Strain identifier

BacDive ID: 7619

Type strain: Yes

Species: Paenarthrobacter ilicis

Strain Designation: Cr-2

Strain history: CIP <- 2001, CCUG <- 1989, LMG <- 1981, NCPPB <- 1962, Mandel: strain Cr-2

NCBI tax ID(s): 43665 (species)

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General

@ref: 8563

BacDive-ID: 7619

DSM-Number: 20138

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

description: Paenarthrobacter ilicis Cr-2 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from american holly .

NCBI tax id

  • NCBI tax id: 43665
  • Matching level: species

strain history

@refhistory
8563<- ATCC <- M. Mandel; (Corynebacterium ilicis)
67770CECT 4207 <-- NCPPB 1228 <-- M. Mandel CR2 <-- M. Mandel and E. F. Guba.
120047CIP <- 2001, CCUG <- 1989, LMG <- 1981, NCPPB <- 1962, Mandel: strain Cr-2

doi: 10.13145/bacdive7619.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Paenarthrobacter
  • species: Paenarthrobacter ilicis
  • full scientific name: Paenarthrobacter ilicis (Collins et al. 1982) Busse 2016

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter ilicis

@ref: 8563

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Paenarthrobacter

species: Paenarthrobacter ilicis

full scientific name: Paenarthrobacter ilicis (Collins et al. 1982) Busse 2016

strain designation: Cr-2

type strain: yes

Morphology

cell morphology

  • @ref: 120047
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
18628Sand yellow (1002)10-14 daysISP 2
18628Zinc yellow (1016)10-14 daysISP 3
18628Colorless10-14 daysISP 6
18628Colorless10-14 daysISP 7
1200471

multicellular morphology

@refforms multicellular complexmedium name
18628noISP 2
18628noISP 3
18628noISP 6
18628noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8563CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: 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 water
18628ISP 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
18628ISP 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:
18628ISP 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
18628ISP 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
41900MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120047CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
8563positivegrowth30
18628positiveoptimum28
41900positivegrowth30
67770positivegrowth28
120047positivegrowth10-37
120047nogrowth41
120047nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
120047obligate aerobe
125439obligate aerobe97.4

halophily

@refsaltgrowthtested relationconcentration
18628NaClpositivemaximum5 %
120047NaClpositivegrowth0-4 %
120047NaClnogrowth6 %
120047NaClnogrowth8 %
120047NaClnogrowth10 %

murein

  • @ref: 8563
  • murein short key: A11.17
  • type: A3alpha L-Lys-L-Ala-L-Thr-L-Ala

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837928087glycogen-fermentation
6837917992sucrose+fermentation
6837917716lactose+fermentation
6837917306maltose+fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose+fermentation
6837917634D-glucose+fermentation
683795291gelatin+hydrolysis
6837916199urea+hydrolysis
683794853esculin+hydrolysis
6837917632nitrate+reduction
12004716947citrate-carbon source
1200474853esculin+hydrolysis
120047606565hippurate+hydrolysis
12004717632nitrate-reduction
12004716301nitrite-reduction
12004717632nitrate-respiration
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

antibiotic resistance

  • @ref: 120047
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
12004735581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-testindole test
12004715688acetoin-
12004717234glucose-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382leucine arylamidase+3.4.11.1
68382trypsin+3.4.21.4
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
120047oxidase-
120047beta-galactosidase+3.2.1.23
120047alcohol dehydrogenase-1.1.1.1
120047gelatinase+
120047amylase-
120047DNase+
120047caseinase+3.4.21.50
120047catalase+1.11.1.6
120047tween esterase-
120047gamma-glutamyltransferase+2.3.2.2
120047lecithinase-
120047lipase-
120047lysine decarboxylase-4.1.1.18
120047ornithine decarboxylase-4.1.1.17
120047phenylalanine ammonia-lyase-4.3.1.24
120047protease+
120047tryptophan deaminase-
120047urease-3.5.1.5
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase+3.2.1.31
68368gelatinase-
68368urease+3.5.1.5
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379alpha-glucosidase+3.2.1.20
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
68368tryptophan deaminase+4.1.99.1
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18628+++-+++++++++--+++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18628+++-++++-++++--+++-
120047+++-+--+-+++++++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18628+++-++++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120047+++++-+++++++++++++-+++--+--+--+++++-----+-------+++-++-+--++++++-+--+-+++-+---++-----+-+++++++-++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
8563american holly (Ilex opaca)Ilex opaca
47870Ilex poacaUSAUSANorth America
67770American holly (Ilex opaca)Ilex opaca
120047American holly, Ilex opacaUnited States of AmericaUSANorth America1989

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Tree

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
186281Hazard group
85631Risk group (German classification)
1200471Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8563A.ilicis 16S rRNA geneX834071486nuccore43665
124043Arthrobacter ilicis partial 16S rRNA gene, type strain CECT 4207TFR8704421460nuccore43665

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenarthrobacter ilicis DSM 20138GCA_016907545contigncbi43665
66792Paenarthrobacter ilicis strain CECT 420743665.5wgspatric43665
66792Paenarthrobacter ilicis strain DSM 2013843665.6wgspatric43665
66792Arthrobacter ilicis CECT 42072824339274draftimg43665
66792Paenarthrobacter ilicis DSM 201382893582668draftimg43665
67770Paenarthrobacter ilicis CECT 4207GCA_011761315scaffoldncbi43665

GC content

@refGC-contentmethod
856361.5
6777061.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes89.786no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.624yes
125438spore-formingspore-formingAbility to form endo- or exosporesno58.719no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.281yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99yes
125438motile2+flagellatedAbility to perform flagellated movementno73no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno79.4
125439BacteriaNetmotilityAbility to perform movementno83.2
125439BacteriaNetgram_stainReaction to gram-stainingpositive85.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.4

External links

@ref: 8563

culture collection no.: DSM 20138, ATCC 14264, NCPPB 1228, CCUG 23889, LMG 3659, LMG 7254, CIP 107004, CCM 4967, JCM 12267, CECT 4207, CFBP 1380, HAMBI 1849, IAM 14586, ICMP 2607, IFO 15514, NBRC 15514, VKM Ac-1987, PDDCC 2607

straininfo link

  • @ref: 77063
  • straininfo: 1002

literature

  • topic: Phylogeny
  • Pubmed-ID: 18676493
  • title: Corynebacterium ilicis is typified by ICMP 2608 =ICPB CI144, Arthrobacter ilicis is typified by DSM 20138 =ATCC 14264 =NCPPB 1228 and the two are not homotypic synonyms, and clarification of the authorship of these two species. Opinion 87.
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.2008/006221-0
  • year: 2008
  • mesh: Arthrobacter/*classification, Corynebacterium/*classification, Species Specificity, *Terminology as Topic

Reference

@idauthorscataloguedoi/urltitle
8563Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20138)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20138
18628Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20138.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
41900Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19196
47870Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23889)https://www.ccug.se/strain?id=23889
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
77063Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1002.1StrainInfo: A central database for resolving microbial strain identifiers
120047Curators of the CIPCollection of Institut Pasteur (CIP 107004)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107004
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1