Bacterial Identification by 16S rRNA Sequencing

Identification of bacteria isolates was based on 16S rRNA fragment sequencing. For this purpose PCR using universal primers 27F and 515R (Supplementary Table S2) was performed as described previously (Kim et al., 2012 (link)) using DNA extracted from bacteria isolates. PCR products then were purified using DNA Clean and Concentrator-5 Kit (D4010, Zymo Research, United States) and identification of the isolates was performed after sequencing and analysis using Molecular Evolutionary Genetic Analysis software (MEGA, version 6). Basic local alignment search tool (BLAST) was used for comparison of obtained sequences with sequences in the database of National Center for Biotechnology Information (NCBI, United States). Species were identified by matching obtained sequences with a sequence showing the highest maximum identity score from the GenBank database. If the identity of the best match was < 99% and query cover < 96% only genus was assigned.