Table 3.
Size (bases) of TRF obtained with: | ||||||||||||
Isolate or organisma | Strain | Alu Ib | Hha Ib | Msp Ib | Rsa Ib | Hha Ic | Sum of differences (SOD) scored | |||||
6-FAM | HEX | 6-FAM | HEX | 6-FAM | HEX | 6-FAM | HEX | 6-FAM | HEX | |||
MCRF-271 / MCRF-412e | 193 | 560 | 561 | 223 | 537 | 247 | UD | UD | 321 | 284 | NA | |
L. rhamnosus | DSM 20021 | 194 | 556 | 561 | 224 | 535 | 246 | UD | UD | 325 | 283 | 14 |
L. rhamnosus | JCM 1136 | 194 | 555 | 560 | 224 | 534 | 246 | UD | UD | 325 | 283 | 17 |
L. plantarum | NCDO 1752 | 175 | 558 | 562 | 224 | 536 | 246 | UD | UD | 320 | 283 | 26 |
L. plantarum | JCM 1149 | 175 | 556 | 560 | 224 | 534 | 246 | UD | UD | 325 | 283 | 33 |
L. plantarum | ATCC 8014 | 175 | 556 | 560 | 224 | 534 | 246 | UD | UD | 325 | 283 | 33 |
L. manihotivorans | LMG 18010 | 174 | 556 | 560 | 224 | 534 | 246 | UD | UD | 325 | 283 | 34 |
L. pentosus | JCM 1588 | 226 | 556 | 560 | 224 | 534 | 246 | UD | UD | 325 | 283 | 48 |
L. casei | ATCC 334 | 194 | 556 | 561 | 172 | 535 | 246 | UD | UD | 325 | 283 | 64 |
L. casei | ATCC 393 | 194 | 556 | 561 | 172 | 535 | 246 | UD | UD | 325 | 283 | 64 |
L. zeae | ATCC 15820 | 194 | 556 | 561 | 172 | 535 | 246 | UD | UD | 325 | 283 | 64 |
L. casei | JCM 1134 | 195 | 555 | 561 | 172 | 535 | 246 | UD | UD | 325 | 283 | 66 |
L. paracasei | JCM 1133 | 194 | 555 | 560 | 172 | 534 | 246 | UD | UD | 325 | 283 | 67 |
L. paracasei | JCM 8130 | 194 | 555 | 560 | 172 | 534 | 246 | UD | UD | 325 | 283 | 67 |
L. paracasei | JCM 1171 | 194 | 555 | 560 | 172 | 534 | 246 | UD | UD | 325 | 283 | 67 |
MCRF-284e | 193 | 560 | 561 | 172 | 537 | 247 | UD | UD | 321 | 284 | NA | |
L. casei | ATCC 334 | 194 | 556 | 561 | 172 | 535 | 246 | UD | UD | 325 | 283 | 13 |
L. casei | ATCC 393 | 194 | 556 | 561 | 172 | 535 | 246 | UD | UD | 325 | 283 | 13 |
L. zeae | ATCC 15820 | 194 | 556 | 561 | 172 | 535 | 246 | UD | UD | 325 | 283 | 13 |
L. casei | JCM 1134 | 195 | 555 | 561 | 172 | 535 | 246 | UD | UD | 325 | 283 | 15 |
L. paracasei | JCM 1133 | 194 | 555 | 560 | 172 | 534 | 246 | UD | UD | 325 | 283 | 16 |
L. paracasei | JCM 8130 | 194 | 555 | 560 | 172 | 534 | 246 | UD | UD | 325 | 283 | 16 |
L. paracasei | JCM 1171 | 194 | 555 | 560 | 172 | 534 | 246 | UD | UD | 325 | 283 | 16 |
L. rhamnosus | DSM 20021 | 194 | 556 | 561 | 224 | 535 | 246 | UD | UD | 325 | 283 | 65 |
L. paracasei | JCM 1181 | 194 | 555 | 612 | 172 | 534 | 246 | UD | UD | 325 | 283 | 66 |
L. rhamnosus | JCM 1136 | 194 | 555 | 560 | 224 | 534 | 246 | UD | UD | 325 | 283 | 68 |
UD: Undigested PCR product (6-FAM and HEX fragment sizes were both >700 bases).
aOrganisms are presented in ascending order of the SOD scores relative to the TRF results for each MCRF strain.
bLabeled fragments derived from the PCR product of (6-FAM)-S-D-Bact-0045-b-S-20 and (HEX)-S-D-Bact-0785-a-A-19 or as predicted from sequence data.
cLabeled fragments derived from the PCR product of (6-FAM)-S-D-Bact-0785-a-S-19 and (HEX)-S-D-Bact-1371-a-A-20 or as predicted from sequence data.
dValue calculated from the differences between the size of the experimentally determined TRF and the sequence predicted fragment sizes for a restriction digest of organisms in the TRF database. The SOD for each organism was then calculated.
eEach TRF size reported was determined from the average of at least two digests.