Strain identifier

BacDive ID: 7591

Type strain: Yes

Species: Arthrobacter gandavensis

Strain Designation: R 5812, R5812

Strain history: CIP <- 2004, DSMZ <- V. Storms, RUG <- L. A. Devriese, Ghent Univ., Ghent, Belgium: strain R5812

NCBI tax ID(s): 169960 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 5684

BacDive-ID: 7591

DSM-Number: 15046

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, animal pathogen

description: Arthrobacter gandavensis R 5812 is an obligate aerobe, mesophilic, Gram-positive animal pathogen that was isolated from caw, mastitic milk.

NCBI tax id

  • NCBI tax id: 169960
  • Matching level: species

strain history

@refhistory
5684<- V. Storms, RUG <- L. A. Devriese; R 5812
67770LMG 21285 <-- V. Storms R-5812 <-- L. A. Devriese 266/2537.
119527CIP <- 2004, DSMZ <- V. Storms, RUG <- L. A. Devriese, Ghent Univ., Ghent, Belgium: strain R5812

doi: 10.13145/bacdive7591.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Arthrobacter
  • species: Arthrobacter gandavensis
  • full scientific name: Arthrobacter gandavensis Storms et al. 2003

@ref: 5684

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter gandavensis

full scientific name: Arthrobacter gandavensis Storms et al. 2003

strain designation: R 5812, R5812

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
119527positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18389Zinc yellow (1018)10-14 daysISP 2
18389Zinc yellow (1018)10-14 daysISP 3
18389Zinc yellow (1018)10-14 daysISP 4
18389Zinc yellow (1018)10-14 daysISP 5
18389Zinc yellow (1018)10-14 daysISP 6
18389Zinc yellow (1018)10-14 daysISP 7
119527

multicellular morphology

@refforms multicellular complexmedium name
18389noISP 2
18389noISP 3
18389noISP 4
18389noISP 5
18389noISP 6
18389noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5684COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
5684TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18389ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18389ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18389ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18389ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18389ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18389ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
37396MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119527CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18389positiveoptimum28mesophilic
5684positivegrowth30mesophilic
37396positivegrowth30mesophilic
67770positivegrowth30mesophilic
119527positivegrowth10-37
119527nogrowth41thermophilic
119527nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119527
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.947

halophily

@refsaltgrowthtested relationconcentration
119527NaClpositivegrowth0-8 %
119527NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1838917234glucose+
1838922599arabinose-
1838917992sucrose+
1838918222xylose-
1838917268myo-inositol-
1838929864mannitol-
1838928757fructose-
1838926546rhamnose-
1838916634raffinose-
1838962968cellulose-
11952716947citrate-carbon source
1195274853esculin+hydrolysis
119527606565hippurate-hydrolysis
11952717632nitrate+reduction
11952716301nitrite-reduction
11952717632nitrate-respiration
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 119527
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119527
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11952715688acetoin-
11952717234glucose-

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
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68379catalase+1.11.1.6
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15
119527oxidase-
119527beta-galactosidase+3.2.1.23
119527alcohol dehydrogenase-1.1.1.1
119527gelatinase+/-
119527amylase+
119527DNase+
119527caseinase-3.4.21.50
119527catalase+1.11.1.6
119527tween esterase-
119527gamma-glutamyltransferase-2.3.2.2
119527lecithinase-
119527lipase-
119527lysine decarboxylase-4.1.1.18
119527ornithine decarboxylase-4.1.1.17
119527phenylalanine ammonia-lyase-4.3.1.24
119527tryptophan deaminase-
119527urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSACNITControlGLURIBXYLMANMALLACGLYGCAT
18389+-+-++-++-+
5684+-+/--+--+-+-+--------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18389+-++++++-++++-++-+-
119527+++-+--+-++++-++-+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119527+++++-++-++++++++++++++++++++--++++++----+++++--+++--+-+++--+++++-++-++-+-++---+-++++-+-+-++---++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5684caw, mastitic milkGhentBelgiumBELEurope
60834Cow,mastitic milkBelgiumBELEurope
67770Mastitic milkBelgiumBELEurope
119527Food, Caw, mastitic milkBelgiumBELEurope

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Fluids#Milk

taxonmaps

  • @ref: 69479
  • File name: preview.99_6941.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_458;97_525;98_603;99_6941&stattab=map
  • Last taxonomy: Arthrobacter
  • 16S sequence: AJ316140
  • Sequence Identity:
  • Total samples: 25
  • soil counts: 8
  • aquatic counts: 2
  • animal counts: 15

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
5684yes2Risk group (German classification)
183892
1195271Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5684
  • description: Arthrobacter gandensis 16S rRNA gene, type strain R5812T
  • accession: AJ316140
  • length: 1445
  • database: ena
  • NCBI tax ID: 169960

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arthrobacter gandavensis strain JCM 13316169960.3wgspatric169960
67770Arthrobacter gandavensis JCM 13316GCA_009192735contigncbi169960
66792Arthrobacter citreus DSM 15046GCA_029023805completencbi1670

GC content

@refGC-contentmethod
568465
6777065high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno62.991no
flagellatedno95.484no
gram-positiveyes91.839no
anaerobicno99.23no
aerobicyes91.567no
halophileno65.454no
spore-formingno87.399no
glucose-fermentno86.067yes
thermophileno98.814yes
glucose-utilyes86.994yes

External links

@ref: 5684

culture collection no.: DSM 15046, CIP 108364, LMG 21285, CCUG 56033, JCM 13316

straininfo link

@refstraininfo
77035127284
77036410886

literature

  • topic: Phylogeny
  • Pubmed-ID: 14657117
  • title: Arthrobacter gandavensis sp. nov., for strains of veterinary origin.
  • authors: Storms V, Devriese LA, Coopman R, Schumann P, Vyncke F, Gillis M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02353-0
  • year: 2003
  • mesh: Animals, Arthrobacter/*classification/genetics/isolation & purification, Cattle/*microbiology, DNA, Bacterial/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
5684Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15046)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15046
18389Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM15046.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
37396Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5978
60834Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56033)https://www.ccug.se/strain?id=56033
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/
68379Automatically annotated from API Coryne
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
77035Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID127284.1StrainInfo: A central database for resolving microbial strain identifiers
77036Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID410886.1StrainInfo: A central database for resolving microbial strain identifiers
119527Curators of the CIPCollection of Institut Pasteur (CIP 108364)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108364