Computational protocol: Bacillus thuringiensis B1(2015b) is a Gram-Positive Bacteria Able to Degrade Naproxen and Ibuprofen

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Protocol publication

[…] Bacterial DNA was isolated from the pure culture using the DNA commercial kit (GenElute Bacterial Genomic DNA Kit, Sigma-Aldrich). For 16S rRNA gene amplification, the bacteria-specific primers: 8 F 5′AGTTTGATCATCGCTCAG 3′ and 1492R 5′GGTTACCTTGTTACGACTT3′ were used. Amplification was carried out through a program consisting of initial denaturation at 94 °C for 300 s, three cycles at 94 °C for 45 s, 57 °C for 30 s, and 72 °C for 120 s; three cycles at 94 °C for 45 s, 56 °C for 30 s, and 72 °C for 120 s; three cycles at 94 °C for 45 s, 55 °C for 30 s, and 72 °C for 120 s; 26 cycles at 94 °C for 45 s, 53 °C for 30 s, and 72 °C for 120 s; and a final elongation step at 72 °C for 300 s. The nucleotide sequencing of the gene was done by using the Big DyeR Terminator Cycle Sequencing Kit (Applied Biosystem) and AbiPrism®3100 Genetic Analyzer. The MegaBLAST program was used for homology searches with the standard default program. Multiple sequence alignments were performed and the neighbor-joining phylogenetic tree was constructed using CLC Sequence Viewer 7.0.2 program. The 16S rRNA gene sequence determined in this study has been deposited in the GeneBank database of NCBI under the accession number KP895873.1. […]

Pipeline specifications

Software tools BLASTN, CLC Sequence Viewer
Application Phylogenetics
Organisms Bacillus thuringiensis, Bacteria, Halalkalicoccus jeotgali
Chemicals Carbon, Glucose, Ibuprofen, Naproxen