Strain identifier

BacDive ID: 3169

Type strain: Yes

Species: Corynebacterium afermentans subsp. lipophilum

Strain Designation: T 18502

Strain history: CIP <- 1993, P. Riegel, Strasbourg Hosp., France: strain T 18502, Corynebacterium group ANF 1

NCBI tax ID(s): 144184 (subspecies)

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General

@ref: 11529

BacDive-ID: 3169

DSM-Number: 44282

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

description: Corynebacterium afermentans subsp. lipophilum T 18502 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from human .

NCBI tax id

  • NCBI tax id: 144184
  • Matching level: subspecies

strain history

@refhistory
11529<- CCUG <- P. Riegel, ULP Strasbourg, T 18502
342911993, P. Riegel, Strasbourg Hosp., France: strain T 18502, Corynebacterium group ANF 1
67770CIP 103500 <-- P. Riegel T18502.
116102CIP <- 1993, P. Riegel, Strasbourg Hosp., France: strain T 18502, Corynebacterium group ANF 1

doi: 10.13145/bacdive3169.20230509.8.1

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 afermentans subsp. lipophilum
  • full scientific name: Corynebacterium afermentans subsp. lipophilum Riegel et al. 1993

@ref: 11529

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium afermentans subsp. lipophilum

full scientific name: Corynebacterium afermentans subsp. lipophilum Riegel et al. 1993

strain designation: T 18502

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
23370positiverod-shaped
23370coccus-shaped
23370no
69480no98.148
69480positive100
116102positiverod-shapedno

colony morphology

  • @ref: 23370
  • colony size: 2 mm
  • colony color: beige
  • medium used: 1% Tween 80 supplemented sheep blood agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11529TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92; with strain-specific modifications) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Tween 80 2.0 g/l Distilled water
11529COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
233701% Tween 80 supplemented sheep blood agaryes
34291MEDIUM 37 - for Corynebacterium afermentans subsp. lipophilumyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Tween80 (10.000 ml)
116102CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
11529positivegrowth37mesophilic
34291positivegrowth37mesophilic
50833positivegrowth37mesophilic
67770positivegrowth37mesophilic
116102positivegrowth37-41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
50833aerobe
50833microaerophile
116102obligate aerobe

spore formation

@refspore formationconfidence
23370no
69481no100
69480no99.998

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2337012936D-galactose-builds acid from
2337017634D-glucose-builds acid from
2337016899D-mannitol-builds acid from
2337016024D-mannose-builds acid from
2337065327D-xylose-builds acid from
2337028087glycogen-builds acid from
2337017716lactose-builds acid from
2337033942ribose-builds acid from
2337017992sucrose-builds acid from
2337027082trehalose-builds acid from
2337030089acetate-carbon source
2337017128adipate-carbon source
2337027689decanoate-carbon source
2337016947citrate-carbon source
2337017634D-glucose-carbon source
2337016899D-mannitol-carbon source
2337016024D-mannose-carbon source
2337024265gluconate-carbon source
2337030849L-arabinose-carbon source
2337025115malate-carbon source
2337017306maltose-carbon source
23370506227N-acetylglucosamine-carbon source
2337017272propionate-carbon source
2337016991dna-degradation
233705291gelatin-degradation
2337018186tyrosine-degradation
2337016199urea-degradation
2337017234glucose-fermentation
233704853esculin-hydrolysis
23370606565hippurate-hydrolysis
2337030089acetate+carbon source
2337024996lactate+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837115824D-fructose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
1161024853esculin-hydrolysis
11610217632nitrate-reduction
11610216301nitrite-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
2337028915fosfomycinyesyes
233702637amikacinyesyes
2337028971ampicillinyesyes
23370204928cefotaximeyesyes
23370124991cefalotinyesyes
23370100241ciprofloxacinyesyes
2337048923erythromycinyesyes
2337071321fusidateyesyes
2337017833gentamicinyesyes
233706919mezlocillinyesyes
233707528netilmycinyesyes
23370100246norfloxacinyesyes
233708232piperacillinyesyes
2337085274pristinamycinyesyes
2337028077rifampicinyesyes
2337029687teicoplaninyesyes
2337027902tetracyclineyesyes
233709587ticarcillinyesyes
2337028001vancomycinyesyes

metabolite production

  • @ref: 116102
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 23370
  • Chebi-ID: 17234
  • metabolite: glucose
  • methylred-test: -

enzymes

@refvalueactivityec
23370acid phosphatase+3.1.3.2
23370alkaline phosphatase+3.1.3.1
23370alpha-galactosidase-3.2.1.22
23370alpha-glucosidase-3.2.1.20
23370alpha-glucuronidase-3.2.1.139
23370beta-galactosidase-3.2.1.23
23370beta-glucosidase-3.2.1.21
23370catalase+1.11.1.6
23370cytochrome oxidase-1.9.3.1
23370esterase+
23370lipase (C 14)+
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
68379catalase+1.11.1.6
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
68379pyrazinamidase-3.5.1.B15
116102oxidase-
116102beta-galactosidase-3.2.1.23
116102alcohol dehydrogenase-1.1.1.1
116102gelatinase-
116102amylase+
116102caseinase-3.4.21.50
116102catalase+1.11.1.6
116102tween esterase-
116102lecithinase-
116102lysine decarboxylase-4.1.1.18
116102ornithine decarboxylase-4.1.1.17
116102urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    50833C16:020.916
    50833C17:02.717
    50833C18:015.818
    50833C16:1 ω7c2.315.819
    50833C18:1 ω9c35.217.769
    50833C18:2 ω6,9c/C18:0 ANTE22.217.724
    50833Unidentified0.916.754
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
11529--------------------+

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116102-+++-+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116102+/----+/------+/--+/---------------------------+/----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116102+------------------+------------------+----------+-------------+-----------+--+++---------+-------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11529human (blood culture)StrasbourgFranceFRAEurope
50833Human bloodStrasbourgFranceFRAEurope
67770Human blood cultureStrasbourgFranceFRAEurope
116102Human, BloodStrasbourgFranceFRAEurope1990

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Blood culture
#Host#Human

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115292Risk group (German classification)
1161022Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium afermentans subsp. lipophilum 16S ribosomal RNA gene, partial sequenceAY438046420ena144184
11529Corynebacterium afermentans subsp. lipophilum 16S ribosomal DNA, type strain CIP 103500TX820551325ena144184

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium afermentans subsp. lipophilum CCUG 32105GCA_015351335contigncbi144184
66792Corynebacterium afermentans subsp. lipophilum strain CCUG 32105144184.3wgspatric144184

GC content

@refGC-contentmethod
1152968
2337068.0high performance liquid chromatography (HPLC)
6777068high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.985yes
gram-positiveyes94.953yes
anaerobicno98.963yes
halophileyes78.291no
spore-formingno94.013no
thermophileno96.069no
glucose-utilyes76.588yes
aerobicno65.527no
flagellatedno96.911yes
glucose-fermentno64.335yes

External links

@ref: 11529

culture collection no.: DSM 44282, ATCC 51404, CCUG 32105, CIP 103500, JCM 10391, LMG 19063

straininfo link

  • @ref: 72685
  • straininfo: 12985

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28950931Corynebacterium gottingense sp. nov., isolated from a clinical patient.Atasayar E, Zimmermann O, Sproer C, Schumann P, Gross UInt J Syst Evol Microbiol10.1099/ijsem.0.0023222017Bacterial Typing Techniques, Base Composition, Blood/*microbiology, Corynebacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Germany, Humans, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny34846289Corynebacterium zhongnanshanii sp. nov. isolated from trachea of Marmota himalayana, Corynebacterium lujinxingii sp. nov. and Corynebacterium wankanglinii sp. nov. from human faeces.Zhang G, Yang J, Lai XH, Jin D, Lu S, Ren Z, Qin T, Pu J, Ge Y, Cheng Y, Yang C, Lv X, Jiao Y, Huang Y, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0050692021Animals, Bacterial Typing Techniques, Base Composition, Corynebacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Humans, *Marmota/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Trachea/microbiology, Vitamin K 2/analogs & derivatives/chemistryPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11529Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44282)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44282
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
23370P. Riegel, D. De Briel, G. Prévost, F. Jehl, H. Monteil, R. Minck10.1099/00207713-43-2-287Taxonomic Study of Corynebacterium Group ANF-1 Strains: Proposal of Corynebacterium afermentans sp. nov. Containing the Subspecies C. afermentans subsp. afermentans subsp. nov. and C. afermentans subsp. lipophilum subsp. nov.IJSEM 43: 287-292 19938494739
34291Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15304
50833Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32105)https://www.ccug.se/strain?id=32105
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/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
72685Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12985.1StrainInfo: A central database for resolving microbial strain identifiers
116102Curators of the CIPCollection of Institut Pasteur (CIP 103500)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103500