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ISSN: 2153-0602
Journal of Data Mining in Genomics & Proteomics
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Insights into Genomic Variation within Salmonella enterica

Serrano PC1, Perez LAM2, Hernandez YE2 and Nava GM2*

1Autonomous University of Mexico, Mexico City, Mexico

2Autonomous University of Queretaro, Mexico City, Mexico

*Corresponding Author:
Nava GM
Department of Research and Graduate Studies in Food Science
Faculty of Chemistry, Autonomous University of Queretaro
Mexico City, Mexico
Tel: +52-4424676817
E-mail: [email protected]

Received date: March 07, 2017; Accepted date: March 08, 2017; Published date: March 23, 2017

Citation: Serrano PC, Perez LAM, Hernandez YE, Nava GM (2017) Insights into Genomic Variation within Salmonella enterica. J Data Mining Genomics Proteomics 8:e128. doi: 10.4172/2153-0602.1000e128

Copyright: © 2017 Serrano PC, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Editorial

Advances in molecular microbiology, comparative genomics and data mining have allowed us to uncover new insights into genome structure within bacterial species. To evolve, Bacteria gains and loses genes and other genomic sequences to adapt to specific ecological niches [1]. Thus, the intraspecies genomic variation found in numerous bacterial species has highlighted the need of analyzing genome composition to define bacterial species [1]. Fortunately, Whole-Genome Sequence Analysis (WGSA) has uncovered the dynamic nature of genomic plasticity and the consequent extensive genetic diversity in Bacteria [2]. Currently, microbiological research has been focused on WGSA within-species to identify molecular or virulence determinants. These studies could accelerate our understanding of bacterial pathogenesis and strains-specific traits of virulence; key factors in improving bacterial surveillance and development of antibacterial treatments or vaccines [3].

Herein, we investigate the genomic variation within Salmonella enterica as an example of the potential of comparative analysis of WGSA to uncover intraspecies variation. A total of 1,604 S. enterica whole genomes were analyzed. This dataset comprised 38 different serotypes (Table 1) retrieved from the Integrated Microbial Genomes (IMG) system [4]. Serotypes with at least 3 genomes available were used for bioinformatics analyses. Intraspecies traits of genomic variation were assessed for each of the selected serotypes. Briefly, it was found that the genome size S. enterica serotypes varies considerably; for example, serotype Muenchen, in average, possess the largest genome size (5.00 Mbp) whereas Paratyphi possess the smallest (4.59 Mbp). Unexpectedly, a high variation in the genome size was observed in each serotype (Figure 1 and Table 1).

Genome size (Mbp)
Serotype Number Mean Smallest Largest Difference
Muenchen 6 5.00 4.64 5.59 0.95
Weltevreden 119 4.99 3.83 5.23 1.40
Senftenberg 14 4.99 4.69 5.59 0.90
Cubana 5 4.98 4.82 5.27 0.44
Typhimurium 457 4.93 3.39 5.53 2.14
Dublin 6 4.91 4.81 5.06 0.24
Derby 4 4.88 4.81 5.08 0.27
Rubislaw 3 4.88 4.74 4.97 0.23
Kentucky 15 4.85 4.70 5.01 0.31
Hartford 3 4.84 4.78 4.88 0.10
Heidelberg 105 4.83 4.63 5.16 0.53
Infantis 10 4.82 4.58 4.98 0.39
Muenster 4 4.82 4.71 4.92 0.21
Hvittingfoss 3 4.81 4.67 4.90 0.23
Tennessee 9 4.79 4.74 4.86 0.13
Schwarzengrund 3 4.79 4.76 4.82 0.06
Saintpaul 6 4.78 4.62 5.05 0.43
Typhi 88 4.78 4.54 5.13 0.59
Newport 68 4.78 4.65 5.08 0.44
Anatum 15 4.77 4.62 4.99 0.37
Mbandaka 3 4.77 4.74 4.83 0.08
Agona 112 4.77 4.69 4.96 0.26
Choleraesuis 4 4.75 4.66 4.94 0.29
Bovismorbificans 29 4.75 4.56 4.90 0.35
Give 3 4.74 4.55 4.97 0.42
Bareilly 105 4.73 4.16 5.14 0.98
Berta 3 4.72 4.72 4.73 0.01
Thompson 6 4.72 4.65 4.88 0.23
Virchow 3 4.72 4.60 4.87 0.27
Hadar 7 4.71 4.66 4.79 0.13
Enteritidis 134 4.70 4.62 4.91 0.29
Pullorum 5 4.70 4.62 4.75 0.13
Cerro 20 4.69 4.52 4.74 0.22
Montevideo 57 4.65 4.32 5.05 0.73
Gallinarum 6 4.65 4.56 4.75 0.19
Javiana 5 4.64 4.55 4.74 0.19
Oranienburg 3 4.61 4.60 4.63 0.02
Paratyphi 156 4.59 4.42 5.02 0.60

Table 1: Genome size variation between different Salmonella enterica serotypes.

data-mining-genomics-proteomics-Genome-size-comparisons

Figure 1: Genome size comparisons between different serotypes of Salmonella enterica . Whole-genomes (n=1,604) covering at least 38 serovars were analyzed. Genomes were obtained from the Integrated Microbial Genomes (IMG) system. Mean values of genome size are presented. Blue dashed lines depict the range between the smallest and largest genome size for each serotype.

Serotypes Typhimurium, Weltevreden, Bareilly, Muenchen, Senftenberg, Montevideo, Paratyphi, Typhi and Heidelberg showed the highest variation (difference between the smallest and the largest chromosome) in genome size. This variation corresponds to differences in genome size ranging between 0.53-2.14 Mbp. These numbers represents from 10% to 43% extra genome. Such differences in genome size have been observed between different bacterial species and genera [5]; thus, it is possible to contemplate the need for reviewing the “bacterial species concept” in S. enterica .

Together, these analyses reveal that the gain and loss of genes is an important mechanism used by S. enterica to adapt to different niches. The intra-species genomic variation reported here highlights the need for deeper WGSA to uncover the extent of the genomic plasticity of this pathogen. Understanding genome diversity will helps us to understand the dynamics of bacterial-host interactions.

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