Molecular Phylogenetic Study on <i>Pseudomonas stutzeri</i> Isolated from Currency Notes in Khartoum State, Sudan and Identified Via16s rRNA Gene Sequence Analysis

Mosab Yahya Al-Nour; Malik Suliman Mohamed; Noha Ahmed Abd Alfadil; Hisham Nouraldayem Altayb; Salah-Eldin Gumaa El-lzaki; Mohamed Ahmed Hassan

doi:doi:10.11648/j.ejb.20170506.12

Molecular Phylogenetic Study on Pseudomonas stutzeri Isolated from Currency Notes in Khartoum State, Sudan and Identified Via16s rRNA Gene Sequence Analysis

Mosab Yahya Al-Nour, Malik Suliman Mohamed, Noha Ahmed Abd Alfadil, Hisham Nouraldayem Altayb, Salah-Eldin Gumaa El-lzaki, Mohamed Ahmed Hassan

Published in European Journal of Biophysics (Volume 5, Issue 6)

Received: 28 November 2017 Accepted: 19 December 2017 Published: 17 January 2018

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Abstract

Pseudomonas stutzeri 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 Pseudomonas stutzeri. 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.

Published in	European Journal of Biophysics (Volume 5, Issue 6)
DOI	10.11648/j.ejb.20170506.12
Page(s)	104-111
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2018. Published by Science Publishing Group

Keywords

Pseudomonas stutzeri, Currency Notes, Molecular Phylogenetic, Khartoum, Sudan

References

[1]	Bio Edit software. (http://www.mbio.ncsu.edu/bioedit/bioedit.html).
[2]	Jukes TH, Cantor CR (1969) Evolution of protein molecules. Mammalian protein metabolism 3: 132.
[3]	Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution: 783-791.
[4]	Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.06. Molecular biology and evolution 30: 2725-2729.
[5]	Lalucat J, Bennasar A, Bosch R, Garcia-Valdes E, Palleroni NJ (2006) Biology of Pseudomonas stutzeri. Microbiol Mol Biol Rev 70: 510-547. doi: 10.1128/MMBR.00047-05.
[6]	Stackebrandt E, Murray RGE, Trüper HG (1988) Proteobacteria classis nov., a Name for the Phylogenetic Taxon That Includes the “Purple Bacteria and Their Relatives”. International Journal of Systematic and Evolutionary Microbiology 38: 321-325. doi:10.1099/00207713-38-3-321.
[7]	Rosselló‐Mora R, Lalucat J, Dott W, Kämpfer P (1994) Biochemical and chemotaxonomic characterization of Pseudomonas stutzeri genomovars. Journal of applied bacteriology 76: 226-233.
[8]	Rosselló R, García-Valdés E, Lalucat J, Ursing J (1991) Genotypic and phenotypic diversity of Pseudomonas stutzeri. Systematic and applied microbiology 14: 150-157.
[9]	García-Valdés E, Mulet M, Lalucat J (2010) Insights into the life styles of Pseudomonas stutzeri Pseudomonas. Springer, pp. 177-198.
[10]	Patwardhan A RS, Roy A (2014) Molecular Markers in Phylogenetic Studies – A Review. J Phylogen Evolution Biol 2. doi: 10.4172/2329-9002-2-131.
[11]	B H (1986) Identification and distribution of Pseudomonas stutzeri in clinical material. J Appl Bacteriol 60: 401-411.
[12]	Kalita M, Palusinska-Szysz M, Turska-Szewczuk A, Wdowiak-Wrobel S, Urbanik-Sypniewska T (2013) Isolation of cultivable microorganisms from Polish notes and coins. Pol J Microbiol 62: 281-286.
[13]	Aradaib MEAaIE (2006) Association of Pseudomonas stutzeri with An Infected Ruptured Pulmonary Hydatid Cyst in A Young Patient. Surgery Journal 1: 32-34.
[14]	Osman TMaES, S. M. (2013) Aerobic Bacteria Isolated from Dead in -Shell Chick Embryo in Khartoum State. The Sudan Journal of Veterinary Research 28: 1-7.
[15]	E. Mohamed Ahmed HAAaIEA (2006) A Clinical Case of Recurrent Pleural Effusions, Culminating in Empyema-thoraces in a Sudanese Woman with Yellow Nail Syndrome. International Journal of Tropical Medicine 1: 137-139.
[16]	El-Hussein AA, Elsalahi RH, Osman AG, Sherif AM, El Siddig MA (2014) Isolation and 16S rRNA-Based Identification of Benomyl-Degrading Bacteria. British Biotechnology Journal 4: 670.
[17]	Lane DJ PB, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proceedings of the National Academy of Sciences of the United States of America 82: 6955-6959.
[18]	Cheesbrough M (2006) District laboratory practice in tropical countries- part 2. Cambridge university press.
[19]	Dart RK (1996) Microbiology for the analytical chemist. Royal Society of Chemistry.
[20]	Giraffa G, Rossetti L, Neviani E (2000) An evaluation of chelex-based DNA purification protocols for the typing of lactic acid bacteria. Journal of Microbiological Methods 42: 175-184.
[21]	Liu W, Bao Q, Qing M, Chen X, Sun T, Li M, Zhang J, Yu J, Bilige M, Sun T (2012) Isolation and identification of lactic acid bacteria from Tarag in Eastern Inner Mongolia of China by 16S rRNA sequences and DGGE analysis. Microbiological research 167: 110-115.
[22]	Lee PY, Costumbrado J, Hsu C-Y, Kim YH (2012) Agarose gel electrophoresis for the separation of DNA fragments. JoVE (Journal of Visualized Experiments): e3923-e3923.
[23]	Finch TV software, (http://www.geospiza.com/ftvdlinfo.html).
[24]	Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of molecular biology 215: 403-410.
[25]	Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2013) GenBank. Nucleic acids research 41: D36-D42.
[26]	Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research 22: 4673-4680.
[27]	Okonechnikov K, Golosova O, Fursov M (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28: 1166-1167.
[28]	Maps of world (www.mapsofworld.com).
[29]	Carlson CA, Pierson LS, Rosen J, Ingraham JL (1983) Pseudomonas stutzeri and related species undergo natural transformation. Journal of Bacteriology 153: 93-99.
[30]	Sikorski J, Rosselló-Mora R, Lorenz MG (1999) Analysis of genotypic diversity and relationships among Pseudomonas stutzeri strains by PCR-based genomic fingerprinting and multilocus enzyme electrophoresis. Systematic and applied microbiology 22: 393-402.
[31]	Scotta C, Gomila M, Mulet M, Lalucat J, García-Valdés E (2013) Whole-cell MALDI-TOF mass spectrometry and multilocus sequence analysis in the discrimination of Pseudomonas stutzeri populations: three novel genomovars. Microbial ecology 66: 522-532.
[32]	Sikorski J, Teschner N, Wackernagel W (2002) Highly different levels of natural transformation are associated with genomic subgroups within a local population of Pseudomonas stutzeri from soil. Applied and environmental microbiology 68: 865-873.
[33]	Alemu A (2014) Microbial contamination of currency notes and coins in circulation: a potential public health hazard. Biomedicine and Biotechnology 2: 46-53.
[34]	Cladera AM, Bennasar A, Barceló M, Lalucat J, García-Valdés E (2004) Comparative genetic diversity of Pseudomonas stutzeri genomovars, clonal structure, and phylogeny of the species. Journal of bacteriology 186: 5239-5248.

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APA Style

Mosab Yahya Al-Nour, Malik Suliman Mohamed, Noha Ahmed Abd Alfadil, Hisham Nouraldayem Altayb, Salah-Eldin Gumaa El-lzaki, et al. (2018). Molecular Phylogenetic Study on Pseudomonas stutzeri Isolated from Currency Notes in Khartoum State, Sudan and Identified Via16s rRNA Gene Sequence Analysis. European Journal of Biophysics, 5(6), 104-111. https://doi.org/10.11648/j.ejb.20170506.12

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ACS Style

Mosab Yahya Al-Nour; Malik Suliman Mohamed; Noha Ahmed Abd Alfadil; Hisham Nouraldayem Altayb; Salah-Eldin Gumaa El-lzaki, et al. Molecular Phylogenetic Study on Pseudomonas stutzeri Isolated from Currency Notes in Khartoum State, Sudan and Identified Via16s rRNA Gene Sequence Analysis. Eur. J. Biophys. 2018, 5(6), 104-111. doi: 10.11648/j.ejb.20170506.12

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AMA Style

Mosab Yahya Al-Nour, Malik Suliman Mohamed, Noha Ahmed Abd Alfadil, Hisham Nouraldayem Altayb, Salah-Eldin Gumaa El-lzaki, et al. Molecular Phylogenetic Study on Pseudomonas stutzeri Isolated from Currency Notes in Khartoum State, Sudan and Identified Via16s rRNA Gene Sequence Analysis. Eur J Biophys. 2018;5(6):104-111. doi: 10.11648/j.ejb.20170506.12

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@article{10.11648/j.ejb.20170506.12,
  author = {Mosab Yahya Al-Nour and Malik Suliman Mohamed and Noha Ahmed Abd Alfadil and Hisham Nouraldayem Altayb and Salah-Eldin Gumaa El-lzaki and Mohamed Ahmed Hassan},
  title = {Molecular Phylogenetic Study on Pseudomonas stutzeri Isolated from Currency Notes in Khartoum State, Sudan and Identified Via16s rRNA Gene Sequence Analysis},
  journal = {European Journal of Biophysics},
  volume = {5},
  number = {6},
  pages = {104-111},
  doi = {10.11648/j.ejb.20170506.12},
  url = {https://doi.org/10.11648/j.ejb.20170506.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ejb.20170506.12},
  abstract = {Pseudomonas stutzeri 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 Pseudomonas stutzeri. 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.},
 year = {2018}
}

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TY  - JOUR
T1  - Molecular Phylogenetic Study on Pseudomonas stutzeri Isolated from Currency Notes in Khartoum State, Sudan and Identified Via16s rRNA Gene Sequence Analysis
AU  - Mosab Yahya Al-Nour
AU  - Malik Suliman Mohamed
AU  - Noha Ahmed Abd Alfadil
AU  - Hisham Nouraldayem Altayb
AU  - Salah-Eldin Gumaa El-lzaki
AU  - Mohamed Ahmed Hassan
Y1  - 2018/01/17
PY  - 2018
N1  - https://doi.org/10.11648/j.ejb.20170506.12
DO  - 10.11648/j.ejb.20170506.12
T2  - European Journal of Biophysics
JF  - European Journal of Biophysics
JO  - European Journal of Biophysics
SP  - 104
EP  - 111
PB  - Science Publishing Group
SN  - 2329-1737
UR  - https://doi.org/10.11648/j.ejb.20170506.12
AB  - Pseudomonas stutzeri 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 Pseudomonas stutzeri. 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.
VL  - 5
IS  - 6
ER  -

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Author Information

Mosab Yahya Al-Nour

Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Khartoum, Sudan
Malik Suliman Mohamed

Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
Noha Ahmed Abd Alfadil

Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Alneelain, Khartoum, Sudan
Hisham Nouraldayem Altayb

Department of Microbiology, College of Medical Laboratory Science, Sudan University of Science and Technology, Khartoum, Sudan
Salah-Eldin Gumaa El-lzaki

Department of Epidemiology, Molecular Epidemiology Laboratory, Tropical Medicine Institute Research, Khartoum, Sudan
Mohamed Ahmed Hassan

Applied Bioinformatics Center, Africa City of Technology, Khartoum, Sudan

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Mosab Yahya Al-Nour, Malik Suliman Mohamed, Noha Ahmed Abd Alfadil, Hisham Nouraldayem Altayb, Salah-Eldin Gumaa El-lzaki, et al. (2018). Molecular Phylogenetic Study on Pseudomonas stutzeri Isolated from Currency Notes in Khartoum State, Sudan and Identified Via16s rRNA Gene Sequence Analysis. European Journal of Biophysics, 5(6), 104-111. https://doi.org/10.11648/j.ejb.20170506.12

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ACS Style

Mosab Yahya Al-Nour; Malik Suliman Mohamed; Noha Ahmed Abd Alfadil; Hisham Nouraldayem Altayb; Salah-Eldin Gumaa El-lzaki, et al. Molecular Phylogenetic Study on Pseudomonas stutzeri Isolated from Currency Notes in Khartoum State, Sudan and Identified Via16s rRNA Gene Sequence Analysis. Eur. J. Biophys. 2018, 5(6), 104-111. doi: 10.11648/j.ejb.20170506.12

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AMA Style

Mosab Yahya Al-Nour, Malik Suliman Mohamed, Noha Ahmed Abd Alfadil, Hisham Nouraldayem Altayb, Salah-Eldin Gumaa El-lzaki, et al. Molecular Phylogenetic Study on Pseudomonas stutzeri Isolated from Currency Notes in Khartoum State, Sudan and Identified Via16s rRNA Gene Sequence Analysis. Eur J Biophys. 2018;5(6):104-111. doi: 10.11648/j.ejb.20170506.12

Copy | Download

@article{10.11648/j.ejb.20170506.12,
  author = {Mosab Yahya Al-Nour and Malik Suliman Mohamed and Noha Ahmed Abd Alfadil and Hisham Nouraldayem Altayb and Salah-Eldin Gumaa El-lzaki and Mohamed Ahmed Hassan},
  title = {Molecular Phylogenetic Study on Pseudomonas stutzeri Isolated from Currency Notes in Khartoum State, Sudan and Identified Via16s rRNA Gene Sequence Analysis},
  journal = {European Journal of Biophysics},
  volume = {5},
  number = {6},
  pages = {104-111},
  doi = {10.11648/j.ejb.20170506.12},
  url = {https://doi.org/10.11648/j.ejb.20170506.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ejb.20170506.12},
  abstract = {Pseudomonas stutzeri 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 Pseudomonas stutzeri. 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.},
 year = {2018}
}

Copy | Download

TY  - JOUR
T1  - Molecular Phylogenetic Study on Pseudomonas stutzeri Isolated from Currency Notes in Khartoum State, Sudan and Identified Via16s rRNA Gene Sequence Analysis
AU  - Mosab Yahya Al-Nour
AU  - Malik Suliman Mohamed
AU  - Noha Ahmed Abd Alfadil
AU  - Hisham Nouraldayem Altayb
AU  - Salah-Eldin Gumaa El-lzaki
AU  - Mohamed Ahmed Hassan
Y1  - 2018/01/17
PY  - 2018
N1  - https://doi.org/10.11648/j.ejb.20170506.12
DO  - 10.11648/j.ejb.20170506.12
T2  - European Journal of Biophysics
JF  - European Journal of Biophysics
JO  - European Journal of Biophysics
SP  - 104
EP  - 111
PB  - Science Publishing Group
SN  - 2329-1737
UR  - https://doi.org/10.11648/j.ejb.20170506.12
AB  - Pseudomonas stutzeri 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 Pseudomonas stutzeri. 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.
VL  - 5
IS  - 6
ER  -

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