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Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut.

Seck E, Rathored J, Khelaifia S, Croce O, Robert C, Couderc C, Di Pinto F, Sokhna C, Raoult D, Lagier JC - New Microbes New Infect (2015)

Bottom Line: It is an aerobic, Gram positive, moderately halophilic, motile bipolar flagellum isolated from a healthy Senegalese man.Here we describe the genomic and phenotypic characteristics of this isolate.The 3 755 098 bp long genome (one chromosome, no plasmid) exhibits a G + C content of 42.9% and contains 3738 protein-coding and 95 RNA genes.

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
Virgibacillus senegalensis SK-1(T) (= CSUR P1101 = DSM 28585) is the type strain of V. senegalensis sp. nov. It is an aerobic, Gram positive, moderately halophilic, motile bipolar flagellum isolated from a healthy Senegalese man. Here we describe the genomic and phenotypic characteristics of this isolate. The 3 755 098 bp long genome (one chromosome, no plasmid) exhibits a G + C content of 42.9% and contains 3738 protein-coding and 95 RNA genes.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree highlighting position of Virgibacillus senegalensis strain SK-1T (= CSUR P1101 = DSM 28585) relative to other type strains of Virgibacillus albus strain YIM 93624 (NR_109613.1), Virgibacillus kekensis strain YIM kkny16 (NR_042744.1), Virgibacillus alimentarius strain J18 (NR_108710.1), Virgibacillus marismortui strain M3-23 (GQ282501.1), Virgibacillus necropolis strain LMG 19488 (NR_025472.1), Virgibacillus carmonensis strain LMG 20964 (NR_025481.1), Virgibacillus subterraneus strain H57B72 (FJ746573.1), Virgibacillus zhanjiangensis strain JSM 079157 (FJ425904.1), Virgibacillus litoralis strain JSM 089168 (FJ425909.1), Virgibacillus dokdonensis strain DSW-10 (NR_043206.1), Virgibacillus siamensis strain MS3-4 (AB365482.1), Virgibacillus salarius strain SA-Vb1 (NR_041270.1), Virgibacillus halophilus strain 5B73C (NR_041358.1), Virgibacillus natechei strain FarD (NR_132721.1), Virgibacillus chiguensis strain NTU-101 (NR_044086.1), Virgibacillus dokdonensis strain DSW-10 (NR_043206.1), Virgibacillus campisalis strain IDS-20 (GU586225.1), Virgibacillus pantothenticus strain NBRC 102447 (AB681789.1), Virgibacillus halodenitrificans strain NBRC 102361 (AB681753.1), Virgibacillus byunsanensis strain ISL-24 (FJ357159.1), Virgibacillus massiliensis strain Vm-5 (HG931931.1) and Paenibacillus polymyxa strain KCTC3717 (AY359637.1). GenBank accession numbers are indicated in parentheses. Sequences were aligned using Clustal W (http://www.clustal.org/clustal2/), and phylogenetic inferences were obtained using maximum-likelihood method within MEGA 6 (http://www.megasoftware.net/mega.php). Paenibacillus polymyxa was used as outgroup. Scale bar = 0.005% nucleotide sequence divergence.
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fig3: Phylogenetic tree highlighting position of Virgibacillus senegalensis strain SK-1T (= CSUR P1101 = DSM 28585) relative to other type strains of Virgibacillus albus strain YIM 93624 (NR_109613.1), Virgibacillus kekensis strain YIM kkny16 (NR_042744.1), Virgibacillus alimentarius strain J18 (NR_108710.1), Virgibacillus marismortui strain M3-23 (GQ282501.1), Virgibacillus necropolis strain LMG 19488 (NR_025472.1), Virgibacillus carmonensis strain LMG 20964 (NR_025481.1), Virgibacillus subterraneus strain H57B72 (FJ746573.1), Virgibacillus zhanjiangensis strain JSM 079157 (FJ425904.1), Virgibacillus litoralis strain JSM 089168 (FJ425909.1), Virgibacillus dokdonensis strain DSW-10 (NR_043206.1), Virgibacillus siamensis strain MS3-4 (AB365482.1), Virgibacillus salarius strain SA-Vb1 (NR_041270.1), Virgibacillus halophilus strain 5B73C (NR_041358.1), Virgibacillus natechei strain FarD (NR_132721.1), Virgibacillus chiguensis strain NTU-101 (NR_044086.1), Virgibacillus dokdonensis strain DSW-10 (NR_043206.1), Virgibacillus campisalis strain IDS-20 (GU586225.1), Virgibacillus pantothenticus strain NBRC 102447 (AB681789.1), Virgibacillus halodenitrificans strain NBRC 102361 (AB681753.1), Virgibacillus byunsanensis strain ISL-24 (FJ357159.1), Virgibacillus massiliensis strain Vm-5 (HG931931.1) and Paenibacillus polymyxa strain KCTC3717 (AY359637.1). GenBank accession numbers are indicated in parentheses. Sequences were aligned using Clustal W (http://www.clustal.org/clustal2/), and phylogenetic inferences were obtained using maximum-likelihood method within MEGA 6 (http://www.megasoftware.net/mega.php). Paenibacillus polymyxa was used as outgroup. Scale bar = 0.005% nucleotide sequence divergence.

Mentions: Strain SK-1T was isolated in February 2014 (Table 1) by aerobic culture on a homemade culture medium at 37°C after 48 hours. No significant MALDI-TOF result for the strain SK-1T against our MALDI-TOF database was obtained, suggesting that our isolate was not a previously known species. We added the specter of SK-1T strain to our database (Fig. 1). The gel view allowed us to observe the spectral differences with other members of Virgibacillus genus (Fig. 2). PCR-based identification of the 16S rRNA of our new isolate (GenBank accession number LK021111) yielded 96.3% 16S rRNA sequence similarity with the reference Virgibacillus kekensis (GenBank accession number NR042744), the phylogenetically closest validated Virgibacillus species (Fig. 3).


Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut.

Seck E, Rathored J, Khelaifia S, Croce O, Robert C, Couderc C, Di Pinto F, Sokhna C, Raoult D, Lagier JC - New Microbes New Infect (2015)

Phylogenetic tree highlighting position of Virgibacillus senegalensis strain SK-1T (= CSUR P1101 = DSM 28585) relative to other type strains of Virgibacillus albus strain YIM 93624 (NR_109613.1), Virgibacillus kekensis strain YIM kkny16 (NR_042744.1), Virgibacillus alimentarius strain J18 (NR_108710.1), Virgibacillus marismortui strain M3-23 (GQ282501.1), Virgibacillus necropolis strain LMG 19488 (NR_025472.1), Virgibacillus carmonensis strain LMG 20964 (NR_025481.1), Virgibacillus subterraneus strain H57B72 (FJ746573.1), Virgibacillus zhanjiangensis strain JSM 079157 (FJ425904.1), Virgibacillus litoralis strain JSM 089168 (FJ425909.1), Virgibacillus dokdonensis strain DSW-10 (NR_043206.1), Virgibacillus siamensis strain MS3-4 (AB365482.1), Virgibacillus salarius strain SA-Vb1 (NR_041270.1), Virgibacillus halophilus strain 5B73C (NR_041358.1), Virgibacillus natechei strain FarD (NR_132721.1), Virgibacillus chiguensis strain NTU-101 (NR_044086.1), Virgibacillus dokdonensis strain DSW-10 (NR_043206.1), Virgibacillus campisalis strain IDS-20 (GU586225.1), Virgibacillus pantothenticus strain NBRC 102447 (AB681789.1), Virgibacillus halodenitrificans strain NBRC 102361 (AB681753.1), Virgibacillus byunsanensis strain ISL-24 (FJ357159.1), Virgibacillus massiliensis strain Vm-5 (HG931931.1) and Paenibacillus polymyxa strain KCTC3717 (AY359637.1). GenBank accession numbers are indicated in parentheses. Sequences were aligned using Clustal W (http://www.clustal.org/clustal2/), and phylogenetic inferences were obtained using maximum-likelihood method within MEGA 6 (http://www.megasoftware.net/mega.php). Paenibacillus polymyxa was used as outgroup. Scale bar = 0.005% nucleotide sequence divergence.
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fig3: Phylogenetic tree highlighting position of Virgibacillus senegalensis strain SK-1T (= CSUR P1101 = DSM 28585) relative to other type strains of Virgibacillus albus strain YIM 93624 (NR_109613.1), Virgibacillus kekensis strain YIM kkny16 (NR_042744.1), Virgibacillus alimentarius strain J18 (NR_108710.1), Virgibacillus marismortui strain M3-23 (GQ282501.1), Virgibacillus necropolis strain LMG 19488 (NR_025472.1), Virgibacillus carmonensis strain LMG 20964 (NR_025481.1), Virgibacillus subterraneus strain H57B72 (FJ746573.1), Virgibacillus zhanjiangensis strain JSM 079157 (FJ425904.1), Virgibacillus litoralis strain JSM 089168 (FJ425909.1), Virgibacillus dokdonensis strain DSW-10 (NR_043206.1), Virgibacillus siamensis strain MS3-4 (AB365482.1), Virgibacillus salarius strain SA-Vb1 (NR_041270.1), Virgibacillus halophilus strain 5B73C (NR_041358.1), Virgibacillus natechei strain FarD (NR_132721.1), Virgibacillus chiguensis strain NTU-101 (NR_044086.1), Virgibacillus dokdonensis strain DSW-10 (NR_043206.1), Virgibacillus campisalis strain IDS-20 (GU586225.1), Virgibacillus pantothenticus strain NBRC 102447 (AB681789.1), Virgibacillus halodenitrificans strain NBRC 102361 (AB681753.1), Virgibacillus byunsanensis strain ISL-24 (FJ357159.1), Virgibacillus massiliensis strain Vm-5 (HG931931.1) and Paenibacillus polymyxa strain KCTC3717 (AY359637.1). GenBank accession numbers are indicated in parentheses. Sequences were aligned using Clustal W (http://www.clustal.org/clustal2/), and phylogenetic inferences were obtained using maximum-likelihood method within MEGA 6 (http://www.megasoftware.net/mega.php). Paenibacillus polymyxa was used as outgroup. Scale bar = 0.005% nucleotide sequence divergence.
Mentions: Strain SK-1T was isolated in February 2014 (Table 1) by aerobic culture on a homemade culture medium at 37°C after 48 hours. No significant MALDI-TOF result for the strain SK-1T against our MALDI-TOF database was obtained, suggesting that our isolate was not a previously known species. We added the specter of SK-1T strain to our database (Fig. 1). The gel view allowed us to observe the spectral differences with other members of Virgibacillus genus (Fig. 2). PCR-based identification of the 16S rRNA of our new isolate (GenBank accession number LK021111) yielded 96.3% 16S rRNA sequence similarity with the reference Virgibacillus kekensis (GenBank accession number NR042744), the phylogenetically closest validated Virgibacillus species (Fig. 3).

Bottom Line: It is an aerobic, Gram positive, moderately halophilic, motile bipolar flagellum isolated from a healthy Senegalese man.Here we describe the genomic and phenotypic characteristics of this isolate.The 3 755 098 bp long genome (one chromosome, no plasmid) exhibits a G + C content of 42.9% and contains 3738 protein-coding and 95 RNA genes.

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
Virgibacillus senegalensis SK-1(T) (= CSUR P1101 = DSM 28585) is the type strain of V. senegalensis sp. nov. It is an aerobic, Gram positive, moderately halophilic, motile bipolar flagellum isolated from a healthy Senegalese man. Here we describe the genomic and phenotypic characteristics of this isolate. The 3 755 098 bp long genome (one chromosome, no plasmid) exhibits a G + C content of 42.9% and contains 3738 protein-coding and 95 RNA genes.

No MeSH data available.


Related in: MedlinePlus