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Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov.

Lagier JC, Gimenez G, Robert C, Raoult D, Fournier PE - Stand Genomic Sci (2012)

Bottom Line: H. massiliense is an aerobic rod.Here we describe the features of this organism, together with the complete genome sequence and annotation.The 4,186,486 bp long genome (one chromosome but no plasmid) contains 3,847 protein-coding and 54 RNA genes, including 3 rRNA genes.

View Article: PubMed Central - PubMed

Affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université

ABSTRACT
Herbaspirillum massiliense strain JC206(T) sp. nov. is the type strain of H. massiliense sp. nov., a new species within the genus Herbaspirillum. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. H. massiliense is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,186,486 bp long genome (one chromosome but no plasmid) contains 3,847 protein-coding and 54 RNA genes, including 3 rRNA genes.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree highlighting the position of Herbaspirillum massiliense strain JC206T relative to other type strains within the Herbaspirillum genus. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are bootstrap values obtained by repeating 500 times the analysis to generate a majority consensus tree. Janthinobacterium lividum was used as an outgroup. The scale bar represents a 0.5% nucleotide sequence divergence.
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f1: Phylogenetic tree highlighting the position of Herbaspirillum massiliense strain JC206T relative to other type strains within the Herbaspirillum genus. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are bootstrap values obtained by repeating 500 times the analysis to generate a majority consensus tree. Janthinobacterium lividum was used as an outgroup. The scale bar represents a 0.5% nucleotide sequence divergence.

Mentions: The fecal specimen was preserved at -80°C after collection and sent to Marseille. Strain JC206T (Table 1) was isolated in June 2011 after passive filtration of the stool sample to select motile species using companion plate, cell culture inserts with 0.4 μm-pore membranes (Becton Dickinson, Heildeberg, Germany) and Leptospira broth (BioMerieux, Marcy l’Etoile, France). Subsequently, we cultivated strain JC206T on 5% sheep blood agar in an aerobic atmosphere at 37°C. This strain exhibited a 96.7% 16S rDNA nucleotide sequence similarity with H. aurantiacum (Carro et al. 2012), the phylogenetically closest validly published Herbaspirillum species (Figure 1), that was cultivated from volcanic soil in Canary Islands. This value was lower than the 98.7% 16S rRNA gene sequence threshold recommended by Stackebrandt and Ebers to delineate a new species without carrying out DNA-DNA hybridization [29].


Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov.

Lagier JC, Gimenez G, Robert C, Raoult D, Fournier PE - Stand Genomic Sci (2012)

Phylogenetic tree highlighting the position of Herbaspirillum massiliense strain JC206T relative to other type strains within the Herbaspirillum genus. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are bootstrap values obtained by repeating 500 times the analysis to generate a majority consensus tree. Janthinobacterium lividum was used as an outgroup. The scale bar represents a 0.5% nucleotide sequence divergence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3569391&req=5

f1: Phylogenetic tree highlighting the position of Herbaspirillum massiliense strain JC206T relative to other type strains within the Herbaspirillum genus. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are bootstrap values obtained by repeating 500 times the analysis to generate a majority consensus tree. Janthinobacterium lividum was used as an outgroup. The scale bar represents a 0.5% nucleotide sequence divergence.
Mentions: The fecal specimen was preserved at -80°C after collection and sent to Marseille. Strain JC206T (Table 1) was isolated in June 2011 after passive filtration of the stool sample to select motile species using companion plate, cell culture inserts with 0.4 μm-pore membranes (Becton Dickinson, Heildeberg, Germany) and Leptospira broth (BioMerieux, Marcy l’Etoile, France). Subsequently, we cultivated strain JC206T on 5% sheep blood agar in an aerobic atmosphere at 37°C. This strain exhibited a 96.7% 16S rDNA nucleotide sequence similarity with H. aurantiacum (Carro et al. 2012), the phylogenetically closest validly published Herbaspirillum species (Figure 1), that was cultivated from volcanic soil in Canary Islands. This value was lower than the 98.7% 16S rRNA gene sequence threshold recommended by Stackebrandt and Ebers to delineate a new species without carrying out DNA-DNA hybridization [29].

Bottom Line: H. massiliense is an aerobic rod.Here we describe the features of this organism, together with the complete genome sequence and annotation.The 4,186,486 bp long genome (one chromosome but no plasmid) contains 3,847 protein-coding and 54 RNA genes, including 3 rRNA genes.

View Article: PubMed Central - PubMed

Affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université

ABSTRACT
Herbaspirillum massiliense strain JC206(T) sp. nov. is the type strain of H. massiliense sp. nov., a new species within the genus Herbaspirillum. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. H. massiliense is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,186,486 bp long genome (one chromosome but no plasmid) contains 3,847 protein-coding and 54 RNA genes, including 3 rRNA genes.

No MeSH data available.


Related in: MedlinePlus