Strain identifier

BacDive ID: 7520

Type strain: Yes

Species: Arthrobacter citreus

Strain Designation: C7

Strain history: CIP <- 1986, DSM <- ATCC <- WRRL <- L.E. Sacks: strain C7

NCBI tax ID(s): 1670 (species)

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General

@ref: 8558

BacDive-ID: 7520

DSM-Number: 20133

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive

description: Arthrobacter citreus C7 is an aerobe, spore-forming, mesophilic bacterium that was isolated from Animal, Chicken, feces.

NCBI tax id

  • NCBI tax id: 1670
  • Matching level: species

strain history

@refhistory
8558<- ATCC <- WRRL. L.E. Sacks, C7
67770K. Suzuki CNF 021 <-- AJ 1423 <-- ATCC 11624 <-- WRRL.
118301CIP <- 1986, DSM <- ATCC <- WRRL <- L.E. Sacks: strain C7

doi: 10.13145/bacdive7520.20230509.8.1

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 citreus
  • full scientific name: Arthrobacter citreus Sacks 1954 (Approved Lists 1980)

@ref: 8558

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter citreus

full scientific name: Arthrobacter citreus Sacks 1954

strain designation: C7

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
18422Golden yellow (1004)10-14 daysISP 2
18422Rapeseed yellow (1021)10-14 daysISP 3
18422Oyster white (1013)10-14 daysISP 4
18422Oyster white (1013)10-14 daysISP 5
18422Colorless10-14 daysISP 6
18422Light ivory (1015)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18422noISP 2
18422noISP 3
18422noISP 4
18422noISP 5
18422noISP 6
18422noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18422ISP 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
18422ISP 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:
18422ISP 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
18422ISP 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
18422ISP 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
18422ISP 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
33071MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8558CORYNEBACTERIUM AGAR (DSMZ Medium 53)yesName: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/53
118301CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18422positiveoptimum28mesophilic
8558positivegrowth30mesophilic
33071positivegrowth30mesophilic
47854positivegrowth22-37
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 47854
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
8558L serine
8558L aspartyl-L-phenylalanine esters

halophily

  • @ref: 18422
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

murein

  • @ref: 8558
  • murein short key: A11.27
  • type: A3alpha L-Lys-L-Thr-L-Ala2

observation

@refobservation
67770Assay of Subtilin
67770quinones: MK-9(H2), MK-9(H2) MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1842217234glucose+
1842222599arabinose+
1842217992sucrose+
1842218222xylose+
1842217268myo-inositol+
1842229864mannitol+
1842228757fructose+
1842226546rhamnose+
1842216634raffinose+
1842262968cellulose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

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
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
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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    47854C14:00.314
    47854C16:01.716
    47854C18:00.618
    47854C13:0 ANTEISO0.812.701
    47854C14:0 ISO2.213.618
    47854C15:0 ANTEISO79.114.711
    47854C15:0 ISO6.614.621
    47854C16:0 iso2.415.626
    47854C17:0 anteiso2.816.722
    47854C18:1 ω9c1.417.769
    47854C18:2 ω6,9c/C18:0 ANTE2.117.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18422-++-+++--++/-+-----+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphatasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18422+++-+++--++-------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18422-----------

Isolation, sampling and environmental information

isolation

  • @ref: 118301
  • sample type: Animal, Chicken, feces

taxonmaps

  • @ref: 69479
  • File name: preview.99_8639.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_458;97_525;98_6307;99_8639&stattab=map
  • Last taxonomy: Arthrobacter citreus subclade
  • 16S sequence: X80737
  • Sequence Identity:
  • Total samples: 422
  • soil counts: 147
  • aquatic counts: 78
  • animal counts: 161
  • plant counts: 36

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184221
85581Risk group (German classification)
1183011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Arthrobacter citreus partial 16S rRNA gene, isolate OS-21.bAM2373461408ena1670
20218Arthrobacter citreus partial 16S rRNA gene, isolate OS-26.aAM2373481268ena1670
20218A.citreus 16S rDNAX807371475ena1670

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arthrobacter citreus strain DSM 201331670.3wgspatric1670
67770Arthrobacter citreus DSM 20133GCA_009192745contigncbi1670

GC content

@refGC-contentmethod
855862.9
6777065.1thermal denaturation, midpoint method (Tm)
6777064.9high performance liquid chromatography (HPLC)
6777068.1thermal denaturation, midpoint method (Tm)
6777068
6777062.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno62.991no
gram-positiveyes91.839no
anaerobicno99.23no
aerobicyes91.567yes
halophileno65.454no
spore-formingno87.399no
thermophileno98.814yes
glucose-utilyes86.994yes
flagellatedno95.484no
glucose-fermentno86.067yes

External links

@ref: 8558

culture collection no.: DSM 20133, ATCC 11624, NCIB 8915, CCUG 23840, CCM 1647, JCM 1331, BCRC 10374, CDA 837, CGMCC 1.1893, CIP 102363, HAMBI 89, IAM 12341, IFO 12671, IFO 12957, IMET 10680, IMSNU 20062, KCTC 1001, LMG 16338, NBIMCC 2008, NBRC 12671, NBRC 12957, NCCB 72019, NCIMB 8915, NRIC 1858, NRRL B-1258, VKM Ac-1106, VKM Ac-1125

straininfo link

  • @ref: 76965
  • straininfo: 386987

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology14529187Identification and differentiation of species and strains of Arthrobacter and Microbacterium barkeri isolated from smear cheeses with Amplified Ribosmal DNA Restriction Analysis (ARDRA) and pulsed field gel electrophoresis (PFGE).Hoppe-Seyler TS, Jaeger B, Bockelmann W, Noordman WH, Geis A, Heller KJSyst Appl Microbiol10.1078/0723202033224974732003Actinomycetales/*classification/genetics/*isolation & purification, Arthrobacter/*classification/genetics/*isolation & purification, Cheese/*microbiology, DNA Restriction Enzymes, DNA, Bacterial/analysis/isolation & purification, DNA, Ribosomal/analysis/chemistry, Electrophoresis, Agar Gel, Electrophoresis, Gel, Pulsed-Field, Food Microbiology, Physical Chromosome Mapping, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityPhylogeny
Phylogeny35103585Arthrobacter sunyaminii sp. nov. and Arthrobacter jiangjiafuii sp. nov., new members in the genus Arthrobacter.Zhang G, Yang J, Jin D, Lai XH, Lu S, Ren Z, Qin T, Liu L, Pu J, Liu Y, Ye L, Zhou J, Lv X, Tao Y, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0051812022Animals, Arthrobacter/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Intestines/microbiology, Marmota/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8558Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20133)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20133
18422Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20133.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
33071Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14041
47854Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23840)https://www.ccug.se/strain?id=23840
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/
68368Automatically annotated from API 20E
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
76965Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID386987.1StrainInfo: A central database for resolving microbial strain identifiers
118301Curators of the CIPCollection of Institut Pasteur (CIP 102363)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102363