This peak was therefore initially not taken into account in the original eT-RFLP profiles. Table 3 T-RF diversity for single phylogenetic descriptions Phylogenetic affiliation dTRF (bp) dTRF shifteda(bp) Countsb(−) Relative contribution to T-RFc(%) AG-881 order Reference OTUd Reference GenBank accession numbere SW mapping scoref(−) Normalized SW mapping scoreg(−) Flocculent and aerobic granular sludge samples from wastewater treatment systems Rhodocyclus tenuis 39 34 37 4.8 3160 AB200295 363 0.917 199 194 1 25.0 3160 AB200295 248 0.648 205 200 3 100.0 3160 AF204247 314 0.858 210 205 1 100.0 3160 AF204247 211 0.699 218 213 11 91.7 3160 AB200295 356 0.942 219 214 769 99.6 3160 AB200295
371 0.949 220 215 6 37.5 3160 AF502230 318 0.817 221 216 1 7.7 3160 AF502230 276 0.865 225 220 2 3.7 3160 AB200295 206 0.703 252 247 3 100.0 3160 AB200295 305 0.762 253 248 9 100.0 3160 AB200295 EPZ015666 ic50 228 0.752 257 252 1 20.0 3160 AF502230 241 0.660 Groundwater samples from aquifers contaminated with chloroethenes Dehalococcoides spp. 166 161 1 100.0 1368 EF059529 290 0.775 168 163 143 100.0 1368 EF059529 241 0.717 169 164 2 100.0 1368 EF059529 331 0.768 170 165 2 100.0 1368 EF059529
241 0.693 171 166 1 50.0 1368 EF059529 303 0.783 173 168 1 100.0 1368 EF059529 241 0.717 176 171 1 100.0 1369 DQ833317 211 0.687 179 174 1 100.0 1369 DQ833317 193 0.629 188 183 4 66.7 1369 DQ833340 Selleckchem SB525334 464 0.947 a Digital T-RF obtained after having shifted the digital dataset with the most probable average cross-correlation lag. b Number of reads of the target phylotype that contribute to the T-RF. c Diverse bacterial affiliates can contribute to the same T-RF. d Reference OTU from the Greengenes public Vildagliptin database obtained after mapping. e GenBank accession numbers provided by Greengenes for reference sequences. f Best SW mapping score obtained. g SW mapping score normalized by the read length. Generation of digital T-RFLP profiles The dT-RFLP profiles were successfully generated with
the standard PyroTRF-ID procedure (Table 1) from denoised bacterial pyrosequencing datasets of the GRW and the AGS sample series (Additional file 4). With HaeIII, 165±29 and 87±11 T-RFs were present in the dT-RFLP profiles of the GRW and AGS series, respectively. For all samples, only a reduced number of dT-RFs above 400 bp were obtained because of the low pyrosequencing quality at sequence lengths between 400 and 500 bp. An additional feature of PyroTRF-ID is the generation of dT-RFLP profiles with any restriction enzyme. Here profiles were obtained with five additional restriction enzymes and compared. Profiles of GRW samples were on average 2.3 times richer than ones of AGS samples, and each restriction enzyme generated characteristic dT-RFLP features regardless of the sample complexity (Figure 2 and Additional file 4). HaeIII provided dT-RFLP profiles with the highest richness.