Strain identifier

BacDive ID: 7495

Type strain: Yes

Species: Rhodoglobus vestalii

Strain Designation: LV3

Strain history: CIP <- 2002, J. Brenchley, Pennstate Univ., Pennsylvania, USA: strain LV3

NCBI tax ID(s): 193384 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 16063

BacDive-ID: 7495

DSM-Number: 21947

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, psychrophilic, Gram-positive

description: Rhodoglobus vestalii LV3 is an obligate aerobe, psychrophilic, Gram-positive bacterium that was isolated from Antarctic Dry Valley lake.

NCBI tax id

  • NCBI tax id: 193384
  • Matching level: species

strain history

@refhistory
16063<- CIP <- J. E. Brenchley, Pennsylvania State Univ., University Park, USA; LV3 <- P. P. Sheridan, Idaho State University, Pocatello, USA
407112002, J. Brenchley, Pennstate Univ., Pennsylvania, USA, strain: LV3
67770CIP 107482 <-- J. E. Brenchley LV3 <-- P. P. Sheridan.
123828CIP <- 2002, J. Brenchley, Pennstate Univ., Pennsylvania, USA: strain LV3

doi: 10.13145/bacdive7495.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Rhodoglobus
  • species: Rhodoglobus vestalii
  • full scientific name: Rhodoglobus vestalii Sheridan et al. 2003

@ref: 16063

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Rhodoglobus

species: Rhodoglobus vestalii

full scientific name: Rhodoglobus vestalii Sheridan et al. 2003 emend. An et al. 2010

strain designation: LV3

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
123828positiverod-shapedyes

colony morphology

  • @ref: 123828

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16063R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
40711MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123828CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16063positivegrowth18psychrophilic
40711positivegrowth18psychrophilic
67770positivegrowth18psychrophilic
123828positivegrowth10-18psychrophilic
123828nogrowth25mesophilic
123828nogrowth30mesophilic
123828nogrowth37mesophilic
123828nogrowth41thermophilic
123828nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123828
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
123828NaClpositivegrowth0-2 %
123828NaClnogrowth4 %
123828NaClnogrowth6 %
123828NaClnogrowth8 %
123828NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-11

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
123828citrate-carbon source16947
123828esculin+hydrolysis4853
123828hippurate+hydrolysis606565
123828nitrate-reduction17632
123828nitrite-reduction16301

antibiotic resistance

  • @ref: 123828
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123828
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12382815688acetoin-
12382817234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
123828oxidase-
123828beta-galactosidase+3.2.1.23
123828alcohol dehydrogenase-1.1.1.1
123828gelatinase-
123828amylase-
123828DNase+
123828caseinase-3.4.21.50
123828catalase+1.11.1.6
123828gamma-glutamyltransferase-2.3.2.2
123828lysine decarboxylase-4.1.1.18
123828ornithine decarboxylase-4.1.1.17
123828phenylalanine ammonia-lyase-4.3.1.24
123828tryptophan deaminase-
123828urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123828-+++-+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123828+/----+/-+/------+/-+/--+/----------+/-------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.countryisolation date
16063Antarctic Dry Valley lakesouth of the Miers and Adams glaciers near Bratina Island on the McMurdo Ice ShelfAustralia and Oceania
67770Cyanobacterial mat from a lake near the McMurdo Ice ShelfAntarcticaAntarcticaATA
123828Pond, cyanobacterial materialAntarcticaAntarcticaATA1997

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Condition#Psychrophilic (<10°C)
#Climate#Cold#Polar

taxonmaps

  • @ref: 69479
  • File name: preview.99_6465.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_895;97_3383;98_4770;99_6465&stattab=map
  • Last taxonomy: Microbacteriaceae
  • 16S sequence: AJ459101
  • Sequence Identity:
  • Total samples: 104
  • soil counts: 30
  • aquatic counts: 62
  • animal counts: 7
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
160631Risk group (German classification)
1238281Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16063
  • description: Rhodoglobus vestalii 16S rRNA gene, strain LV3
  • accession: AJ459101
  • length: 1426
  • database: ena
  • NCBI tax ID: 193384

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodoglobus vestalii strain DSM 21947193384.3wgspatric193384
66792Rhodoglobus vestalii DSM 219472811994966draftimg193384
67770Rhodoglobus vestalii DSM 21947GCA_006788895contigncbi193384

GC content

  • @ref: 16063
  • GC-content: 62
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.435no
gram-positiveyes93.578no
anaerobicno99.041no
aerobicyes93.188no
halophileno68.762no
spore-formingno94.042no
glucose-utilyes85.171no
flagellatedno97.503no
thermophileno99.21yes
glucose-fermentno88.465no

External links

@ref: 16063

culture collection no.: DSM 21947, ATCC BAA 534, CIP 107482, JCM 12695, NBRC 103084, CGMCC 1.7091, IAM 15169

straininfo link

  • @ref: 76941
  • straininfo: 126082

literature

  • topic: Phylogeny
  • Pubmed-ID: 12892115
  • title: Rhodoglobus vestalii gen. nov., sp. nov., a novel psychrophilic organism isolated from an Antarctic Dry Valley lake.
  • authors: Sheridan PP, Loveland-Curtze J, Miteva VI, Brenchley JE
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02415-0
  • year: 2003
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Antarctic Regions, Base Composition, DNA, Bacterial/chemistry/genetics, Fatty Acids/metabolism, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Conformation, Phylogeny, RNA, Bacterial/chemistry/genetics, RNA, Ribosomal, 16S/chemistry/genetics, Terminology as Topic
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
16063Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21947)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21947
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
40711Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4922
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
76941Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID126082.1StrainInfo: A central database for resolving microbial strain identifiers
123828Curators of the CIPCollection of Institut Pasteur (CIP 107482)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107482