The forward primer Arch21F was shortened to match

The forward primer Arch21F was shortened to match see more the new annealing temperature of the reverse primer. The cycle profiles had an initial 5 min at 95°C for Taq polymerase activation followed by denaturation at 94°C for 1 min, annealing at 58°C for 30 s and elongation at 72°C for 1 min. The annealing temperature was decreased 1°C every 3 cycles until reaching 55°C where the number of cycles was 30. The reactions were ended with a final elongation step

at 72°C for 7 min. Cloning The PCR-products of nine PCR replicates, generated from two DNA extraction replicates, were pooled and purified using Qiagen MinElute PCR Purification Kit (Qiagen). 8 ng and 15 ng of purified PCR-product were ligated into the plasmid vector pCR 4 TOPO (Invitrogen) in duplicate reactions. One Shot DH5alpha-T1R competent Escherichia coli cells (Invitrogen) were transformed with the vector constructs according to the manufacturer’s instructions in two separate reactions. The transformed cells were plated on LB-agar plates with 50 μg/ml Kanamycin

and incubated at 37°C over night. 95 cloned sequences were amplified directly from transformed single colonies from the two cloning reactions by PCR using the vector specific primers T3 (ATTAACCCTCACTAAAGGGA) and T7 (TAATACGACTCACTATAGGG). The bacterial cells were lysed by five minutes incubation at 94°C followed by PCR-cycles as described above but with a starting annealing temperature of 57°C. Sequencing and Liproxstatin-1 clinical trial sequence analysis Cloned sequences were sequenced from find more both ends using Big Dye Sequencing Kit (Applied Biosystems) and primers T3 and T7 as sequencing primers. Sequence data was generated by capillary gel electrophoresis (3730 DNA analyzer, Applied Biosystems). Raw data sequences were manually inspected using SeqScape (Applied Biosystems). Sequences sequenced from different ends of the PCR-product were aligned using BioEdit (version 5.0.9) [61]. Consensus sequences were generated for 82 clones with overlaps between the 5’ and 3’ end sequences ranging from 80 to 496 bases. The sequences were aligned using the alignment tool of the SILVA rRNA database [26]

and checked for PIK3C2G chimeras using the Bellerophon server [62]. The sequences were also aligned with a reference E. Coli sequence, accession number U00096, and checked for chimeras using Mallard [63]. No chimeric sequences were detected with either of the two methods. The similarity between the 16S rRNA gene sequences was determined by generating a similarity matrix using the DNADIST program in the PHYLIP package [64]. The sequences were then assigned to OTUs based on different similarity thresholds. For Bacteria, 16S rRNA gene sequence similarities of 80%, 90%, 95% and 98.7% approximately represent the division in phylum, family/class, genus and species levels, respectively [23, 24], and we use the same criteria for Archaea.

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