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Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut.

Lagier JC, Khelaifia S, Azhar EI, Croce O, Bibi F, Jiman-Fatani AA, Yasir M, Helaby HB, Robert C, Fournier PE, Raoult D - Stand Genomic Sci (2015)

Bottom Line: The draft genome sequence of Oceanobacillus picturae has a similar size to the Oceanobacillus kimchii (respectively 3.67 Mb versus 3.83 Mb).The G + C content was higher compared with Oceanobacillus kimchii (respectively 39.15 % and 35.2 %).Oceanobacillus picturae shared almost identical number of genes (3823 genes versus 3879 genes), with a similar ratio of genes per Mb (1041 genes/Mb versus 1012 genes/Mb).

View Article: PubMed Central - PubMed

Affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L'Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France.

ABSTRACT
Oceanobacillus picturae is a strain of a moderately halophilic bacterium, first isolated from a mural painting. We demonstrate, for the first time, the culture of human Oceanobacillus picturae, strain S1(T), whose genome is described here, from a stool sample collected from a 25-year-old Saoudian healthy individual. We used a slightly modified standard culture medium adding 100¬†g/L of NaCl. We provide a short description of this strain including its MALDI-TOF spectrum, the main identification tool currently used in clinical microbiology. The 3,675,175¬†bp long genome exhibits a G‚ÄČ+‚ÄČC content of 39.15¬†% and contains 3666 protein-coding and 157 RNA genes. The draft genome sequence of Oceanobacillus picturae has a similar size to the Oceanobacillus kimchii (respectively 3.67¬†Mb versus 3.83¬†Mb). The G‚ÄČ+‚ÄČC content was higher compared with Oceanobacillus kimchii (respectively 39.15¬†% and 35.2¬†%). Oceanobacillus picturae shared almost identical number of genes (3823 genes versus 3879 genes), with a similar ratio of genes per Mb (1041 genes/Mb versus 1012 genes/Mb). The genome sequencing of Oceanobacillus picturae strain S1 isolated for the first time in a human, will be added to the 778 genome projects from the gastrointestinal tract listed by the international consortium Human Microbiome Project.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree highlighting the position of Oceanobacillus picturae strain S1T relative to other strains of the genus Oceanobacillus. Strain S1T (CSUR P1091‚ÄČ=‚ÄČDSM 28586) relative to other type strains within the genus Oceanobacillus. The strains and their corresponding GenBank accession numbers for 16S rRNA genes are (type‚ÄČ=‚ÄČT): Oceanobacillus indicireducens strain A21T, NR_113330, Oceanobacillus chironomi strain T3944DT, NR_043700, Oceanobacillus caeni strain S-11 T, NR_041533, Oceanobacillus chungangensis strain CAU 1051T, NR_109672, Oceanobacillus picturae strain R-5321T, NR_028952, Oceanobacillus manasiensis strain YD3-56T, NR_116624, Oceanobacillus kapialis strain SSK2-2T, NR-112740, Oceanobacillus polygoni strain SA9T, NR_114348, Oceanobacillus profundus strain CL-MP28T, NR_043778, Oceanobacillus kimchii strain X50T, NR_117544, Oceanobacillus iheyensis strain HTE831T, NR_075027, Oceanobacillus iheyensis strain HTE831T, NR_028001, Oceanobacillus oncorhynchi subsp.incalanensis strain 20AGT, NR_042257, Oceanobacillus locisalsi strain CHL-21T, NR_116461, Oceanobacillus sojae strain Y27T, NR_112845 and Oceanobacillus neutriphilus strain A1gT, NR_116424. Phylogeny pipeline [28] was used, wherein sequences were aligned using MUSCLE [29] alignment curation by Gblocks [30] and construction of phylogenic tree performed using PhyML [31]. Numbers at the nodes are bootstrap values obtained by repeating the analysis 100 times. The scale bar represents a 2¬†% nucleotides sequences divergence
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Fig1: Phylogenetic tree highlighting the position of Oceanobacillus picturae strain S1T relative to other strains of the genus Oceanobacillus. Strain S1T (CSUR P1091‚ÄČ=‚ÄČDSM 28586) relative to other type strains within the genus Oceanobacillus. The strains and their corresponding GenBank accession numbers for 16S rRNA genes are (type‚ÄČ=‚ÄČT): Oceanobacillus indicireducens strain A21T, NR_113330, Oceanobacillus chironomi strain T3944DT, NR_043700, Oceanobacillus caeni strain S-11 T, NR_041533, Oceanobacillus chungangensis strain CAU 1051T, NR_109672, Oceanobacillus picturae strain R-5321T, NR_028952, Oceanobacillus manasiensis strain YD3-56T, NR_116624, Oceanobacillus kapialis strain SSK2-2T, NR-112740, Oceanobacillus polygoni strain SA9T, NR_114348, Oceanobacillus profundus strain CL-MP28T, NR_043778, Oceanobacillus kimchii strain X50T, NR_117544, Oceanobacillus iheyensis strain HTE831T, NR_075027, Oceanobacillus iheyensis strain HTE831T, NR_028001, Oceanobacillus oncorhynchi subsp.incalanensis strain 20AGT, NR_042257, Oceanobacillus locisalsi strain CHL-21T, NR_116461, Oceanobacillus sojae strain Y27T, NR_112845 and Oceanobacillus neutriphilus strain A1gT, NR_116424. Phylogeny pipeline [28] was used, wherein sequences were aligned using MUSCLE [29] alignment curation by Gblocks [30] and construction of phylogenic tree performed using PhyML [31]. Numbers at the nodes are bootstrap values obtained by repeating the analysis 100 times. The scale bar represents a 2¬†% nucleotides sequences divergence

Mentions: A stool specimen was collected from a 25-year-old Saudi obese patient. The patient gave informed and signed consent. The study and the assent procedure were approved by the Ethics Committees of the King Abdulaziz University, King Fahd medical Research Center, Saudi Arabia, under agreement number 014-CEGMR-2-ETH-P, and of the Institut F√©d√©ratif de Recherche 48, Faculty of Medicine, Marseille, France, under agreement number 09‚Äď022. The stool sample was preserved at ‚ąí80¬†¬įC after collection and sent to Marseille. O. picturae strain S1T (Table¬†1) was isolated in December 2013 by aerobic cultivation on a culture medium consisting of a Columbia broth culture medium (Sigma-Aldrich, Saint-Quentin Fallavier, France) modified by the addtion of 100¬†g/L of NaCl with a pH adjusted to 7.5. O. picturae strain S1 had a 16S rRNA sequence similarity of 99.8¬†% with the reference strain O. picturae strain LMG19492T (Genbank accession number NR_028952) (Fig.¬†1). This strain was deposited in the CSUR (under number P887).Table 1


Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut.

Lagier JC, Khelaifia S, Azhar EI, Croce O, Bibi F, Jiman-Fatani AA, Yasir M, Helaby HB, Robert C, Fournier PE, Raoult D - Stand Genomic Sci (2015)

Phylogenetic tree highlighting the position of Oceanobacillus picturae strain S1T relative to other strains of the genus Oceanobacillus. Strain S1T (CSUR P1091‚ÄČ=‚ÄČDSM 28586) relative to other type strains within the genus Oceanobacillus. The strains and their corresponding GenBank accession numbers for 16S rRNA genes are (type‚ÄČ=‚ÄČT): Oceanobacillus indicireducens strain A21T, NR_113330, Oceanobacillus chironomi strain T3944DT, NR_043700, Oceanobacillus caeni strain S-11 T, NR_041533, Oceanobacillus chungangensis strain CAU 1051T, NR_109672, Oceanobacillus picturae strain R-5321T, NR_028952, Oceanobacillus manasiensis strain YD3-56T, NR_116624, Oceanobacillus kapialis strain SSK2-2T, NR-112740, Oceanobacillus polygoni strain SA9T, NR_114348, Oceanobacillus profundus strain CL-MP28T, NR_043778, Oceanobacillus kimchii strain X50T, NR_117544, Oceanobacillus iheyensis strain HTE831T, NR_075027, Oceanobacillus iheyensis strain HTE831T, NR_028001, Oceanobacillus oncorhynchi subsp.incalanensis strain 20AGT, NR_042257, Oceanobacillus locisalsi strain CHL-21T, NR_116461, Oceanobacillus sojae strain Y27T, NR_112845 and Oceanobacillus neutriphilus strain A1gT, NR_116424. Phylogeny pipeline [28] was used, wherein sequences were aligned using MUSCLE [29] alignment curation by Gblocks [30] and construction of phylogenic tree performed using PhyML [31]. Numbers at the nodes are bootstrap values obtained by repeating the analysis 100 times. The scale bar represents a 2¬†% nucleotides sequences divergence
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4627390&req=5

Fig1: Phylogenetic tree highlighting the position of Oceanobacillus picturae strain S1T relative to other strains of the genus Oceanobacillus. Strain S1T (CSUR P1091‚ÄČ=‚ÄČDSM 28586) relative to other type strains within the genus Oceanobacillus. The strains and their corresponding GenBank accession numbers for 16S rRNA genes are (type‚ÄČ=‚ÄČT): Oceanobacillus indicireducens strain A21T, NR_113330, Oceanobacillus chironomi strain T3944DT, NR_043700, Oceanobacillus caeni strain S-11 T, NR_041533, Oceanobacillus chungangensis strain CAU 1051T, NR_109672, Oceanobacillus picturae strain R-5321T, NR_028952, Oceanobacillus manasiensis strain YD3-56T, NR_116624, Oceanobacillus kapialis strain SSK2-2T, NR-112740, Oceanobacillus polygoni strain SA9T, NR_114348, Oceanobacillus profundus strain CL-MP28T, NR_043778, Oceanobacillus kimchii strain X50T, NR_117544, Oceanobacillus iheyensis strain HTE831T, NR_075027, Oceanobacillus iheyensis strain HTE831T, NR_028001, Oceanobacillus oncorhynchi subsp.incalanensis strain 20AGT, NR_042257, Oceanobacillus locisalsi strain CHL-21T, NR_116461, Oceanobacillus sojae strain Y27T, NR_112845 and Oceanobacillus neutriphilus strain A1gT, NR_116424. Phylogeny pipeline [28] was used, wherein sequences were aligned using MUSCLE [29] alignment curation by Gblocks [30] and construction of phylogenic tree performed using PhyML [31]. Numbers at the nodes are bootstrap values obtained by repeating the analysis 100 times. The scale bar represents a 2¬†% nucleotides sequences divergence
Mentions: A stool specimen was collected from a 25-year-old Saudi obese patient. The patient gave informed and signed consent. The study and the assent procedure were approved by the Ethics Committees of the King Abdulaziz University, King Fahd medical Research Center, Saudi Arabia, under agreement number 014-CEGMR-2-ETH-P, and of the Institut F√©d√©ratif de Recherche 48, Faculty of Medicine, Marseille, France, under agreement number 09‚Äď022. The stool sample was preserved at ‚ąí80¬†¬įC after collection and sent to Marseille. O. picturae strain S1T (Table¬†1) was isolated in December 2013 by aerobic cultivation on a culture medium consisting of a Columbia broth culture medium (Sigma-Aldrich, Saint-Quentin Fallavier, France) modified by the addtion of 100¬†g/L of NaCl with a pH adjusted to 7.5. O. picturae strain S1 had a 16S rRNA sequence similarity of 99.8¬†% with the reference strain O. picturae strain LMG19492T (Genbank accession number NR_028952) (Fig.¬†1). This strain was deposited in the CSUR (under number P887).Table 1

Bottom Line: The draft genome sequence of Oceanobacillus picturae has a similar size to the Oceanobacillus kimchii (respectively 3.67 Mb versus 3.83 Mb).The G + C content was higher compared with Oceanobacillus kimchii (respectively 39.15 % and 35.2 %).Oceanobacillus picturae shared almost identical number of genes (3823 genes versus 3879 genes), with a similar ratio of genes per Mb (1041 genes/Mb versus 1012 genes/Mb).

View Article: PubMed Central - PubMed

Affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L'Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France.

ABSTRACT
Oceanobacillus picturae is a strain of a moderately halophilic bacterium, first isolated from a mural painting. We demonstrate, for the first time, the culture of human Oceanobacillus picturae, strain S1(T), whose genome is described here, from a stool sample collected from a 25-year-old Saoudian healthy individual. We used a slightly modified standard culture medium adding 100¬†g/L of NaCl. We provide a short description of this strain including its MALDI-TOF spectrum, the main identification tool currently used in clinical microbiology. The 3,675,175¬†bp long genome exhibits a G‚ÄČ+‚ÄČC content of 39.15¬†% and contains 3666 protein-coding and 157 RNA genes. The draft genome sequence of Oceanobacillus picturae has a similar size to the Oceanobacillus kimchii (respectively 3.67¬†Mb versus 3.83¬†Mb). The G‚ÄČ+‚ÄČC content was higher compared with Oceanobacillus kimchii (respectively 39.15¬†% and 35.2¬†%). Oceanobacillus picturae shared almost identical number of genes (3823 genes versus 3879 genes), with a similar ratio of genes per Mb (1041 genes/Mb versus 1012 genes/Mb). The genome sequencing of Oceanobacillus picturae strain S1 isolated for the first time in a human, will be added to the 778 genome projects from the gastrointestinal tract listed by the international consortium Human Microbiome Project.

No MeSH data available.


Related in: MedlinePlus