Abstract
<i>Pseudomonas stutzeri</i> is a valuable bacteria for understanding of the taxonomical and the phylogenetic relationships. The study of genetic relationships between organisms or genes is carried out by molecular phylogeny. We aim to study the relationships according to16S rRNA gene sequences between our samples and the closest strains from other countries over the world. To our knowledge, the phylogenetic studies between strains from Sudan with strains from other countries were not done before. A total of 140 currency notes in different denominations were collected randomly from several locations including hospitals, food sellers and transporters. From the collected notes, a total of 135 bacterial colonies were isolated and from them 14 isolates were identified as a <i>Pseudomonas stutzeri</i>. In the study, streaking plate method was used for the isolation of pure bacterial culture, Chelex 100 method was used for DNA extraction, conventional PCR was used for amplification of the targeted gene, agarose gel electrophoresis and various bioinformatics tools were used for nucleotide sequence analysis. The PCR products were sent for Macrogen Company-Netherlands for purification and nucleotide sequencing. After sequencing 3 samples were noisy, hence they were excluded. According to phylogenetic analysis, we found that the samples were closely related to strains from south-east Asia (Indonesia), east Asia (China), south-central Asia (Bangladesh), south Asia (India), north Africa (Tunisia) and south Europe (Italy and Greece). Despite the samples were from the same source (currency notes), we found that there is broad sequence variation between them.
Highlights
Pseudomonas stutzeri is a gram negative straight rod [5] belonging to gamma-Proteobacteria [6].Strains of P. stutzeri exhibit broad genotypic diversity [7], [8] P. stutzeri is a valuable bacteria for understanding of the taxonomical and the phylogenetic relationships [9].The study of genetic relationships between organisms or genes is carried out by molecular phylogeny via the European Journal of Biophysics 2018; 5(6): 104-111 comparing of protein or homologous DNA sequences such as ribosomal RNA and mitochondrial genes
P. stutzeri strains have almost a universal environmental distribution [5], it is not strange to be isolated from currency notes
Identification of bacteria and the phylogenetic analysis, we found that sample 1 clustered with strain SC-04 from Indonesia in the same phylogenetic sub branch (100% sequence identity), sample 2 was closely related to strain N55 from China (100% sequence identity) and Bd8 from Sudan (99% sequence identity)
Summary
Pseudomonas stutzeri is a gram negative straight rod [5] belonging to gamma-Proteobacteria [6].Strains of P. stutzeri exhibit broad genotypic diversity [7], [8] P. stutzeri is a valuable bacteria for understanding of the taxonomical and the phylogenetic relationships [9].The study of genetic relationships between organisms or genes is carried out by molecular phylogeny via the European Journal of Biophysics 2018; 5(6): 104-111 comparing of protein or homologous DNA sequences such as ribosomal RNA and mitochondrial genes. P. stutzeri strains are characterized by their ability to grow in broad range of temperature, anaerobically, and organotrophically (via utilization of many organic substrates) as well as the resistance to heavy metals. They were isolated from various environments including soil, groundwater, rhizosphere marine water, sediment, wastewater [5], clinical materials [11] and currency notes [12]. Many studies on the genotypic identification and phylogenetic analysis of P. stutzeri were performed via several highly specific and sensitive molecular markers including 16S rRNA gene [5]. In Sudan, it was isolated and identified via conventional methods [13], [14], [15] as well as 16S rRNA gene [16]
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