Strain identifier

BacDive ID: 3209

Type strain: Yes

Species: Corynebacterium halotolerans

Strain history: CIP <- 2005, DSMZ <- W. J. Li <- CCTCC <- YIM: strain YIM 70093

NCBI tax ID(s): 1121362 (strain), 225326 (species)

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General

@ref: 11998

BacDive-ID: 3209

DSM-Number: 44683

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

description: Corynebacterium halotolerans CCUG 54529 is an aerobe, halotolerant, mesophilic bacterium that was isolated from saline soil.

NCBI tax id

NCBI tax idMatching level
1121362strain
225326species

strain history

@refhistory
11998<- W.-J. Li <- CCTCC <- YIM
67770DSM 44683 <-- W.-J. Li YIM 70093.
119824CIP <- 2005, DSMZ <- W. J. Li <- CCTCC <- YIM: strain YIM 70093

doi: 10.13145/bacdive3209.20230509.8.1

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 halotolerans
  • full scientific name: Corynebacterium halotolerans Chen et al. 2004

@ref: 11998

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium halotolerans

full scientific name: Corynebacterium halotolerans Chen et al. 2004 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
23194positiverod-shapedno
30093positiverod-shapedno
69480no95.825
69480positive100
119824positiveoval-shapedno

colony morphology

@refcolony colorincubation periodmedium usedcolony sizecolony shape
20094Zinc yellow (1018)10-14 daysISP 2
2009410-14 daysISP 3
2009410-14 daysISP 4
2009410-14 daysISP 5
20094Zinc yellow (1018)10-14 daysISP 6
2009410-14 daysISP 7
23194yellow1 dayISP 5 medium, trypticase/soy agar and Mueller-Hinton agar0.5-1.5 mmcircular
602172 days
119824

multicellular morphology

@refforms multicellular complexmedium name
20094noISP 2
20094noISP 3
20094noISP 4
20094noISP 5
20094noISP 6
20094noISP 7

pigmentation

  • @ref: 30093
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11998TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
11998COLUMBIA 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
20094ISP 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
20094ISP 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:
20094ISP 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
20094ISP 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
20094ISP 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
20094ISP 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
23194ISP 5 medium, trypticase/soy agar and Mueller-Hinton agaryes
37454MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119824CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20094positiveoptimum37mesophilic
11998positivegrowth37mesophilic
23194positiveoptimum28mesophilic
30093positiveoptimum28mesophilic
37454positivegrowth37mesophilic
60217positivegrowth37mesophilic
67770positivegrowth28mesophilic

culture pH

  • @ref: 30093
  • ability: positive
  • type: optimum
  • pH: 7.2

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23194aerobe
30093aerobe
60217aerobe
119824obligate aerobe

spore formation

@refspore formationconfidence
23194no
30093no
69481no100
69480no99.997

halophily

@refhalophily levelsaltgrowthtested relationconcentration
23194halotolerantKClpositiveoptimum10 %
23194NaClpositiveoptimum10 %
23194MgCl2positiveoptimum10 %
30093NaClpositiveoptimum10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2009417234glucose+
2009422599arabinose-
2009417992sucrose-
2009418222xylose-
2009417268myo-inositol-
2009429864mannitol+
2009428757fructose+
2009426546rhamnose-
2009416634raffinose-
2009462968cellulose-
2319427613amygdalin-carbon source
2319417057cellobiose-carbon source
2319428757fructose-carbon source
2319417716lactose-carbon source
2319417632nitrate-reduction
2319417234glucose+builds acid from
2319440585alpha-cyclodextrin+carbon source
2319422599arabinose+carbon source
2319428260galactose+carbon source
2319417234glucose+carbon source
2319417306maltose+carbon source
2319429864mannitol+carbon source
2319437684mannose+carbon source
2319433942ribose+carbon source
2319417814salicin+carbon source
2319428017starch+carbon source
2319417992sucrose+carbon source
2319418222xylose+carbon source
2319428017starch+hydrolysis
2319417632nitrate+reduction
3009322599arabinose+carbon source
3009323652dextrin+carbon source
3009328260galactose+carbon source
300935291gelatin+carbon source
3009317234glucose+carbon source
3009317306maltose+carbon source
3009329864mannitol+carbon source
3009337684mannose+carbon source
3009333942ribose+carbon source
3009317814salicin+carbon source
3009317992sucrose+carbon source
3009316199urea+carbon source
3009318222xylose+carbon source
3009317632nitrate+reduction
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
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
6837117754glycerol-builds acid from
11982417632nitrate+reduction
11982416301nitrite-reduction
683794853esculin-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose+fermentation

metabolite production

  • @ref: 119824
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
23194alpha-galactosidase-3.2.1.22
23194arginine dihydrolase-3.5.3.6
23194beta-galactosidase-3.2.1.23
23194beta-glucosidase-3.2.1.21
23194beta-glucuronidase+3.2.1.31
23194lipase (C 14)+
23194lysine decarboxylase-4.1.1.18
23194N-acetyl-beta-glucosaminidase-3.2.1.52
23194ornithine decarboxylase-4.1.1.17
30093catalase+1.11.1.6
30093gelatinase+
30093urease+3.5.1.5
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
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
68379gelatinase-
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
119824oxidase+
119824alcohol dehydrogenase-1.1.1.1
119824catalase+1.11.1.6
119824lysine decarboxylase-4.1.1.18
119824ornithine decarboxylase-4.1.1.17
119824urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
20094+-+-----+/--+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20094+++-+--------+-----
119824+++-+--+-----+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119824----+/------+/-+/-+/------------------------------------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11998saline soilAiding Lake in Xinnjiang provinceChinaCHNAsia
60217Saline soilChinaCHNAsia
67770Saline soilXinjiang ProvinceChinaCHNAsia
119824Environment, Saline soilChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119981Risk group (German classification)
1198242Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium halotolerans strain DSM 44683 16S ribosomal RNA gene, partial sequenceDQ002919420ena1121362
11998Corynebacterium halophilum 16S ribosomal RNA gene, partial sequenceAY2265091492ena1121362

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium halotolerans YIM 70093 = DSM 44683GCA_000341345completencbi1121362
66792Corynebacterium halotolerans YIM 70093 = DSM 446831121362.3completepatric1121362
66792Corynebacterium halotolerans YIM 70093 = DSM 446831121362.6wgspatric1121362
66792Corynebacterium halotolerans YIM 70093 = DSM 446831121362.10plasmidpatric1121362
66792Corynebacterium halotolerans YIM 70093, DSM 446832524023198completeimg1121362
66792Corynebacterium halotolerans YIM 70093, DSM 446832556921045draftimg1121362
67770Corynebacterium halotolerans YIM 70093 = DSM 44683GCA_000688435contigncbi1121362

GC content

@refGC-contentmethod
1199863
2319463.0Thermal denaturation, fluorometry
6777063thermal denaturation, midpoint method (Tm)
6777068.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.347yes
flagellatedno98.696yes
gram-positiveyes92.884yes
anaerobicno99.403yes
aerobicyes89.554yes
halophileyes84.8yes
spore-formingno92.436yes
glucose-utilyes87.519yes
thermophileno98.038yes
glucose-fermentno54.751no

External links

@ref: 11998

culture collection no.: CCUG 54529, DSM 44683, CCTCC AA 001024, CIP 108972, JCM 12676, YIM 70093, KCTC 19015

straininfo link

  • @ref: 72724
  • straininfo: 132014

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143024Corynebacterium halotolerans sp. nov., isolated from saline soil in the west of China.Chen HH, Li WJ, Tang SK, Kroppenstedt RM, Stackebrandt E, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.02919-02004Cell Wall/chemistry, China, Corynebacterium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Membrane Lipids/analysis, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sodium Chloride, Soil MicrobiologyGenetics
Phylogeny19622641Corynebacterium maris sp. nov., a marine bacterium isolated from the mucus of the coral Fungia granulosa.Ben-Dov E, Ben Yosef DZ, Pavlov V, Kushmaro AInt J Syst Evol Microbiol10.1099/ijs.0.007468-02009Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Corynebacterium/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny19783605Corynebacterium marinum sp. nov. isolated from coastal sediment.Du ZJ, Jordan EM, Rooney AP, Chen GJ, Austin BInt J Syst Evol Microbiol10.1099/ijs.0.018523-02009Corynebacterium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Genetics23408721Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093(T) (= DSM 44683(T)).Ruckert C, Albersmeier A, Al-Dilaimi A, Niehaus K, Szczepanowski R, Kalinowski JStand Genomic Sci10.4056/sigs.32366912012

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
11998Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44683)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44683
20094Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44683.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
23194Hua-Hong Chen, Wen-Jun Li, Shu-Kun Tang, Reiner M. Kroppenstedt, Erko Stackebrandt, Li-Hua Xu, Cheng-Lin Jiang10.1099/ijs.0.02919-0Corynebacterium halotolerans sp. nov., isolated from saline soil in the west of ChinaIJSEM 54: 779-782 200415143024
30093Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126450
37454Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6661
60217Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54529)https://www.ccug.se/strain?id=54529
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
72724Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132014.1StrainInfo: A central database for resolving microbial strain identifiers
119824Curators of the CIPCollection of Institut Pasteur (CIP 108972)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108972