1b 400 609 1% Thermoplasmatales/RCIII 515 264 1% Methanocorpusculum 551 609 10% Thermoplasmatales/RCIII ND 80 1% Methanosaeta ND 613 1% Thermoplasmatales/Cluster C ND ND 4% Methanosaeta a Observed PD-0332991 clinical trial and predicted TRF lengths from T-RFLP and clone library analysis of a sample from 2007-05-22. b Relative abundance based on total fluorescence. c Relative abundance based on frequency in clone library. d ND indicates cases where a TRF could not be predicted or where the predicted TRF was outside the detection range. Figure 7 Relative abundances of AluI TRFs. Relative abundances of TRFs in normalized TRF profiles generated by digestion with
AluI. Together with the RsaI TRFs, the AluI TRFs were compared with the predicted TRFs of the clone library Quisinostat datasheet sequences (identities in
bold) and the sequences from the RDP database (identities in italics) (Table 4). Figure 8 Relative abundances of RsaI TRFs. Relative abundances of TRFs in normalized TRF profiles generated by digestion with RsaI. Together with the AluI TRFs, the RsaI TRFs were compared with the predicted TRFs of the clone KU55933 in vitro library sequences (identities in bold) and the sequences from the RDP database (identities in italics) (Table 4). To identify the TRFs the observed TRF lengths were compared with the predicted TRF lengths of sequences in the clone library. The predicted TRFs from the sequences in the clone library were between 4 and 6 bases longer than the observed TRFs (Table 3). Such a discrepancy Ribose-5-phosphate isomerase between observed and predicted
TRF sizes is commonly observed [32, 33]. Not all observed TRFs in the time series could be matched with the predicted TRFs of the clone library sequences. To explore the possibility that the TRFs in the TRF profiles from the samples from 2003 and 2004 come from sequences other than those found in the clone library a comparison was also made with a database of 5802 archaeal 16S rRNA gene sequences matching the primers used in this study. The database was checked for sequences that would result in any of the observed combinations of TRFs generated by AluI and RsaI. The result of the analysis was a number of possible identities for each observed combination of AluI and RsaI TRFs (Table 4). Although the database comparison may result in false identities of the TRFs, it is valuable because it gives an indication about the range of species that could give the observed TRF combinations. By comparison with the clone library sequences the dominating TRFs (AluI 176, AluI 184, RsaI 74 and RsaI 238) were determined to represent Methanosaeta-like species. Comparisons with the predicted TRFs of 5802 Archaea sequences in the database (Table 4) showed that it is possible that the dominating TRFs are from other species of the Euryarchaeota than Methanosaeta.