Computational protocol: Assessment of the Bacteriocinogenic Potential of Marine Bacteria Reveals Lichenicidin Production by Seaweed-Derived Bacillus spp.

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Protocol publication

[…] Marine isolates were initially characterized phenotypically by Gram staining, spore staining and oxidase and catalase tests. In addition, 16S rRNA gene sequencing was performed on each isolate, by amplifying the 16S rRNA gene in a 15 µL reaction volume using primers 63f and 1387r, purifying the PCR products and sequencing them on an AB 310 genetic analyzer (Applied Biosystems, CA, USA), as outlined by Coffey et al. []. Nucleotide sequences were compared with those in the GenBank database using the blast program [] through the National Center for Biotechnology Information (NCBI) server []. TreeView 1.6.6 [] was used to construct a phylogram from a ClustalW alignment (ClustalX) [].Molecular fingerprinting of the marine isolates was then performed by pulsed-field gel electrophoresis (PFGE), as described previously [], using ApaI, XbaI and NotI. Electrophoresis conditions used were 200 V for 17 h with a pulse time from 1 to 15 s for ApaI; 10 h at 200 V with a pulse time from 1 to 15 s for XbaI and 15 h at 200 V with a pulse time from 1 to 12 s for NotI. A low-range molecular weight DNA marker (0.13–194.0 Kb; New England Biolabs, Beverly, MA) was used. […]

Pipeline specifications

Software tools TreeViewX, Clustal W
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Bacillus licheniformis