Strain identifier

BacDive ID: 3134

Type strain: Yes

Species: Corynebacterium amycolatum

Strain Designation: S160

Strain history: NCFB 2768 <-- R. R. Marples S160.

NCBI tax ID(s): 43765 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2888

BacDive-ID: 3134

DSM-Number: 6922

keywords: 16S sequence, genome sequence, Bacteria, mesophilic, human pathogen

description: Corynebacterium amycolatum S160 is a mesophilic human pathogen that was isolated from human skin.

NCBI tax id

  • NCBI tax id: 43765
  • Matching level: species

strain history

doi: 10.13145/bacdive3134.20220920.7

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 amycolatum
  • full scientific name: Corynebacterium amycolatum Collins et al. 1988

@ref: 2888

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium amycolatum

full scientific name: Corynebacterium amycolatum Collins et al. 1988

strain designation: S160

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
20198Light ivory (1015)10-14 daysISP 2
20198Oyster white (1013)10-14 daysISP 4
20198Ivory (1014)10-14 daysISP 5
20198Sand yellow (1002)10-14 daysISP 6
20198Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20198noISP 2
20198noISP 4
20198noISP 5
20198noISP 6
20198noISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
2888https://www.dsmz.de/microorganisms/photos/DSM_6922-1.jpg© Leibniz-Institut DSMZ
2888https://www.dsmz.de/microorganisms/photos/DSM_6922.jpg© Leibniz-Institut DSMZMedium 535a 37°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2888TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://bacmedia.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
2888COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://bacmedia.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
20198ISP 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
20198ISP 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
20198ISP 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
20198ISP 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
20198ISP 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
34280MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)

culture temp

@refgrowthtypetemperaturerange
20198positiveoptimum28mesophilic
2888positivegrowth37mesophilic
34280positivegrowth37mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

halophily

  • @ref: 20198
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

murein

  • @ref: 2888
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2) (MK-8(H2))

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2019817234glucose+
2019822599arabinose-
2019817992sucrose-
2019818222xylose-
2019817268myo-inositol-
2019829864mannitol-
2019828757fructose+
2019826546rhamnose-
2019816634raffinose-
2019862968cellulose-
6837917992sucrose-fermentation
6837917306maltose+fermentation
6837917634D-glucose+fermentation
683795291gelatin-hydrolysis
6837916199urea+hydrolysis
683794853esculin-hydrolysis
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
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
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
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
20198+--+-----+-++++++-+
2888---+-----+-++/---+----+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20198+++++----++--------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARA
20198------+--+-+--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
2888human skin
52916Human cutaneousUnited KingdomGBREurope
67770Human skin

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Organ#Skin, Nail, Hair

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
2888yesyes2Risk group (German classification)
201982German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium amycolatum partial 16S rRNA gene, culture collection CCUG:35685FN6687351378ena43765
20218Corynebacterium amycolatum partial 16S rRNA gene, type strain CCUG 35685THE5862711304ena43765
20218Corynebacterium amycolatum partial 16S-23S rRNA IGS, type strain CCUG 35685THE586286361ena43765
20218C.amycolatum 16S ribosomal DNAX820571401ena43765
20218Corynebacterium amycolatum strain DSM 6922 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536502394ena43765
20218Corynebacterium amycolatum gene for 16S rRNA, partial sequenceAB470624544ena43765
20218Corynebacterium amycolatum DNA, 16S-23S ribosomal RNA intergenic spacer, partial sequenceAB477423762ena43765
20218Corynebacterium amycolatum 16S rRNA gene, strain NCFB 2768X842441476ena43765

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium amycolatum strain FDAARGOS_1189 strain Not applicable43765.128completepatric43765
66792Corynebacterium amycolatum strain LK2343765.79wgspatric43765
66792Corynebacterium amycolatum DSM 6922 Genome Sequencing2617270851completeimg43765

GC content

  • @ref: 2888
  • GC-content: 61
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 2888

culture collection no.: DSM 6922, ATCC 49368, NCFB 2768, CCUG 35685, LMG 19043, JCM 7447, CCM 4123, CECT 4163, CGMCC 1.1939, CIP 103452, IFO 15207, KCTC 3432, NBRC 15207, NCIMB 13130

straininfo link

@refpassport
20218http://www.straininfo.net/strains/48859
20218http://www.straininfo.net/strains/48857
20218http://www.straininfo.net/strains/48861

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology8370733Comparative chemotaxonomic studies of mycolic acid-free coryneform bacteria of human origin.Barreau C, Bimet F, Kiredjian M, Rouillon N, Bizet CJ Clin Microbiol10.1128/jcm.31.8.2085-2090.19931993Actinomycetales/*chemistry/classification, Chromatography, Thin Layer, Electrophoresis, Polyacrylamide Gel, Humans, Mycolic Acids/*analysis, PhenotypePathogenicity
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
Metabolism23811360Identification and characterization of the channel-forming protein in the cell wall of Corynebacterium amycolatum.Soltan Mohammadi N, Mafakheri S, Abdali N, Barcena-Uribarri I, Tauch A, Benz RBiochim Biophys Acta10.1016/j.bbamem.2013.06.0242013Amino Acid Sequence, Bacterial Proteins/chemistry/genetics/*metabolism, Base Sequence, Cell Wall/*metabolism, Cloning, Molecular, Corynebacterium/*metabolism, DNA Primers, Drug Resistance, Microbial, Lipid Bilayers, Molecular Sequence Data, Porins/chemistry/genetics/*metabolism, Recombinant Proteins/genetics/metabolism, Sequence Homology, Amino AcidEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2888Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6922)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6922
20198Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM6922.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
34280Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15251
52916Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 35685)https://www.ccug.se/strain?id=35685
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