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, Gram-positive, coccus-shaped

description: Arthrobacter tumbae R-5305 is an aerobe, Gram-positive, coccus-shaped 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/bacdive7607.20240916.9.1

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
123684positivecoccus-shapedno
69480positive92.639

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

@refgrowthtypetemperature
6435positivegrowth28
31342positivegrowth04-37
31342positiveoptimum26
37386positivegrowth30
67770positivegrowth28
123684positivegrowth10-30
123684nogrowth37
123684nogrowth41
123684nogrowth45

culture pH

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

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31342aerobe
123684obligate aerobe
69480aerobe90.693

spore formation

  • @ref: 31342
  • spore formation: no

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: nuccore
  • 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

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno89no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes92.639yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.946yes
69480spore-formingspore-formingAbility to form endo- or exosporesno79.49yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.693yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.447no
69480flagellatedmotile2+Ability to perform flagellated movementno89.5no

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)
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
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