Pati A, Sikorski J, Gronow S, Munk C, Lapidus A, Copeland A, Glavina Del Tio T, Nolan M, Lucas S, Chen F, et al. Complete genome sequence of Brachyspira murdochii type strain (56-150). Stand Genomic Sci 2010, 2(3):260-269. 10.4056/sigs.831993, 3035287, 21304710.
21. Wanchanthuek P, Bellgard MI, La T, Ryan K, Moolhuijzen P, Chapman B, Black M, Schibeci D, Hunter A, Barrero R, et al. The complete genome sequence of the pathogenic intestinal spirochete Brachyspira pilosicoli and comparison with other Brachyspira genomes. PLoS One 2010, 5(7):e11455. 10.1371/journal.pone.0011455, 2897892, 20625514.
22. La T, Phillips ND, Wanchanthuek P, Bellgard MI, O'Hara AJ, Hampson DJ. Evidence that the 36 kb plasmid of Brachyspira hyodysenteriae contributes to virulence. Vet Microbiol 2011,
23. Humphrey SB, Stanton TB, Jensen NS, Zuerner RL. Purification and characterization of VSH-1, a generalized transducing bacteriophage of Serpulina hyodysenteriae. J Bacteriol 1997, 179(2):323-329. 178700, 8990282.
24. Segerman B, De Medici D, Ehling Schulz M, Fach P, Fenicia L, Fricker M, Wielinga P, Van Rotterdam B, Knutsson R. Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain. Int J Food Microbiol 2011, 145:167-176.
25. Gao F, Zhang CT. Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics 2008, 9(79):79. 2275245, 18237442.
26. Mrazek J, Karlin S. Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci USA 1998, 95(7):3720-3725. 10.1073/pnas.95.7.3720, 19903, 9520433.
27. Tillier ER, Collins RA. Genome rearrangement by replication-directed translocation. Nat Genet 2000, 26(2):195-197. 10.1038/79918, 11017076.
28. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997, 278(5338):631-637. 10.1126/science.278.5338.631, 9381173.
29. Andersson SG, Kurland CG. Reductive evolution of resident genomes. Trends Microbiol 1998, 6(7):263-268. 10.1016/S0966-842X(98)01312-2, 9717214.
30. Stanton TB, Humphrey SB, Bayles DO, Zuerner RL. Identification of a divided genome for VSH-1, the prophage-like gene transfer agent of Brachyspira hyodysenteriae. J Bacteriol 2009, 191(5):1719-1721. 10.1128/JB.01359-08, 2648187, 19103931.
31. Song H, Hwang J, Yi H, Ulrich RL, Yu Y, Nierman WC, Kim HS. The early stage of bacterial genome-reductive evolution in the host. PLoS Pathog 6(5):e1000922.
32. Chain PS, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, Regala WM, Georgescu AM, Vergez LM, Land ML, Motin VL, et al. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci USA 2004, 101(38):13826-13831. 10.1073/pnas.0404012101, 518763, 15358858.
33. Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998, 8(3):195-202.
34. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27(23):4636-4641. 10.1093/nar/27.23.4636, 148753, 10556321.
35. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000, 16(10):944-945. 10.1093/bioinformatics/16.10.944, 11120685.
36. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25(5):955-964. 10.1093/nar/25.5.955, 146525, 9023104.
37. 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.
38. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol 2004, 5(2):R12. 10.1186/gb-2004-5-2-r12, 395750, 14759262.
39. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. ACT: the Artemis Comparison Tool. Bioinformatics 2005, 21(16):3422-3423. 10.1093/bioinformatics/bti553, 15976072.