Strain identifier

BacDive ID: 3131

Type strain: Yes

Species: Corynebacterium xerosis

Strain history: CIP <- 1984, ATCC <- J.G. Fitzgerald

NCBI tax ID(s): 1223513 (strain), 1725 (species)

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General

@ref: 9052

BacDive-ID: 3131

DSM-Number: 20743

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

description: Corynebacterium xerosis CCUG 56051 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from ear discharge of child.

NCBI tax id

NCBI tax idMatching level
1725species
1223513strain

strain history

@refhistory
9052<- ATCC <- J.G. Fitzgerald
67770ATCC 373 <-- J. G. Fitzgerald.
123976CIP <- 1984, ATCC <- J.G. Fitzgerald

doi: 10.13145/bacdive3131.20230509.8.1

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 xerosis
  • full scientific name: Corynebacterium xerosis (Lehmann and Neumann 1896) Lehmann and Neumann 1899 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacillus xerosis

@ref: 9052

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium xerosis

full scientific name: Corynebacterium xerosis (Lehmann and Neumann 1896) Lehmann and Neumann 1899 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

  • @ref: 123976
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18458Beige (1001)10-14 daysISP 2
18458Light ivory (1015)10-14 daysISP 4
18458Colorless10-14 daysISP 5
18458Colorless10-14 daysISP 6
18458Salmon orange (2012)10-14 daysISP 7
123976

multicellular morphology

@refforms multicellular complexmedium name
18458noISP 2
18458noISP 4
18458noISP 5
18458noISP 6
18458noISP 7

multimedia

  • @ref: 9052
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_20743.jpg
  • caption: Medium 535a 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18458ISP 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
18458ISP 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
18458ISP 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
18458ISP 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
18458ISP 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
9052TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yesName: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535
40238MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
123976CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
18458positiveoptimum37mesophilic
9052positivegrowth37mesophilic
40238positivegrowth30mesophilic
60846positivegrowth37mesophilic
67770positivegrowth37mesophilic
123976positivegrowth15-41
123976nogrowth10psychrophilic
123976nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60846aerobe
123976facultative anaerobe

compound production

  • @ref: 9052
  • compound: L aspartyl-L-phenylalanine esters

halophily

@refsaltgrowthtested relationconcentration
18458NaClpositivemaximum10 %
123976NaClpositivegrowth0-4 %
123976NaClnogrowth6 %
123976NaClnogrowth8 %
123976NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1845817234glucose+
1845822599arabinose+
1845817992sucrose+
1845818222xylose-
1845817268myo-inositol+
1845829864mannitol-
1845828757fructose-
1845826546rhamnose+
1845816634raffinose+/-
1845862968cellulose+/-
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
6837132528turanose-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
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-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
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836930849L-arabinose-assimilation
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12397616947citrate-carbon source
1239764853esculin-hydrolysis
123976606565hippurate+hydrolysis
12397617632nitrate+reduction
12397616301nitrite-reduction
12397617632nitrate+respiration
6837917632nitrate+reduction
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12397635581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin+
6836835581indole-
12397615688acetoin+

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
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)-
68379gelatinase-
68379urease-3.5.1.5
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
68379pyrrolidonyl arylamidase-3.4.19.3
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
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
123976oxidase-
123976beta-galactosidase-3.2.1.23
123976alcohol dehydrogenase-1.1.1.1
123976gelatinase-
123976amylase+
123976DNase-
123976caseinase-3.4.21.50
123976catalase+1.11.1.6
123976tween esterase-
123976gamma-glutamyltransferase-2.3.2.2
123976lecithinase-
123976lipase-
123976lysine decarboxylase-4.1.1.18
123976ornithine decarboxylase-4.1.1.17
123976urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControl
18458+--+--+-+--++----+-
9052++----+----++--+-+--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18458+-+-+--+-++---+----
9052-++-+---------+-----
9052-+/-+/------------+-----
123976+++-+----++---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18458------+--++

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
9052+----+/-+/--+/--+/-+/-+/-+/----+/-+/-+/-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123976-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123976++-++--+--+--------+---------------+-------------+-----------------------------++-----+-+----------

Isolation, sampling and environmental information

isolation

@refsample typesampling dateisolation date
9052ear discharge of child
60846Human ear discharge,child1924
67770Ear discharge of a child
123976Human, Child, ear discharge1924

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body-Site#Organ#Ear
#Host Body Product#Fluids
#Host#Human#Child

taxonmaps

  • @ref: 69479
  • File name: preview.99_1838.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1038;97_1212;98_1453;99_1838&stattab=map
  • Last taxonomy: Corynebacterium xerosis
  • 16S sequence: X84446
  • Sequence Identity:
  • Total samples: 6520
  • soil counts: 495
  • aquatic counts: 698
  • animal counts: 5206
  • plant counts: 121

Safety information

risk assessment

@refbiosafety levelbiosafety level commentpathogenicity animal
184582German classification
90521Risk group (German classification)yes, in single cases
1239762Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium xerosis small subunit ribosomal RNA sequenceM590581462ena1725
20218Corynebacterium xerosis ATCC 373 16S rRNA gene, partial sequenceU02895313ena1725
20218C.xerosis 16S rRNA gene (ATCC 373T)X819141317ena1725
20218Corynebacterium xerosis partial 16S rRNA gene, strain DSM 20743X844461488ena1725

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium paraputrificum NCTC11861GCA_900461265contigncbi29363
66792Clostridium paraputrificum strain NCTC1186129363.59wgspatric29363
66792Corynebacterium xerosis NBRC 167211223513.5wgspatric1223513
66792Corynebacterium xerosis strain ATCC 3731725.5wgspatric1725
66792Clostridium paraputrificum NCTC 118612811995212draftimg1725
66792Corynebacterium xerosis NBRC 167212690315859draftimg1223513
66792Corynebacterium xerosis DSM 20743 Genome Sequencing2617270853completeimg1725
66792Corynebacterium xerosis ATCC 3732648501103draftimg1725
67770Corynebacterium xerosis NBRC 16721GCA_001552415contigncbi1223513
67770Corynebacterium xerosis ATCC 373GCA_000988235contigncbi1725

GC content

@refGC-contentmethod
905267.3
6777071high performance liquid chromatography (HPLC)
6777068thermal denaturation, midpoint method (Tm)
6777067.3thermal denaturation, midpoint method (Tm)
6777069.7genome sequence analysis

External links

@ref: 9052

culture collection no.: CCUG 56051, CCM 2824, NCTC 11861, CIP 100653, IFO 15287, DSM 20743, ATCC 373, JCM 1971, BCRC 14413, CCM 1.1919, CCUG 27544, CECT 4160, IFO 16721, KCCM 40941, KCTC 3435, LMG 19544, NBRC 15287, NBRC 16721

straininfo link

  • @ref: 72648
  • straininfo: 13152

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8727888Most Corynebacterium xerosis strains identified in the routine clinical laboratory correspond to Corynebacterium amycolatum.Funke G, Lawson PA, Bernard KA, Collins MDJ Clin Microbiol10.1128/jcm.34.5.1124-1128.19961996Bacterial Typing Techniques/standards, Bacteriological Techniques/standards, Corynebacterium/*classification/genetics/metabolism, Corynebacterium Infections/diagnosis, Drug Resistance, Microbial, Genes, Bacterial, Humans, Phenotype, Polymerase Chain Reaction, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Reference Standards, Species SpecificityPathogenicity
Phylogeny11594602Corynebacterium freneyi sp. nov., alpha-glucosidase-positive strains related to Corynebacterium xerosis.Renaud FN, Aubel D, Riegel P, Meugnier H, Bollet CInt J Syst Evol Microbiol10.1099/00207713-51-5-17232001Anti-Bacterial Agents/pharmacology, Corynebacterium/chemistry/*classification/drug effects/*enzymology/genetics, Corynebacterium Infections/*microbiology, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, DNA, Ribosomal Spacer/genetics, Humans, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, alpha-Glucosidases/*metabolismPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9052Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20743)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20743
18458Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20743.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
40238Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12141
60846Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56051)https://www.ccug.se/strain?id=56051
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
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
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
72648Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13152.1StrainInfo: A central database for resolving microbial strain identifiers
123976Curators of the CIPCollection of Institut Pasteur (CIP 100653)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20100653