Strain identifier

BacDive ID: 132694

Type strain: Yes

Species: Arthrobacter rhombi

Strain Designation: F.98.3HR.69

Strain history: CIP <- 2002, CCUG <- 1997, M.D. Collins, IFR, Reading, UK <- C.R. Osori and J.L. Barja, Santiago di Compostela, Spain

NCBI tax ID(s): 71253 (species)

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General

@ref: 24484

BacDive-ID: 132694

DSM-Number: 15838

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped

description: Arthrobacter rhombi F.98.3HR.69 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from organs of Greenland halibut .

NCBI tax id

  • NCBI tax id: 71253
  • Matching level: species

strain history

@refhistory
24484<- JCM <- M. D. Collins; F.98.3HR.69 <- C. R. Osorio and J. L. Barja
67770CCUG 38813 <-- M. D. Collins F.98.3HR.69 <-- C. R. Osorio and J. L. Barja.
122231CIP <- 2002, CCUG <- 1997, M.D. Collins, IFR, Reading, UK <- C.R. Osori and J.L. Barja, Santiago di Compostela, Spain

doi: 10.13145/bacdive132694.20241212.9.2

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 rhombi
  • full scientific name: Arthrobacter rhombi Osorio et al. 1999

@ref: 24484

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter rhombi

full scientific name: Arthrobacter rhombi Osorio et al. 1999

strain designation: F.98.3HR.69

type strain: yes

Morphology

cell morphology

  • @ref: 122231
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 122231
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24484TRYPTICASE 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
37306MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122231CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
24484positivegrowth28
37306positivegrowth30
54484positivegrowth30
54484nogrowth37
67770positivegrowth30
122231positivegrowth25-30
122231nogrowth10
122231nogrowth15
122231nogrowth37
122231nogrowth41
122231nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
54484aerobe
122231obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
122231NaClpositivegrowth0-4 %
122231NaClnogrowth6 %
122231NaClnogrowth8 %
122231NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12223116947citrate-carbon source
1222314853esculin+hydrolysis
12223117632nitrate-reduction
12223116301nitrite-reduction
12223117632nitrate+respiration

antibiotic resistance

  • @ref: 122231
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122231
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12223115688acetoin-
12223117234glucose-

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-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase-
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
122231oxidase-
122231beta-galactosidase+3.2.1.23
122231alcohol dehydrogenase-1.1.1.1
122231gelatinase+/-
122231amylase+
122231DNase-
122231caseinase+3.4.21.50
122231catalase+1.11.1.6
122231tween esterase-
122231gamma-glutamyltransferase-2.3.2.2
122231lysine decarboxylase+4.1.1.18
122231ornithine decarboxylase+4.1.1.17
122231phenylalanine ammonia-lyase-4.3.1.24
122231tryptophan deaminase-
122231urease-3.5.1.5
68382esterase (C 4)+

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    54484C14:00.414
    54484C16:00.716
    54484C14:0 ISO0.213.618
    54484C15:0 ANTEISO77.914.711
    54484C15:0 ISO7.314.621
    54484C16:0 iso0.415.626
    54484C17:0 anteiso1.716.722
    54484Unidentified0.914.928
    54484Unidentified10.215.029
    54484Unidentified0.317.026
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122231-+++----------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122231+++++-++-+++++++++++---+--+----+-+-+-----------+++---+----+-+++-++++---+++-+--+++-+---+-+-++---+---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
24484organs of Greenland halibut (Reinhardtius hippoglossoides)Reinhardtius hippoglossoidesNW Atlantic, Newfoundland, Flemish Cap
54484Greenland halibut (Reinhardtius hippoglossoides)NW,Newfoundland,Flemish CapAtlantic Ocean
67770Spleen of Greenland halibut (Reinhardtius hippoglossoides)Reinhardtius hippoglossoides
122231Greenland halibutAtlantic, NewfoundlandCanadaCANNorth America

isolation source categories

Cat1Cat2
#Host#Fishes
#Host Body-Site#Organ

taxonmaps

  • @ref: 69479
  • File name: preview.99_8848.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_158;97_5075;98_6468;99_8848&stattab=map
  • Last taxonomy: Arthrobacter rhombi subclade
  • 16S sequence: Y15885
  • Sequence Identity:
  • Total samples: 1150
  • soil counts: 324
  • aquatic counts: 101
  • animal counts: 451
  • plant counts: 274

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
244841Risk group (German classification)
1222311Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
24484Arthrobacter rhombi 16S rRNA gene, strain F58.3CB57Y158841423nuccore71253
67770Arthrobacter rhombi 16S rRNA gene, strain F98.3HR69Y158851423nuccore71253

GC content

@refGC-contentmethod
2448461
6777061thermal denaturation, midpoint method (Tm)

External links

@ref: 24484

culture collection no.: DSM 15838, CCUG 38813, CIP 107337, JCM 11678, LMG 22201, NCIMB 13909

straininfo link

  • @ref: 91002
  • straininfo: 100511

literature

  • topic: Phylogeny
  • Pubmed-ID: 10425782
  • title: Arthrobacter rhombi sp. nov., isolated from Greenland halibut (Reinhardtius hippoglossoides).
  • authors: Osorio CR, Barja JL, Hutson RA, Collins MD
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-49-3-1217
  • year: 1999
  • mesh: Animals, Arthrobacter/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Flatfishes/*microbiology, Genes, rRNA, Greenland, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24484Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-15838Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15838)
37306Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4762
54484Curators of the CCUGhttps://www.ccug.se/strain?id=38813Culture Collection University of Gothenburg (CCUG) (CCUG 38813)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91002Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID100511.1
122231Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107337Collection of Institut Pasteur (CIP 107337)