Computational protocol: Bioprospection of actinobacteria derived from freshwater sediments for their potential to produce antimicrobial compounds

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Protocol publication

[…] Genomic DNA was isolated and purified using a DNA extraction kit (Invitrogen) as described in previous studies []. Ribosomal RNA (16S rRNA) genes were amplified using universal bacterial primers []. The reactions and conditions of the PCR were performed exactly as reported in our previous studies [], and sequencing was done commercially at Sci Genome Pvt. Ltd. Cochin, India. Sequences were compared with the reference strains of actinobacteria from the NCBI genomic database using a BLASTn search to determine similarity percentages. The strains with highest similarity percentages were retrieved from the EzTaxon database [], and multiple sequence alignment was performed using Clustal W software packaged in MEGA 6.0 []. The evolutionary models were selected based on the lowest Bayesian information criterion (BIC) scores and the highest Akaike information criterion (AIC) values using MEGA 6.0 []. Phylogenetic analysis was performed using MEGA 6 software using the maximum-likelihood method and using the Tamura Nei parameters algorithm taking E. coli as the outgroup []. The significance of the branching order was determined by bootstrap analysis of 1000 alternative trees. The obtained nucleotide sequences of the 16S rRNA gene fragments were deposited, and accession numbers were acquired. Trees were viewed and edited using the FigTree 1.3.1 program. […]

Pipeline specifications

Software tools BLASTN, Clustal W, MEGA, FigTree
Databases EzBioCloud
Application Phylogenetics
Organisms Hemisus marmoratus, Saccharomyces cerevisiae
Diseases Bacterial Infections, Communicable Diseases, Multiple Sclerosis
Chemicals Ketoconazole, Rifampin, Trimethoprim, Fluconazole