Computational protocol: Cellulolytic potential of a novel strain of Paenibacillus sp. isolated from the armored catfish Parotocinclus maculicauda gut

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Protocol publication

[…] Total DNA was extracted from the selected strain (P118) as described in Seldin and Dubnau (). The procedure described by Massol-Deya et al. () was employed for PCR amplification of the 16S rRNA coding gene using the pair of universal primers (pA and pH). The amplification conditions were: a hot start (2 min 10 s at 92°C) and 35 cycles of 92°C (1 min 10 s), 48°C (30 s) and 72°C (2 min 10 s). A final extension step was run for 6 min 10 s at 72°C and the reaction tubes were then cooled to 4°C. DNA preparation and PCR products were visualized after electrophoresis respectively in 0.8% and 1.2% agarose gel in 1x TBE buffer ().PCR product of the 16S rRNA coding gene from P118 was sequenced by using an ABI Prism 3100 automatic sequencer. All sequences were identified using the Blastn facility (www.ncbi.nlm.nih.gov/blast) of the National Center for Biotechnology Information with GenBank non-redundant database. The 16S rRNA coding gene sequences of closely related strains were recovered from GenBank database and aligned with the sequences obtained in this study using the package software Clustal X (). BioEdit version 7.0.5.3 (http://www.mbio.ncsu.edu/Bioedit/bioedit.html) was used for manual editing of the sequences.Phylogenetic trees were constructed based on complete 16S rDNA sequences, using the Neighbor-Joining (NJ) method (), whereas MEGA 4.1 software () was used to calculate pairwise p-distance values for 16S rRNA gene sequences among the different species studied here. […]

Pipeline specifications

Software tools BLASTN, Clustal W, BioEdit, MEGA
Applications Phylogenetics, 16S rRNA-seq analysis
Chemicals Acetoin, Carbohydrates, Carbon, Carboxymethylcellulose Sodium, Fatty Acids