Computational protocol: Cellulolytic and proteolytic ability of bacteria isolated from gastrointestinal tract and composting of a hippopotamus

Similar protocols

Protocol publication

[…] All the phylogenetic analyzes were developed using Mega 4.1 program (Molecular Evolutionary Genetics Analysis). Partial 16S rRNA gene sequences obtained from the pure cultures using the described primers were assembled in a contiguous sequence using the Chromas Pro Current Version 1:34 software. Identification was achieved by comparing the contiguous 16S rRNA gene sequences (~1000 bp in length) generated for isolates with 16S rRNA sequence data from reference and type strains, available at the public databases Genbank (http://www.ncbi.nem.nih.gov) and RDP (Ribosomal Database Project, Wisconsin, USA, http://www.cme.msu.edu/RDP/html/index.html), by using BLASTN and RDP sequence match routines. The sequences were aligned using Clustal W (Thompson et al. ) and analyzed using Neighbour-Joining method and p distance model. phylogenetic trees were constructed by parsimonium maximum and Neighbour-Joining with bootstrap test in 1000 replicates.The nucleotide sequences determined in this study for the bacterial isolates were deposited at the Genbank database under the accession numbers: KT884746-KT884759 (Table ). […]

Pipeline specifications

Software tools MEGA, BLASTN, Clustal W
Application Phylogenetics
Organisms Hippopotamus amphibius
Chemicals Ethanol