Strain identifier

BacDive ID: 7605

Type strain: Yes

Species: Arthrobacter pigmenti

Strain Designation: R-5117

Strain history: CIP <- 2005, DSMZ

NCBI tax ID(s): 271432 (species)

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General

@ref: 6432

BacDive-ID: 7605

DSM-Number: 16403

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

description: Arthrobacter pigmenti R-5117 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Mural painting, biofilm.

NCBI tax id

  • NCBI tax id: 271432
  • Matching level: species

strain history

@refhistory
6432<- J. Heyrman, R-5117
373042005, DSMZ
67770IAM 15322 <-- LMG 22284 <-- J. Heyrman R-5117.
121830CIP <- 2005, DSMZ

doi: 10.13145/bacdive7605.20230509.8.1

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

@ref: 6432

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter pigmenti

full scientific name: Arthrobacter pigmenti Heyrman et al. 2005

strain designation: R-5117

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
31342positive0.9 µmcoccus-shapedno
69480positive100
121830positivecoccus-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18402Lemon yellow (1012)10-14 daysISP 2
18402Lemon yellow (1012)10-14 daysISP 3
18402Lemon yellow (1012)10-14 daysISP 4
18402Lemon yellow (1012)10-14 daysISP 5
18402Lemon yellow (1012)10-14 daysISP 6
18402Lemon yellow (1012)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18402noISP 2
18402noISP 3
18402noISP 4
18402noISP 5
18402noISP 6
18402noISP 7

pigmentation

  • @ref: 31342
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6432BACTO 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
18402ISP 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
18402ISP 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:
18402ISP 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
18402ISP 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
18402ISP 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
18402ISP 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
37304MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121830CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18402positiveoptimum28mesophilic
6432positivegrowth28mesophilic
31342positivegrowth10-37
31342positiveoptimum26mesophilic
37304positivegrowth25mesophilic
67770positivegrowth28mesophilic
121830positivegrowth15-37
121830nogrowth10psychrophilic
121830nogrowth41thermophilic
121830nogrowth45thermophilic

culture pH

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

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31342aerobe
121830obligate aerobe

spore formation

@refspore formationconfidence
31342no
69481no100
69480no99.747

halophily

@refsaltgrowthtested relationconcentration
31342NaClpositivegrowth05-15 %
31342NaClpositiveoptimum10 %
121830NaClpositivegrowth0-10 %

murein

  • @ref: 6432
  • murein short key: A11.07
  • type: A3alpha L-Lys-L-Ala4

observation

@refobservation
31342aggregates in chains
67770quinones: MK-9(H2), MK-7(H2), MK-10(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1840217234glucose+
1840222599arabinose+
1840217992sucrose+
1840218222xylose-
1840217268myo-inositol+
1840229864mannitol+
1840228757fructose+
1840226546rhamnose-
1840216634raffinose+
1840262968cellulose-
313425291gelatin+carbon source
3134217234glucose+carbon source
3134217306maltose+carbon source
3134237684mannose+carbon source
3134217992sucrose+carbon source
313424853esculin+hydrolysis
3134217632nitrate+reduction
12183016947citrate-carbon source
1218304853esculin-hydrolysis
121830606565hippurate+hydrolysis
12183017632nitrate+reduction
12183016301nitrite-reduction
12183017632nitrate-respiration
683794853esculin-hydrolysis
6837916199urea-hydrolysis
6837917992sucrose+fermentation

metabolite production

  • @ref: 121830
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12183015688acetoin-
12183017234glucose-

enzymes

@refvalueactivityec
31342acid phosphatase+3.1.3.2
31342alkaline phosphatase+3.1.3.1
31342alpha-galactosidase+3.2.1.22
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
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
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
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase+3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
121830oxidase-
121830beta-galactosidase+3.2.1.23
121830alcohol dehydrogenase-1.1.1.1
121830gelatinase+/-
121830amylase+
121830DNase+
121830caseinase+3.4.21.50
121830catalase+1.11.1.6
121830tween esterase-
121830gamma-glutamyltransferase-2.3.2.2
121830lecithinase-
121830lipase-
121830lysine decarboxylase-4.1.1.18
121830ornithine decarboxylase-4.1.1.17
121830phenylalanine ammonia-lyase-4.3.1.24
121830protease+
121830tryptophan deaminase-
121830urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18402--++++---+/-+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18402+++-+--+-++-+++--+-
121830+++-+--+--+-++---+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6432Mural painting, biofilmHerbersteinAustriaAUTEurope
67770Rosy biofilm overgrowing a mural painting in the Saint-Catherine chapelcastle of HerbersteinAustriaAUTEurope
121830Mural paintingHerberstein castle, HimsdorfAustriaAUTEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Engineered#Other#Painting
#Environmental#Biofilm

taxonmaps

  • @ref: 69479
  • File name: preview.99_75052.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1023;97_1193;98_1429;99_75052&stattab=map
  • Last taxonomy: Arthrobacter pigmenti
  • 16S sequence: AJ639827
  • Sequence Identity:
  • Total samples: 140
  • soil counts: 32
  • aquatic counts: 7
  • animal counts: 86
  • plant counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64321Risk group (German classification)
184022
1218301Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6432
  • description: Arthrobacter pigmenti partial 16S rRNA gene, type strain LMG 22284T
  • accession: AJ639827
  • length: 1489
  • database: ena
  • NCBI tax ID: 271432

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arthrobacter pigmenti strain DSM 16403271432.3wgspatric271432
66792Arthrobacter pigmenti DSM 164032831304190draftimg271432
67770Arthrobacter pigmenti DSM 16403GCA_011927905contigncbi271432

GC content

@refGC-contentmethod
643261.6
6777061.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes52.607no
gram-positiveyes91.956no
anaerobicno99.566no
halophileno69.335no
spore-formingno88.763no
glucose-utilyes84.778yes
aerobicyes95.453no
flagellatedno92.32no
thermophileno99.18yes
glucose-fermentno87.575no

External links

@ref: 6432

culture collection no.: DSM 16403, LMG 22284, JCM 21771, CIP 108899, IAM 15322

straininfo link

  • @ref: 77049
  • straininfo: 362265

literature

  • topic: Phylogeny
  • Pubmed-ID: 16014466
  • title: Six novel Arthrobacter species isolated from deteriorated mural paintings.
  • authors: Heyrman J, Verbeeren J, Schumann P, Swings J, De Vos P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63358-0
  • year: 2005
  • mesh: Arthrobacter/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, Spain
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6432Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16403)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16403
18402Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16403.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
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
37304Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6580
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
77049Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362265.1StrainInfo: A central database for resolving microbial strain identifiers
121830Curators of the CIPCollection of Institut Pasteur (CIP 108899)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108899