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Genome sequence and description of Pantoea septica strain FF5.

Lo CI, Padhmanabhan R, Mediannikov O, Nguyen TT, Raoult D, Fournier PE, Fenollar F - Stand Genomic Sci (2015)

Bottom Line: Currently, 17 genomes have been sequenced within the genus Pantoea but none for Pantoea septica.Herein, we compared the genomic properties of strain FF5 to those of other species within the genus Pantoea.We also performed an extensive phenotypic analysis showing new phenotypic characteristics such as the production of alkaline phosphatase, acid phosphatase and naphthol-AS-BI-phosphohydrolase.

View Article: PubMed Central - PubMed

Affiliation: Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France ; Campus international UCAD-IRD, Dakar, Senegal.

ABSTRACT
Strain FF5 was isolated from the skin flora of a healthy Senegalese 35-year-old woman. This strain was identified as belonging to the species Pantoea septica based on rpoB sequence identity of 99.7 % with Pantoea septica strain LMG 5345(T) and a highest MALDI-TOF-MS score of 2.3 with Pantoea septica. Like P. septica, this FF5 strain is a Gram-negative, aerobic, motile, and rod-shaped bacterium. Currently, 17 genomes have been sequenced within the genus Pantoea but none for Pantoea septica. Herein, we compared the genomic properties of strain FF5 to those of other species within the genus Pantoea. The genome of this strain is 4,548,444 bp in length (1 chromosome, no plasmid) with a G + C content of 59.1 % containing 4125 protein-coding and 68 RNA genes (including 2 rRNA operons). We also performed an extensive phenotypic analysis showing new phenotypic characteristics such as the production of alkaline phosphatase, acid phosphatase and naphthol-AS-BI-phosphohydrolase.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree showing the position of Pantoea septica strain FF5 relative to other strains within the genus Pantoea. The rpoB sequences were aligned using MUSCLE [31], and the phylogenetic tree was inferred using the Maximum Likelihood method with Kimura 2-parameter model from MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 1,000 times to generate a majority consensus tree. The scale bar represents a rate of substitution per site of 0.02
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Fig1: Phylogenetic tree showing the position of Pantoea septica strain FF5 relative to other strains within the genus Pantoea. The rpoB sequences were aligned using MUSCLE [31], and the phylogenetic tree was inferred using the Maximum Likelihood method with Kimura 2-parameter model from MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 1,000 times to generate a majority consensus tree. The scale bar represents a rate of substitution per site of 0.02

Mentions: A skin sample was collected with a swab from a healthy Senegalese volunteer living in Dielmo (a rural village in the Guinean-Sudanian area in Senegal) in December 2012 (Table 1). This 35-year-old woman was included in a research project that was approved by the Ministry of Health of Senegal, the assembled village population and the National Ethics Committee of Senegal (CNERS, agreement numbers 09–022), as published elsewhere [7]. Strain FF5 (Table 1) was isolated by aerobic cultivation on 5 % sheep blood-enriched Columbia agar (BioMérieux, Marcy l’Etoile, France). As the 16S rRNA gene sequence cannot be used as a means of identifying Pantoea species, a comparative rpoB nucleotide sequences analysis between strain FF5 and other Pantoea species was performed. Strain FF5 exhibited a 99.7 % sequence identity with P. septica, its phylogenetically closest validly published Pantoea species (Fig. 1) [8]. This strain is motile and its cells grown on agar are Gram-negative rods (and have a mean diameter of 0.79-1.06 μm and a mean length of 1.25-2.04 μm).Table 1


Genome sequence and description of Pantoea septica strain FF5.

Lo CI, Padhmanabhan R, Mediannikov O, Nguyen TT, Raoult D, Fournier PE, Fenollar F - Stand Genomic Sci (2015)

Phylogenetic tree showing the position of Pantoea septica strain FF5 relative to other strains within the genus Pantoea. The rpoB sequences were aligned using MUSCLE [31], and the phylogenetic tree was inferred using the Maximum Likelihood method with Kimura 2-parameter model from MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 1,000 times to generate a majority consensus tree. The scale bar represents a rate of substitution per site of 0.02
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4644298&req=5

Fig1: Phylogenetic tree showing the position of Pantoea septica strain FF5 relative to other strains within the genus Pantoea. The rpoB sequences were aligned using MUSCLE [31], and the phylogenetic tree was inferred using the Maximum Likelihood method with Kimura 2-parameter model from MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 1,000 times to generate a majority consensus tree. The scale bar represents a rate of substitution per site of 0.02
Mentions: A skin sample was collected with a swab from a healthy Senegalese volunteer living in Dielmo (a rural village in the Guinean-Sudanian area in Senegal) in December 2012 (Table 1). This 35-year-old woman was included in a research project that was approved by the Ministry of Health of Senegal, the assembled village population and the National Ethics Committee of Senegal (CNERS, agreement numbers 09–022), as published elsewhere [7]. Strain FF5 (Table 1) was isolated by aerobic cultivation on 5 % sheep blood-enriched Columbia agar (BioMérieux, Marcy l’Etoile, France). As the 16S rRNA gene sequence cannot be used as a means of identifying Pantoea species, a comparative rpoB nucleotide sequences analysis between strain FF5 and other Pantoea species was performed. Strain FF5 exhibited a 99.7 % sequence identity with P. septica, its phylogenetically closest validly published Pantoea species (Fig. 1) [8]. This strain is motile and its cells grown on agar are Gram-negative rods (and have a mean diameter of 0.79-1.06 μm and a mean length of 1.25-2.04 μm).Table 1

Bottom Line: Currently, 17 genomes have been sequenced within the genus Pantoea but none for Pantoea septica.Herein, we compared the genomic properties of strain FF5 to those of other species within the genus Pantoea.We also performed an extensive phenotypic analysis showing new phenotypic characteristics such as the production of alkaline phosphatase, acid phosphatase and naphthol-AS-BI-phosphohydrolase.

View Article: PubMed Central - PubMed

Affiliation: Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France ; Campus international UCAD-IRD, Dakar, Senegal.

ABSTRACT
Strain FF5 was isolated from the skin flora of a healthy Senegalese 35-year-old woman. This strain was identified as belonging to the species Pantoea septica based on rpoB sequence identity of 99.7 % with Pantoea septica strain LMG 5345(T) and a highest MALDI-TOF-MS score of 2.3 with Pantoea septica. Like P. septica, this FF5 strain is a Gram-negative, aerobic, motile, and rod-shaped bacterium. Currently, 17 genomes have been sequenced within the genus Pantoea but none for Pantoea septica. Herein, we compared the genomic properties of strain FF5 to those of other species within the genus Pantoea. The genome of this strain is 4,548,444 bp in length (1 chromosome, no plasmid) with a G + C content of 59.1 % containing 4125 protein-coding and 68 RNA genes (including 2 rRNA operons). We also performed an extensive phenotypic analysis showing new phenotypic characteristics such as the production of alkaline phosphatase, acid phosphatase and naphthol-AS-BI-phosphohydrolase.

No MeSH data available.


Related in: MedlinePlus