TABLE 1.
Sequences of PCR amplicons derived from DGGE gels and identities based on the BLAST database
| Sequence no. and closest relative (% sequence similarity)a | Sequence length (bp)b | Incidencec
|
|
|---|---|---|---|
| Healthy | Diseased | ||
| 1. Fusobacterium nucleatumAF287812 (89) | 158 (10) | 33 | 31 |
| 2. Streptococcus mitisAY281077 (88) | 185 (3) | 50 | 45 |
| 3. Streptococcus oralisAY281080 (96) | 186 (6) | 39 | 52 |
| 4. Corynebacterium sp. AB242687 (98) | 180 (12) | 33 | 21 |
| 5. Prevotella sp. AY350613 (89) | 164 (7) | 28 | 28 |
| 6. Streptococcus sanguinisAY281086 (96) | 180 (3) | 44 | 38 |
| 7. Enterococcus sp. AB0756928 (90) | 158 (11) | 28 | 21 |
| 8. Fusobacterium nucleatum subsp. vincentiiAJ006964 (95) | 161 (3) | 22 | 48 |
| 9. Bacteroides sp. AF529225 (96) | 176 (2) | 33 | 24 |
| 10. Chryseobacterium indologenesAY050493 (88) | 174 (3) | 28 | 45 |
| 11. Fusobacterium nucleatumAF543300 (97) | 153 (7) | 44 | 38 |
| 12. Pseudomonas sp. AY365082 (99) | 177 (4) | 56 | 38 |
| 13. Sphingomonas sp. AY834344 (97) | 145 (2) | 39 | 24 |
| 14. Streptococcus gordoniiAF481950 (83) | 183 (11) | 17 | 17 |
| 15. Flexibacter roseolusM58787 (97) | 180 (3) | 17 | 10 |
| 16. Porphyromonas endodontalisAY253728 (97) | 180 (4) | 39 | 31 |
| 17. Streptococcus parasanguinisAY281087 (87) | 180 (6) | 33 | 31 |
| 18. Bacillus subtilisDQ301917 (98) | 180 (11) | 11 | 14 |
| 19. Treponema amylovorumY09959 (99) | 180 (2) | 6 | 17 |
| 20. Streptococcus cristatusAY2810904 (97) | 181 (2) | 39 | 24 |
| 21. Prevotella nigrescensAF414844 (98) | 168 (4) | 33 | 3 |
| 22. Prevotella sp. DQ188617 (83) | 185 (6) | 11 | 7 |
| 23. Putative new phylotyped | 177 (8) | 0 | 3 |
| 24. Staphylococcus sp. AB167056 (93) | 188 (8) | 17 | 0 |
| 25. Veillonella sp. DQ188766 (90) | 180 (10) | 0 | 24 |
| 26. Alcaligenes latusD88007 (98) | 180 (3) | 0 | 17 |
| 27. Streptococcus oligofermentansAY099095 (95) | 185 (3) | 28 | 24 |
| 28. Shewanella sp. AB059264 (95) | 130 (2) | 22 | 7 |
| 29. Treponema sp. AF023044 (85) | 180 (9) | 17 | 14 |
| 30. Holdemania filiformisY11466 (91) | 178 (4) | 28 | 17 |
| 31. Scardovia genomospecies AY278626 (100) | 180 (6) | 22 | 24 |
| 32. Bulleidia extructaAF22064 (87) | 177 (3) | 33 | 14 |
| 33. Prevotella sp. DQ188583 (94) | 176 (4) | 6 | 0 |
| 34. Streptococcus sp. DQ188664 (94) | 174 (6) | 0 | 37 |
| 35. Streptococcus pneumoniaeAY281084 (98) | 178 (5) | 17 | 7 |
| 36. Sphingomonas sp. AY167827 (92) | 164 (4) | 33 | 21 |
| 37. Veillonella disparAF4396394 (91) | 180 (3) | 33 | 21 |
| 38. Staphylococcus epidermidisAJ717377 (89) | 174 (4) | 0 | 17 |
| 39. Sphingobium yanoikuyaeAJ627009 (98) | 154 (4) | 17 | 0 |
| 40. Leptotrichia sp. AY267541 (87) | 180 (4) | 17 | 28 |
| 41. Corynebacterium matruchotiiX82065 (94) | 157 (8) | 17 | 0 |
| 42. Tannerella forsythensisAB053947 (95) | 180 (10) | 6 | 24 |
| 43. Streptococcus sp. AY494661 (87) | 187 (5) | 28 | 28 |
| 44. Streptococcus mutansAE014854 (84) | 180 (5) | 17 | 0 |
| 45. Sphingobium yanoikuyaeAF541931 (100) | 151 (3) | 28 | 21 |
| 46. Neisseria sp. AJ586614 (87) | 184 (7) | 44 | 24 |
| 47. Capnocytophaga granulosaX97248 (88) | 190 (3) | 11 | 17 |
| 48. Streptococcus oligofermentansAY099095 (91) | 187 (8) | 11 | 3 |
| 49. Treponema socranskii subsp. buccaleAY369255 (99) | 180 (5) | 17 | 10 |
| 50. Citromicrobium sp. AY456209 (100) | 157 (4) | 22 | 7 |
| 51. Anaerococcus sp. AY738694 (92) | 184 (11) | 0 | 3 |
| 52. Veillonella caviaeAY355140 (91) | 197 (3) | 0 | 3 |
a
Similarities are based on pairwise alignments with published sequences according to BLAST searches and indicate similarity, not guaranteed identity. Sequence numbers 1 to 52 refer to consecutive DGGE band positions from the top to the bottom of the synthetic reference ladder.
b
The number of ambiguous bases for an individual band is given in parentheses.
c
Refers to the percent incidence of each unique band in healthy or diseased individuals.
d
Refers to a sequence that did not generate a database match. Each sequence was derived from a unique, discrete gel band.