Strain identifier

BacDive ID: 7647

Type strain: Yes

Species: Kocuria rhizophila

Strain Designation: TA68

Strain history: CIP <- 1999, DSMZ <- 1995, G. Kovacs: strain TA68

NCBI tax ID(s): 72000 (species)

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General

@ref: 4541

BacDive-ID: 7647

DSM-Number: 11926

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

description: Kocuria rhizophila TA68 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from rhizosphere of Typha angustiflora.

NCBI tax id

  • NCBI tax id: 72000
  • Matching level: species

strain history

@refhistory
4541<- E. Stackebrandt <- G. Kovács; TA68
67770IFO 16319 <-- DSM 11926 <-- E. Stackebrandt <-- G. Kovács TA68.
122201CIP <- 1999, DSMZ <- 1995, G. Kovacs: strain TA68

doi: 10.13145/bacdive7647.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Kocuria
  • species: Kocuria rhizophila
  • full scientific name: Kocuria rhizophila Kovács et al. 1999

@ref: 4541

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Kocuria

species: Kocuria rhizophila

full scientific name: Kocuria rhizophila Kovács et al. 1999

strain designation: TA68

type strain: yes

Morphology

cell morphology

  • @ref: 122201
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18361Sulfur yellow (1016)10-14 daysISP 2
18361Sulfur yellow (1016)10-14 daysISP 3
18361Sulfur yellow (1016)10-14 daysISP 4
18361Sulfur yellow (1016)10-14 daysISP 5
18361Sulfur yellow (1016)10-14 daysISP 6
18361Sulfur yellow (1016)10-14 daysISP 7
122201

multicellular morphology

@refforms multicellular complexmedium name
18361noISP 2
18361noISP 3
18361noISP 4
18361noISP 5
18361noISP 6
18361noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4541TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.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
18361ISP 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
18361ISP 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
18361ISP 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
18361ISP 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
18361ISP 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
18361ISP 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:
41794MEDIUM 307 - for Kocuria rhizophilayesDistilled water make up to (1000.000 ml);Yeast extract (3.000 g);Tryptocasein soy agar (40.000 g)
122201CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122201CIP Medium 307yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=307

culture temp

@refgrowthtypetemperaturerange
18361positiveoptimum28mesophilic
4541positivegrowth30mesophilic
41794positivegrowth30mesophilic
60716positivegrowth30-37mesophilic
67770positivegrowth30mesophilic
122201positivegrowth25-37mesophilic
122201nogrowth41thermophilic
122201nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60716aerobe
122201obligate aerobe

halophily

  • @ref: 122201
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 6.5 %

murein

  • @ref: 4541
  • murein short key: A11.06
  • type: A3alpha L-Lys-L-Ala3

observation

  • @ref: 67770
  • observation: quinones: MK-7(H2), MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
122201606565hippurate-hydrolysis
12220117632nitrate-reduction
12220116301nitrite-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

  • @ref: 122201
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122201
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 122201
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
122201oxidase-
122201beta-galactosidase-3.2.1.23
122201alcohol dehydrogenase-1.1.1.1
122201gelatinase+/-
122201amylase-
122201DNase-
122201caseinase+3.4.21.50
122201catalase+1.11.1.6
122201coagulase-
122201tween esterase-
122201gamma-glutamyltransferase+2.3.2.2
122201lecithinase-
122201lipase-
122201lysine decarboxylase-4.1.1.18
122201ornithine decarboxylase-4.1.1.17
122201protease-
122201urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18361--+---+--+-+---+---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18361-+++++++------+----
122201+++++----++---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122201++-++--+--+--------------------+---+-------------+---+------++----------++-+-++++-------+-++----++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
4541rhizosphere of Typha angustifloraTypha angustifoliaSoroksar river (tributary of Danube river)HungaryHUNEurope
60716Rhizosphere of narrow-leaved cattailDanube riverHungaryHUNEurope
67770Rhizosphere of narrow-leaved cattail (Typha angustifolia) from a floating mat in the Soroksár tributary of the River DanubeTypha angustifoliaHungaryHUNEurope
122201Environment, Rhizosphere of Typha angustifloraSoroksar riverHungaryHUNEurope1995

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
45411Risk group (German classification)
183611
1222011Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Kocuria rhizophila 16S rRNA gene
  • accession: Y16264
  • length: 1471
  • database: ena
  • NCBI tax ID: 72000

Genome sequences

  • @ref: 67770
  • description: Kocuria rhizophila TA68
  • accession: GCA_003667225
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 72000

GC content

  • @ref: 4541
  • GC-content: 69.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.861no
flagellatedno97.644no
gram-positiveyes94.292no
anaerobicno99.322yes
aerobicyes86.529no
halophileyes55.561no
spore-formingno93.841no
glucose-utilyes88.165no
thermophileno93.085no
glucose-fermentno79.043no

External links

@ref: 4541

culture collection no.: DSM 11926, CCM 4950, IFO 16319, NBRC 16319, CCUG 55752, ATCC BAA 50, CIP 105972, JCM 11653, IAM 15065, LMG 19168

straininfo link

  • @ref: 77091
  • straininfo: 12993

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10028258Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia).Kovacs G, Burghardt J, Pradella S, Schumann P, Stackebrandt E, Marialigeti KInt J Syst Bacteriol10.1099/00207713-49-1-1671999Actinobacteria/*classification, Base Sequence, DNA, Bacterial/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plants/*microbiologyGenetics
Phylogeny12656171Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample.Reddy GSN, Prakash JSS, Prabahar V, Matsumoto GI, Stackebrandt E, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.02336-02003Antarctic Regions, Cyanobacteria/isolation & purification, Ecosystem, Micrococcaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, Pigmentation, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Water MicrobiologyEnzymology
Phylogeny30514593Kocuria tytonicola, new bacteria from the preen glands of American barn owls (Tyto furcata).Braun MS, Wang E, Zimmermann S, Boutin S, Wagner H, Wink MSyst Appl Microbiol10.1016/j.syapm.2018.11.0042018Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Germany, Micrococcaceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Strigiformes/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny30556804Kocuria tytonis sp. nov., isolated from the uropygial gland of an American barn owl (Tyto furcata).Braun MS, Wang E, Zimmermann S, Wagner H, Wink MInt J Syst Evol Microbiol10.1099/ijsem.0.0031702019Animal Structures/*microbiology, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Germany, Micrococcaceae/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Strigiformes/*microbiology, United States, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
4541Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11926)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11926
18361Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM11926.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
41794Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18050
60716Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55752)https://www.ccug.se/strain?id=55752
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
77091Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12993.1StrainInfo: A central database for resolving microbial strain identifiers
122201Curators of the CIPCollection of Institut Pasteur (CIP 105972)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105972