Strain identifier

BacDive ID: 3230

Type strain: Yes

Species: Corynebacterium lubricantis

Strain Designation: KSS-3Se

Strain history: CIP <- 2009, P. Kämpfer, Giessen Univ., Giessen, Germany: strain KSS-3Se

NCBI tax ID(s): 1121363 (strain), 541095 (species)

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General

@ref: 15809

BacDive-ID: 3230

DSM-Number: 45231

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

description: Corynebacterium lubricantis KSS-3Se is an aerobe, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from coolant lubricant.

NCBI tax id

NCBI tax idMatching level
541095species
1121363strain

strain history

@refhistory
15809<- P. Kämpfer, Univ. Giessen; KSS-3Se
67770CCM 7546 <-- P. Kämpfer KSS-3Se.
120657CIP <- 2009, P. Kämpfer, Giessen Univ., Giessen, Germany: strain KSS-3Se

doi: 10.13145/bacdive3230.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Corynebacteriaceae
  • genus: Corynebacterium
  • species: Corynebacterium lubricantis
  • full scientific name: Corynebacterium lubricantis Kämpfer et al. 2009

@ref: 15809

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium lubricantis

full scientific name: Corynebacterium lubricantis Kämpfer et al. 2009 emend. Nouioui et al. 2018

strain designation: KSS-3Se

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotility
29106positive1 µmrod-shapedno
120657positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19925Ivory10-14 daysISP 2
19925Peeble grey10-14 daysISP 3
19925Beige10-14 daysISP 4
19925Ivory10-14 daysISP 5
19925Sand yellow10-14 daysISP 6
19925Ivory10-14 daysISP 7
610231 day

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19925yesAerial MyceliumIvoryISP 2
19925noISP 3
19925noISP 4
19925noISP 5
19925noISP 6
19925noISP 7

pigmentation

  • @ref: 29106
  • production: yes

multimedia

  • @ref: 15809
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45231.jpg
  • caption: Medium 535a 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15809TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a)yeshttps://mediadive.dsmz.de/medium/535aName: TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) Composition: None 50.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
19925ISP 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
19925ISP 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:
19925ISP 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
19925ISP 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
19925ISP 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
19925ISP 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
37916MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120657CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
19925positiveoptimum28mesophilic
15809positivegrowth28mesophilic
29106positivegrowth25-30mesophilic
29106positiveoptimum27.5mesophilic
37916positivegrowth30mesophilic
61023positivegrowth37mesophilic
67770positivegrowth28mesophilic

culture pH

  • @ref: 29106
  • ability: positive
  • type: optimum
  • pH: 7.2

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
61023aerobe
120657facultative anaerobe

spore formation

  • @ref: 29106
  • spore formation: no

observation

@refobservation
29106aggregates in clumps
67770quinones: MK-9(H2), MK-8(H2), MK-7(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2910630089acetate+carbon source
2910628757fructose+carbon source
2910617234glucose+carbon source
2910624996lactate+carbon source
2910627082trehalose+carbon source
291064853esculin+hydrolysis
6836925115malate-assimilation
6836917128adipate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12065717632nitrate+reduction
12065716301nitrite-reduction
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12065735581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)-
68379gelatinase-
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
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120657oxidase-
120657catalase+1.11.1.6
120657urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    61023C14:00.714
    61023C16:02916
    61023C17:02.317
    61023C18:02.818
    61023C17:1 ω9c22.616.773
    61023C18:1 ω9c36.317.769
    61023C18:2 ω6,9c/C18:0 ANTE317.724
    61023TBSA 10Me18:03.318.392
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19925-+/---+---+--+/-+/---+/--+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19925-++-+----++--+-+---
15809-+/---+/-----------+/-----
120657+++-+----++--+-+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
15809+----+--+------+/---+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15809coolant lubricantGiessenGermanyDEUEurope
61023Coolant lubricantGiessenGermanyDEUEurope
67770Coolant lubricantGiessenGermanyDEUEurope
120657Coolant lubricantGiessen, HessenGermanyDEUEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Industrial
  • Cat3: #Engineered product

taxonmaps

  • @ref: 69479
  • File name: preview.99_17167.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_8817;97_10598;98_12997;99_17167&stattab=map
  • Last taxonomy: Corynebacterium lubricantis subclade
  • 16S sequence: FM173119
  • Sequence Identity:
  • Total samples: 587
  • soil counts: 53
  • aquatic counts: 25
  • animal counts: 509

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
158091Risk group (German classification)
1206572Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15809
  • description: Corynebacterium lubricantis partial 16S rRNA gene, type strain KSS-3SeT
  • accession: FM173119
  • length: 1428
  • database: ena
  • NCBI tax ID: 541095

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium lubricantis DSM 452311121363.3wgspatric1121363
66792Corynebacterium lubricantis DSM 452312515154018draftimg1121363
67770Corynebacterium lubricantis DSM 45231GCA_000379425scaffoldncbi1121363

GC content

  • @ref: 67770
  • GC-content: 56.8
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.09yes
flagellatedno98.032no
gram-positiveyes93.251yes
anaerobicno99.218yes
aerobicyes67.773no
halophileyes68.599no
spore-formingno94.391yes
thermophileno95.98yes
glucose-utilyes85.9no
glucose-fermentno68.075yes

External links

@ref: 15809

culture collection no.: DSM 45231, CCM 7546, CCUG 56567, JCM 16607, CIP 110047

straininfo link

  • @ref: 72744
  • straininfo: 362780

literature

  • topic: Phylogeny
  • Pubmed-ID: 19406802
  • title: Corynebacterium lubricantis sp. nov., isolated from a coolant lubricant.
  • authors: Kampfer P, Lodders N, Warfolomeow I, Falsen E, Busse HJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.006379-0
  • year: 2009
  • mesh: *Air Conditioning, Bacterial Typing Techniques, Corynebacterium/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, *Lubricants, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15809Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45231)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45231
19925Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45231.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
29106Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2553428776041
37916Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7861
61023Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56567)https://www.ccug.se/strain?id=56567
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/
68369Automatically annotated from API 20NE
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
72744Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362780.1StrainInfo: A central database for resolving microbial strain identifiers
120657Curators of the CIPCollection of Institut Pasteur (CIP 110047)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110047