Computational protocol: Isolation and characterization of a novel gossypol-degrading bacteria Bacillus subtilis strain Rumen Bacillus Subtilis

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Protocol publication

[…] The thalli of the isolated strain were inoculated into liquid LB medium and cultured for 24 h at 39°C with shaking, then harvested from the liquid medium by centrifugation. DNA was extracted using the sodium dodecyl sulfate (SDS)-proteinase K method [] and purified DNA samples were stored at −20°C. The genomic DNA was amplified by polymerase chain reaction (PCR) using universal primers F1: 5′-AGAGTTTGATCCTGGCTCAG-3′ and R1: 5′-ACGGTTACCTTGTTACGACTT-3′ [] and the PCR reaction was conducted using the following conditions: 5 min at 94°C, followed by 35 cycles of 30 s at 94°C, 30 s at 56°C, and 90 s at 72°C, and a final extension of 10 min at 72°C. The isolated strain 16S rRNA genes were sequenced by Shanghai Huada, China. The product of 16S rRNA genes of the isolates in the present study were compared against National Center for Biotechnology Information (NCBI) database reported sequences with the Basic Local Alignment Search Tool (BLAST) hosted at website of NCBI. A phylogenetic tree was then drawn using the Neighbor joining method []. Phylogenetic and molecular evolutionary analyses were conducted at 1000 bootstrap value using Molecular Evolutionary Genetics analysis (MEGA) version 5.0 software (Center of Evolutionary Functional Genomics, Biodesign Institute, Arizona State University, Tempe, AZ, USA) []. […]

Pipeline specifications

Software tools BLASTN, MEGA
Application Phylogenetics
Organisms Escherichia coli, Bacillus subtilis, Bos taurus, Bacteria
Diseases Dysentery, Bacillary, Protein Deficiency
Chemicals Amino Acids, Carbon, Gossypol