Strain identifier

BacDive ID: 7643

Type strain: Yes

Species: Kocuria palustris

Strain Designation: TAGA27

Strain history: CIP <- 1999, DSMZ <- E. Stackebrandt <- G. Kovacs: strain TAGA27

NCBI tax ID(s): 71999 (species)

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General

@ref: 4540

BacDive-ID: 7643

DSM-Number: 11925

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

description: Kocuria palustris TAGA27 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from rhizosphere of Typha angustiflora.

NCBI tax id

  • NCBI tax id: 71999
  • Matching level: species

strain history

@refhistory
4540<- E. Stackebrandt <- G. Kovács; TAGA27
67770IFO 16318 <-- DSM 11925 <-- E. Stackebrandt <-- G. Kovács TAGA27.
121518CIP <- 1999, DSMZ <- E. Stackebrandt <- G. Kovacs: strain TAGA27

doi: 10.13145/bacdive7643.20250331.9.3

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 palustris
  • full scientific name: Kocuria palustris Kovács et al. 1999

@ref: 4540

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Kocuria

species: Kocuria palustris

full scientific name: Kocuria palustris Kovács et al. 1999

strain designation: TAGA27

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121518positivecoccus-shapedno
125438no93.5
125438positive91.894
125439positive99.4

colony morphology

@refcolony colorincubation periodmedium used
18437Beige (1001)10-14 daysISP 2
18437Colorless10-14 daysISP 3
18437Beige (1001)10-14 daysISP 4
18437Sulfur yellow (1016)10-14 daysISP 5
18437Sulfur yellow (1016)10-14 daysISP 6
18437Sulfur yellow (1016)10-14 daysISP 7
121518

multicellular morphology

@refforms multicellular complexmedium name
18437noISP 2
18437noISP 3
18437noISP 4
18437noISP 5
18437noISP 6
18437noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4540TRYPTICASE 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
18437ISP 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
18437ISP 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:
18437ISP 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
18437ISP 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
18437ISP 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
18437ISP 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
38595MEDIUM 307 - for Kocuria rhizophilayesDistilled water make up to (1000.000 ml);Yeast extract (3.000 g);Tryptocasein soy agar (40.000 g)
121518CIP Medium 307yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=307

culture temp

@refgrowthtypetemperature
18437positiveoptimum28
4540positivegrowth30
38595positivegrowth30
59536positivegrowth30
67770positivegrowth30
121518positivegrowth25-37
121518nogrowth10
121518nogrowth41
121518nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59536aerobe
121518obligate aerobe

halophily

  • @ref: 121518
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 6.5 %

murein

  • @ref: 4540
  • murein short key: A11.06
  • type: A3alpha L-Lys-L-Ala3

observation

  • @ref: 67770
  • observation: quinones: MK-7(H2), MK-6(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837928087glycogen-fermentation
6837917992sucrose+fermentation
6837917716lactose+fermentation
6837917306maltose+fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose+fermentation
683795291gelatin-hydrolysis
6837916199urea+hydrolysis
683794853esculin-hydrolysis
6837917632nitrate+reduction
121518606565hippurate+hydrolysis
12151817632nitrate+reduction
12151816301nitrite-reduction
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
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
6837128053melibiose-builds acid from
6837117716lactose+builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837159640N-acetylglucosamine-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
6837116024D-mannose-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
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
12151835581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
12151815688acetoin-
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
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)-
68382valine arylamidase-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
121518oxidase-
121518beta-galactosidase+3.2.1.23
121518alcohol dehydrogenase-1.1.1.1
121518gelatinase-
121518amylase-
121518DNase-
121518caseinase-3.4.21.50
121518catalase+1.11.1.6
121518coagulase-
121518tween esterase-
121518gamma-glutamyltransferase+2.3.2.2
121518lecithinase-
121518lipase-
121518lysine decarboxylase-4.1.1.18
121518ornithine decarboxylase-4.1.1.17
121518protease-
121518urease+3.5.1.5
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alkaline phosphatase+3.1.3.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368arginine dihydrolase-3.5.3.6
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368lysine decarboxylase-4.1.1.18
68368beta-galactosidase-3.2.1.23

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18437++-+-++--+-+---+++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18437+---+--+-+--+-+----
121518+--------+--+-+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18437------+--+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121518-----+/----+++----------------+-+/---------+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121518++++---+-+++++------------+----+-+-+------------++-------------++--------------++---------+-+++-+-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
4540rhizosphere of Typha angustifloraTypha angustifoliaSoroksar river (tributary of Danube river)HungaryHUNEurope
59536Rhizosphere of Typha angustifloraHungaryHUNEurope
67770Rhizosphere of narrow-leaved cattail (Typha angustifolia) from a floating mat in the Soroksár tributary of the River DanubeTypha angustifoliaHungaryHUNEurope
121518Environment, 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
184371Hazard group
45401Risk group (German classification)
1215181Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Kocuria palustris 16S rRNA gene
  • accession: Y16263
  • length: 1467
  • database: nuccore
  • NCBI tax ID: 71999

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kocuria palustris TAGA27GCA_016907795contigncbi71999
66792Kocuria palustris strain TAGA2771999.21wgspatric71999
66792Kocuria palustris DSM 119252893684298draftimg71999
66792Kocuria palustris TAGA272562617128draftimg71999

GC content

  • @ref: 4540
  • GC-content: 69.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.894no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.762yes
125438spore-formingspore-formingAbility to form endo- or exosporesno82.792no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.663no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.5yes
125438motile2+flagellatedAbility to perform flagellated movementno93.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno77.6
125439BacteriaNetmotilityAbility to perform movementno77.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe85.6

External links

@ref: 4540

culture collection no.: DSM 11925, CCM 4949, IFO 16318, NBRC 16318, CCUG 52395, CIP 105971, JCM 11652, IAM 15064, LMG 19167

straininfo link

  • @ref: 77087
  • straininfo: 12992

literature

  • topic: Phylogeny
  • Pubmed-ID: 10028258
  • title: Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia).
  • authors: Kovacs G, Burghardt J, Pradella S, Schumann P, Stackebrandt E, Marialigeti K
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-49-1-167
  • year: 1999
  • mesh: Actinobacteria/*classification, Base Sequence, DNA, Bacterial/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plants/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
4540Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11925)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11925
18437Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM11925.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
38595Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18049
59536Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52395)https://www.ccug.se/strain?id=52395
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
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
77087Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12992.1StrainInfo: A central database for resolving microbial strain identifiers
121518Curators of the CIPCollection of Institut Pasteur (CIP 105971)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105971
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1