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, Gram-positive, coccus-shaped

description: Kocuria rhizophila TA68 is an aerobe, Gram-positive, coccus-shaped 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/bacdive7647.20240916.9.1

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

@refgram staincell shapemotilityconfidence
122201positivecoccus-shapedno
69480positive94.126
69480no94

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

@refgrowthtypetemperature
18361positiveoptimum28
4541positivegrowth30
41794positivegrowth30
60716positivegrowth30-37
67770positivegrowth30
122201positivegrowth25-37
122201nogrowth41
122201nogrowth45

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: nuccore
  • 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

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes94.126no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.948yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.76no
69480spore-formingspore-formingAbility to form endo- or exosporesno77.282no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97yes
69480flagellatedmotile2+Ability to perform flagellated movementno94no

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
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)
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