Strain identifier

BacDive ID: 10507

Type strain: Yes

Species: Vogesella indigofera

Strain Designation: Ml, M1

Strain history: CIP <- 1989, DSM <- ATCC <- B.A. McFadden: strain M1

NCBI tax ID(s): 45465 (species)

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General

@ref: 1352

BacDive-ID: 10507

DSM-Number: 3303

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Vogesella indigofera Ml is a mesophilic, Gram-negative bacterium that was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 45465
  • Matching level: species

strain history

@refhistory
1352<- ATCC <- B.A. McFadden; Ml
120090CIP <- 1989, DSM <- ATCC <- B.A. McFadden: strain M1

doi: 10.13145/bacdive10507.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Chromobacteriaceae
  • genus: Vogesella
  • species: Vogesella indigofera
  • full scientific name: Vogesella indigofera (Voges 1893) Grimes et al. 1997

  • synonyms

    @refsynonym
    20215Bacillus indigoferus
    20215Pseudomonas indigofera

@ref: 1352

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Chromobacteriaceae

genus: Vogesella

species: Vogesella indigofera

full scientific name: Vogesella indigofera (Voges 1893) Grimes et al. 1997

strain designation: Ml, M1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.997
120090negativerod-shapedyes

pigmentation

  • @ref: 120090
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1352NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
1352PSEUDOMONAS INDIGOFERA MEDIUM (DSMZ Medium 365)yeshttps://mediadive.dsmz.de/medium/365Name: PSEUDOMONAS INDIGOFERA MEDIUM (DSMZ Medium 365) Composition: Agar 12.0 g/l Yeast extract 10.0 g/l Glucose 5.0 g/l Na-acetate 0.5 g/l Distilled water
35524MEDIUM 18 - for Hydrogenophaga, Vogesella and Pseudomonas generayesDistilled water make up to (1000.000 ml);Sodium chloride (3.000 g);Agar(12.000 g);Yeast extract (3.000 g);Peptone (0.600 g)
120090CIP Medium 18yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=18

culture temp

@refgrowthtypetemperaturerange
1352positivegrowth30mesophilic
35524positivegrowth25mesophilic
120090positivegrowth10-30
120090nogrowth5psychrophilic
120090nogrowth37mesophilic
120090nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

compound production

@refcompound
1352indigoidine
1352isocitrate lyase
20216Indigoidine
20216isocitrate lyase

halophily

@refsaltgrowthtested relationconcentration
120090NaClpositivegrowth0 %
120090NaClnogrowth2 %
120090NaClnogrowth4 %
120090NaClnogrowth6 %
120090NaClnogrowth8 %
120090NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan+energy source
6836917632nitrate+reduction
12009016947citrate-carbon source
1200904853esculin-hydrolysis
12009017632nitrate+reduction
12009016301nitrite+reduction
12009017632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleyes
12009035581indoleyes

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120090oxidase+
120090beta-galactosidase-3.2.1.23
120090alcohol dehydrogenase-1.1.1.1
120090gelatinase-
120090amylase-
120090DNase-
120090caseinase-3.4.21.50
120090catalase+1.11.1.6
120090tween esterase-
120090lecithinase-
120090lipase-
120090lysine decarboxylase-4.1.1.18
120090ornithine decarboxylase-4.1.1.17
120090protease-
120090tryptophan deaminase-
120090urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120090-+++-++---+---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
1352++------+---+-++-+--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120090++-----------------------------++----------------+---------++-+++-------++-+---++-++----++++++--++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
1352garden soilUSAUSANorth America
120090Environment, Garden soil

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
13521Risk group (German classification)
1200901Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Vogesella indigofera gene for 16S rRNA, strain: ATCC 19706
  • accession: AB021385
  • length: 1488
  • database: ena
  • NCBI tax ID: 45465

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vogesella indigofera DSM 3303GCA_003633895scaffoldncbi45465
66792Vogesella indigofera strain DSM 330345465.3wgspatric45465
66792Vogesella indigofera DSM 33032756170386draftimg45465

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.114no
flagellatedyes90.775no
gram-positiveno98.561no
anaerobicno98.269no
aerobicyes90.096no
halophileno92.171no
spore-formingno95.502no
glucose-utilyes89.517yes
thermophileno98.31yes
glucose-fermentno87.065no

External links

@ref: 1352

culture collection no.: DSM 3303, ATCC 19706, CIP 103306, IMET 10724, LMG 6867, NCIMB 9441

straininfo link

  • @ref: 79784
  • straininfo: 4115

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8995797Systematic study of the genus Vogesella gen. nov. and its type species, Vogesella indigofera comb. nov.Grimes DJ, Woese CR, MacDonell MT, Colwell RRInt J Syst Bacteriol10.1099/00207713-47-1-191997Bacteriological Techniques, Culture Media/chemistry/metabolism, DNA, Bacterial/analysis, Molecular Sequence Data, Phylogeny, Pseudomonas/*classification/growth & development/ultrastructure, RNA, Ribosomal, 16S/analysis, RNA, Ribosomal, 5S/analysisGenetics
Phylogeny18842860Pseudogulbenkiania subflava gen. nov., sp. nov., isolated from a cold spring.Lin MC, Chou JH, Arun AB, Young CC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.65755-02008Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Genes, Bacterial, Genes, rRNA, Genotype, Molecular Sequence Data, Neisseriaceae/genetics, Phenotype, Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/chemistry/*classification/*genetics/isolation & purification, Sequence Analysis, DNA, Taiwan, *Water MicrobiologyGenetics
Phylogeny19060039Vogesella perlucida sp. nov., a non-pigmented bacterium isolated from spring water.Chou YJ, Chou JH, Lin MC, Arun AB, Young CC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.65766-02008Fatty Acids/chemistry, Fresh Water/*microbiology, Genotype, Molecular Sequence Data, Neisseriaceae/*classification/genetics/isolation & purification/*physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, TaiwanGenetics
Phylogeny19625439Vogesella lacus sp. nov., isolated from a soft-shell turtle culture pond.Chou JH, Chou YJ, Arun AB, Young CC, Chen CA, Wang JT, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.009266-02009Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Fresh Water/*microbiology, Molecular Sequence Data, Neisseriaceae/chemistry/classification/genetics/*isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, *TurtlesGenetics
Phylogeny19946047Vogesella mureinivorans sp. nov., a peptidoglycan-degrading bacterium from lake water.Jorgensen NOG, Brandt KK, Nybroe O, Hansen MInt J Syst Evol Microbiol10.1099/ijs.0.018630-02009Bacterial Typing Techniques, Base Composition, Chitinases/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Denmark, Fatty Acids/analysis, Fresh Water/*microbiology, Microscopy, Electron, Scanning, Microscopy, Electron, Transmission, Molecular Sequence Data, Muramidase/metabolism, Neisseriaceae/*classification/genetics/isolation & purification/*metabolism, Nucleic Acid Hybridization, Peptidoglycan/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny23178725Vogesella alkaliphila sp. nov., isolated from an alkaline soil, and emended description of the genus Vogesella.Subhash Y, Tushar L, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.046300-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, India, Molecular Sequence Data, Neisseriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Triterpenes/analysisGenetics
Phylogeny23396722Vogesella fluminis sp. nov., isolated from a freshwater river, and emended description of the genus Vogesella.Sheu SY, Chen JC, Young CC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.048629-02013Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Taiwan, *Water MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1352Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3303)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3303
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
35524Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15088
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
79784Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4115.1StrainInfo: A central database for resolving microbial strain identifiers
120090Curators of the CIPCollection of Institut Pasteur (CIP 103306)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103306