Strain identifier

BacDive ID: 7607

Type strain: Yes

Species: Arthrobacter tumbae

Strain Designation: R-5305

Strain history: CIP <- 2005, DSMZ

NCBI tax ID(s): 163874 (species)

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General

@ref: 6435

BacDive-ID: 7607

DSM-Number: 16406

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

description: Arthrobacter tumbae R-5305 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Biofilm covering the Servilia tomb, Roman necropolis of Carmona.

NCBI tax id

  • NCBI tax id: 163874
  • Matching level: species

strain history

@refhistory
6435<- J. Heyrman, R-5305
373862005, DSMZ
67770IAM 15324 <-- LMG 19501 <-- J. Heyrman R-5305.
123684CIP <- 2005, DSMZ

doi: 10.13145/bacdive7607.20230509.8.1

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 tumbae
  • full scientific name: Arthrobacter tumbae Heyrman et al. 2005

@ref: 6435

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter tumbae

full scientific name: Arthrobacter tumbae Heyrman et al. 2005

strain designation: R-5305

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
31342positive0.9 µmcoccus-shapedno
69480no92.028
69480positive100
123684positivecoccus-shapedno

colony morphology

  • @ref: 123684

pigmentation

  • @ref: 31342
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6435TRYPTICASE 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
6435BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
37386MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123684CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6435positivegrowth28mesophilic
31342positivegrowth04-37
31342positiveoptimum26mesophilic
37386positivegrowth30mesophilic
67770positivegrowth28mesophilic
123684positivegrowth10-30
123684nogrowth37mesophilic
123684nogrowth41thermophilic
123684nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
31342positivegrowth07-10alkaliphile
31342positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31342aerobe
123684obligate aerobe

spore formation

@refspore formationconfidence
31342no
69480no99.978

halophily

@refsaltgrowthtested relationconcentration
31342NaClpositivegrowth05-10 %
31342NaClpositiveoptimum7.5 %
123684NaClpositivegrowth0 %
123684NaClnogrowth2 %
123684NaClnogrowth4 %
123684NaClnogrowth6 %
123684NaClnogrowth8 %
123684NaClnogrowth10 %

murein

  • @ref: 6435
  • murein short key: A11.28
  • type: A3alpha L-Lys-L-Thr-L-Ala3

observation

@refobservation
31342aggregates in clumps
67770quinones: MK-9(H2), MK-10(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
313425291gelatin+carbon source
12368416947citrate-carbon source
1236844853esculin-hydrolysis
123684606565hippurate+hydrolysis
12368417632nitrate+reduction
12368416301nitrite-reduction

metabolite production

  • @ref: 123684
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12368415688acetoin-
12368417234glucose-

enzymes

@refvalueactivityec
31342catalase+1.11.1.6
31342gelatinase+
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
123684oxidase-
123684beta-galactosidase+3.2.1.23
123684alcohol dehydrogenase-1.1.1.1
123684gelatinase-
123684amylase+
123684DNase-
123684caseinase+3.4.21.50
123684catalase+1.11.1.6
123684tween esterase-
123684gamma-glutamyltransferase-2.3.2.2
123684lecithinase-
123684lipase-
123684lysine decarboxylase-4.1.1.18
123684ornithine decarboxylase-4.1.1.17
123684phenylalanine ammonia-lyase-4.3.1.24
123684protease+
123684tryptophan deaminase-
123684urease-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
123684--+--+------+--+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6435Biofilm covering the Servilia tomb, Roman necropolis of CarmonaCarmonaSpainESPEurope
67770Biofilm overgrowing a mural painting in the Servilia tombRoman necropolis of CarmonaSpainESPEurope
123684Mural paintings sitesServilia tomb, CarmonaSpainESPEurope

isolation source categories

Cat1Cat2
#Environmental#Biofilm
#Environmental#Terrestrial

taxonmaps

  • @ref: 69479
  • File name: preview.99_5961.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_803;97_937;98_1098;99_5961&stattab=map
  • Last taxonomy: Arthrobacter
  • 16S sequence: AJ315069
  • Sequence Identity:
  • Total samples: 5651
  • soil counts: 2709
  • aquatic counts: 534
  • animal counts: 1557
  • plant counts: 851

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64351Risk group (German classification)
1236841Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6435
  • description: Arthrobacter tumbae 16S rRNA gene, type strain LMG 19501
  • accession: AJ315069
  • length: 1475
  • database: ena
  • NCBI tax ID: 163874

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arthrobacter tumbae DSM 16406GCA_016907495contigncbi163874
66792Arthrobacter tumbae strain DSM 16406163874.3wgspatric163874
66792Arthrobacter tumbae DSM 164062893579105draftimg163874

GC content

@refGC-contentmethod
643564.7
6777064.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno89no
motileno90.142yes
gram-positiveyes92.749yes
anaerobicno99.598yes
aerobicyes95.027no
halophileno54.694yes
spore-formingno92.623yes
glucose-utilyes85.907no
flagellatedno97.282yes
thermophileno99.078no
glucose-fermentno87.824no

External links

@ref: 6435

culture collection no.: DSM 16406, LMG 19501, JCM 21773, CIP 108900, IAM 15324, VTT E-072668

straininfo link

  • @ref: 77051
  • straininfo: 13191

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16014466Six novel Arthrobacter species isolated from deteriorated mural paintings.Heyrman J, Verbeeren J, Schumann P, Swings J, De Vos PInt J Syst Evol Microbiol10.1099/ijs.0.63358-02005Arthrobacter/chemistry/*classification/genetics/*isolation & purification, Austria, Bacterial Typing Techniques, Base Composition, Biofilms/*growth & development, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, *Paintings, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, SpainGenetics
Phylogeny23223813Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments.Vaishampayan P, Moissl-Eichinger C, Pukall R, Schumann P, Sproer C, Augustus A, Roberts AH, Namba G, Cisneros J, Salmassi T, Venkateswaran KInt J Syst Evol Microbiol10.1099/ijs.0.047134-02012Arthrobacter/classification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Environment, Controlled, *Environmental Microbiology, Fatty Acids/analysis, Florida, French Guiana, Micrococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spacecraft, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6435Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16406)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16406
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
31342Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2765628776041
37386Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6581
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/
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)
77051Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13191.1StrainInfo: A central database for resolving microbial strain identifiers
123684Curators of the CIPCollection of Institut Pasteur (CIP 108900)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108900