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Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut.

Khelaifia S, Croce O, Lagier JC, Robert C, Couderc C, Di Pinto F, Davoust B, Djossou F, Raoult D, Fournier PE - New Microbes New Infect (2015)

Bottom Line: Here we describe its phenotypic characteristics and complete genome sequence.The 4 353 177 bp long genome exhibits a G + C content of 36.87% and contains 4394 protein-coding and 125 predicted RNA genes.Phylogenetically and genetically, strain Vm-c is a member of the genus Virgibacillus but is distinct enough to be classified as a new species.

View Article: PubMed Central - PubMed

Affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France.

ABSTRACT
Strain Vm-5(T) was isolated from the stool specimen of a 10-year-old Amazonian boy. This bacterium is a Gram-positive, strictly aerobic rod, motile by a polar flagellum. Here we describe its phenotypic characteristics and complete genome sequence. The 4 353 177 bp long genome exhibits a G + C content of 36.87% and contains 4394 protein-coding and 125 predicted RNA genes. Phylogenetically and genetically, strain Vm-c is a member of the genus Virgibacillus but is distinct enough to be classified as a new species. We propose the creation of V. massiliensis sp. nov., whose type strain is strain Vm-5(T) (CSUR P971 = DSM 28587).

No MeSH data available.


Related in: MedlinePlus

Unrooted phylogenetic tree based on comparison of 16S rRNA sequences highlighting position of Virgibacillus massiliensis strain Vm-5T relative to other type strains within genus Virgibacillus and to type strains of other closely related genera. Sequences were aligned using Clustal W (http://www.clustal.org/clustal2/), and phylogenetic inferences were obtained using maximum-likelihood method within MEGA 6 software (http://www.megasoftware.net/mega.php). Similar phylogenetic organization was obtained using neighbor-joining method. GenBank accession numbers are displayed in parentheses. Scale bar = 0.5% nucleotide sequence divergence. Bootstrap values of 70% or more are indicated at nodes.
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fig1: Unrooted phylogenetic tree based on comparison of 16S rRNA sequences highlighting position of Virgibacillus massiliensis strain Vm-5T relative to other type strains within genus Virgibacillus and to type strains of other closely related genera. Sequences were aligned using Clustal W (http://www.clustal.org/clustal2/), and phylogenetic inferences were obtained using maximum-likelihood method within MEGA 6 software (http://www.megasoftware.net/mega.php). Similar phylogenetic organization was obtained using neighbor-joining method. GenBank accession numbers are displayed in parentheses. Scale bar = 0.5% nucleotide sequence divergence. Bootstrap values of 70% or more are indicated at nodes.

Mentions: Strain Vm-5T (Table 1) was isolated in December 2013 by aerobic culture on a homemade culture medium consisting of a Columbia agar culture medium (Sigma-Aldrich, Saint-Quentin Fallavier, France) modified by adding (per liter) the following: MgCl2 6H2O, 5 g; MgSO4 7H2O, 5 g; KCl, 2 g; CaCl2 2H2O, 1 g; NaBr, 0.5 g; NaHCO3, 0.5 g, glucose, 2 g and 100 g/L of NaCl. The pH was adjusted to 7.5 with 10 M NaOH before autoclaving. Strain Vm-5T (GenBank accession number HG931931) exhibited a 16S rRNA sequence identity of 97.3% with Virgibacillus olivae strain E308T (NR043572), its phylogenetically closest bacterial species with standing in nomenclature (Fig. 1).


Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut.

Khelaifia S, Croce O, Lagier JC, Robert C, Couderc C, Di Pinto F, Davoust B, Djossou F, Raoult D, Fournier PE - New Microbes New Infect (2015)

Unrooted phylogenetic tree based on comparison of 16S rRNA sequences highlighting position of Virgibacillus massiliensis strain Vm-5T relative to other type strains within genus Virgibacillus and to type strains of other closely related genera. Sequences were aligned using Clustal W (http://www.clustal.org/clustal2/), and phylogenetic inferences were obtained using maximum-likelihood method within MEGA 6 software (http://www.megasoftware.net/mega.php). Similar phylogenetic organization was obtained using neighbor-joining method. GenBank accession numbers are displayed in parentheses. Scale bar = 0.5% nucleotide sequence divergence. Bootstrap values of 70% or more are indicated at nodes.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4644261&req=5

fig1: Unrooted phylogenetic tree based on comparison of 16S rRNA sequences highlighting position of Virgibacillus massiliensis strain Vm-5T relative to other type strains within genus Virgibacillus and to type strains of other closely related genera. Sequences were aligned using Clustal W (http://www.clustal.org/clustal2/), and phylogenetic inferences were obtained using maximum-likelihood method within MEGA 6 software (http://www.megasoftware.net/mega.php). Similar phylogenetic organization was obtained using neighbor-joining method. GenBank accession numbers are displayed in parentheses. Scale bar = 0.5% nucleotide sequence divergence. Bootstrap values of 70% or more are indicated at nodes.
Mentions: Strain Vm-5T (Table 1) was isolated in December 2013 by aerobic culture on a homemade culture medium consisting of a Columbia agar culture medium (Sigma-Aldrich, Saint-Quentin Fallavier, France) modified by adding (per liter) the following: MgCl2 6H2O, 5 g; MgSO4 7H2O, 5 g; KCl, 2 g; CaCl2 2H2O, 1 g; NaBr, 0.5 g; NaHCO3, 0.5 g, glucose, 2 g and 100 g/L of NaCl. The pH was adjusted to 7.5 with 10 M NaOH before autoclaving. Strain Vm-5T (GenBank accession number HG931931) exhibited a 16S rRNA sequence identity of 97.3% with Virgibacillus olivae strain E308T (NR043572), its phylogenetically closest bacterial species with standing in nomenclature (Fig. 1).

Bottom Line: Here we describe its phenotypic characteristics and complete genome sequence.The 4 353 177 bp long genome exhibits a G + C content of 36.87% and contains 4394 protein-coding and 125 predicted RNA genes.Phylogenetically and genetically, strain Vm-c is a member of the genus Virgibacillus but is distinct enough to be classified as a new species.

View Article: PubMed Central - PubMed

Affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France.

ABSTRACT
Strain Vm-5(T) was isolated from the stool specimen of a 10-year-old Amazonian boy. This bacterium is a Gram-positive, strictly aerobic rod, motile by a polar flagellum. Here we describe its phenotypic characteristics and complete genome sequence. The 4 353 177 bp long genome exhibits a G + C content of 36.87% and contains 4394 protein-coding and 125 predicted RNA genes. Phylogenetically and genetically, strain Vm-c is a member of the genus Virgibacillus but is distinct enough to be classified as a new species. We propose the creation of V. massiliensis sp. nov., whose type strain is strain Vm-5(T) (CSUR P971 = DSM 28587).

No MeSH data available.


Related in: MedlinePlus