Strain identifier

BacDive ID: 3214

Type strain: Yes

Species: Corynebacterium caspium

Strain Designation: M106/00/5

Strain history: CIP <- 2003, CCUG <- L. Hoyles, Reading, UK <- G. Foster, SAC, Inverness, Scotland, UK: strain M106/00/5

NCBI tax ID(s): 1121355 (strain), 234828 (species)

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General

@ref: 12120

BacDive-ID: 3214

DSM-Number: 44850

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, rod-shaped, animal pathogen

description: Corynebacterium caspium M106/00/5 is a facultative anaerobe, mesophilic, Gram-positive animal pathogen that was isolated from caspian seal, penis.

NCBI tax id

NCBI tax idMatching level
1121355strain
234828species

strain history

@refhistory
12120<- CCUG <- L. Hoyles and M. D. Collins; M106/00/5 <- G. Foster, SAC, Inverness
67770CCUG 44566 <-- L. Hoyles and M. D. Collins M/106/00/5 <-- G. Foster.
117204CIP <- 2003, CCUG <- L. Hoyles, Reading, UK <- G. Foster, SAC, Inverness, Scotland, UK: strain M106/00/5

doi: 10.13145/bacdive3214.20230509.8.1

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 caspium
  • full scientific name: Corynebacterium caspium Collins et al. 2004

@ref: 12120

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium caspium

full scientific name: Corynebacterium caspium Collins et al. 2004 emend. Nouioui et al. 2018

strain designation: M106/00/5

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
23199positiverod-shapedno
69480no97.328
69480positive100
117204positiverod-shapedno

colony morphology

@refincubation periodmedium usedtype of hemolysiscolony sizecolony shape
1971110-14 daysISP 2
1971110-14 daysISP 3
1971110-14 daysISP 4
1971110-14 daysISP 5
1971110-14 daysISP 6
1971110-14 daysISP 7
231993 daysgamma0.5-2 mmcircular
117204

multicellular morphology

@refforms multicellular complexmedium name
19711noISP 2
19711noISP 3
19711noISP 4
19711noISP 5
19711noISP 6
19711noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12120COLUMBIA 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
19711ISP 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
19711ISP 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:
19711ISP 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
19711ISP 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
19711ISP 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
19711ISP 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
33863MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
117204CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
19711positiveoptimum37mesophilic
12120positivegrowth37mesophilic
33863positivegrowth37mesophilic
56384positivegrowth22-42
67770positivegrowth37mesophilic
117204positivegrowth30-37mesophilic
117204nogrowth10psychrophilic
117204nogrowth15psychrophilic
117204nogrowth41thermophilic
117204nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23199facultative anaerobe
56384aerobe
117204facultative anaerobe

spore formation

@refspore formationconfidence
23199no
69481no100
69480no99.985

halophily

@refsaltgrowthtested relationconcentration
117204NaClpositivegrowth0-4 %
117204NaClnogrowth6 %
117204NaClnogrowth8 %
117204NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2319965327D-xylose-builds acid from
2319928087glycogen-builds acid from
2319917716lactose-builds acid from
2319917306maltose-builds acid from
2319929864mannitol-builds acid from
2319917992sucrose-builds acid from
231994853esculin-hydrolysis
231995291gelatin-hydrolysis
2319917632nitrate-reduction
2319916988D-ribose+builds acid from
2319917234glucose+builds acid from
2319916199urea+hydrolysis
68371Potassium 2-ketogluconate-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
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
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836930849L-arabinose-assimilation
683695291gelatin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11720416947citrate-carbon source
1172044853esculin-hydrolysis
117204606565hippurate+hydrolysis
11720417632nitrate-reduction
11720416301nitrite-reduction
11720445285pyrazinamide-hydrolysis
11720417632nitrate+respiration
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11720435581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
11720415688acetoin-
11720417234glucose+

enzymes

@refvalueactivityec
23199acid phosphatase-3.1.3.2
23199alkaline phosphatase-3.1.3.1
23199alpha-fucosidase-3.2.1.51
23199alpha-galactosidase-3.2.1.22
23199alpha-glucosidase-3.2.1.20
23199alpha-mannosidase-3.2.1.24
23199beta-galactosidase-3.2.1.23
23199beta-glucosidase-3.2.1.21
23199beta-glucuronidase-3.2.1.31
23199catalase+1.11.1.6
23199chymotrypsin-3.4.4.5
23199cystine arylamidase-3.4.11.3
23199cytochrome oxidase-1.9.3.1
23199esterase (C 4)+
23199esterase lipase (C 8)+
23199leucine arylamidase-3.4.11.1
23199lipase (C 14)-
23199N-acetyl-beta-glucosaminidase-3.2.1.52
23199phosphoamidase-3.9.1.1
23199pyrazinamidase+3.5.1.B15
23199pyrrolidonyl arylamidase-3.4.19.3
23199trypsin+3.4.21.4
23199valine arylamidase-
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
68382lipase (C 14)-
68382alkaline phosphatase-3.1.3.1
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
68369gelatinase-
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
117204oxidase-
117204beta-galactosidase-3.2.1.23
117204alcohol dehydrogenase-1.1.1.1
117204gelatinase-
117204amylase-
117204DNase+
117204catalase+1.11.1.6
117204tween esterase-
117204gamma-glutamyltransferase-2.3.2.2
117204lecithinase-
117204lipase-
117204lysine decarboxylase-4.1.1.18
117204ornithine decarboxylase+4.1.1.17
117204phenylalanine ammonia-lyase-4.3.1.24
117204tryptophan deaminase-
117204urease+3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
19711+-------+--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19711-++-++++-----------
12120-+/-+/-----+/-------------
117204-++-+----++---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
12120----++/---+/--+/----+/---+/---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117204----+-----+++/----------------------------------+/--+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
117204++-----------------+-----------------------------+----------+--------------+---++------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datehost species
12120caspian seal, penisInverness, Caspian seaUnited KingdomGBREurope
56384Caspian seal,penisCaspian sea2000-06-01
67770Penis of Caspian seal (Phoca caspica)Phoca caspica
117204Caspian seal, penis and lung

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Host#Mammals#Aquatic mammal
#Host Body-Site#Urogenital tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_162628.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_61094;97_79140;98_106953;99_162628&stattab=map
  • Last taxonomy: Corynebacterium caspium subclade
  • 16S sequence: AJ566641
  • Sequence Identity:
  • Total samples: 47
  • soil counts: 2
  • aquatic counts: 3
  • animal counts: 42

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
12120yes, in single cases1Risk group (German classification)
197112Risk group (German classification)
1172042Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium caspium strain CIP 107965 16S ribosomal RNA gene, partial sequenceAY965876443ena234828
23199Corynebacterium caspium partial 16S rRNA gene, type strain CCUG 44566TAJ5666411351nuccore234828

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium caspium DSM 448501121355.3wgspatric1121355
66792Corynebacterium caspium DSM 448502515154055draftimg1121355
67770Corynebacterium caspium DSM 44850GCA_000379705scaffoldncbi1121355

GC content

  • @ref: 67770
  • GC-content: 49.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.998yes
flagellatedno97.855yes
gram-positiveyes94.118yes
anaerobicno97.817no
aerobicno89.738no
halophileyes82.638no
spore-formingno94.651yes
glucose-utilyes88.328no
thermophileno96.479yes
glucose-fermentno51.222yes

External links

@ref: 12120

culture collection no.: DSM 44850, CCUG 44566, CIP 107965, JCM 13387

straininfo link

  • @ref: 72729
  • straininfo: 100452

literature

  • topic: Phylogeny
  • Pubmed-ID: 15143043
  • title: Corynebacterium caspium sp. nov., from a Caspian seal (Phoca caspica).
  • authors: Collins MD, Hoyles L, Foster G, Falsen E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02950-0
  • year: 2004
  • mesh: Animals, Corynebacterium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Male, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seals, Earless/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12120Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44850)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44850
19711Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44850.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
23199Matthew D. Collins, Lesley Hoyles, Geoffrey Foster, Enevold Falsen10.1099/ijs.0.02950-0Corynebacterium caspium sp. nov., from a Caspian seal (Phoca caspica)IJSEM 54: 925-928 200415143043
33863Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5534
56384Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 44566)https://www.ccug.se/strain?id=44566
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
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
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
72729Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100452.1StrainInfo: A central database for resolving microbial strain identifiers
117204Curators of the CIPCollection of Institut Pasteur (CIP 107965)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107965