Strain identifier

BacDive ID: 7609

Type strain: Yes

Species: Paeniglutamicibacter kerguelensis

Strain Designation: KGN15

Strain history: CIP <- 2005, JCM <- S. Shivaji: strain KGN15

NCBI tax ID(s): 254788 (species)

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General

@ref: 6109

BacDive-ID: 7609

DSM-Number: 15797

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

description: Paeniglutamicibacter kerguelensis KGN15 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sea water.

NCBI tax id

  • NCBI tax id: 254788
  • Matching level: species

strain history

@refhistory
6109<- S. Shivaji; KGN15
67770S. Shivaji KGN15.
120405CIP <- 2005, JCM <- S. Shivaji: strain KGN15

doi: 10.13145/bacdive7609.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Paeniglutamicibacter
  • species: Paeniglutamicibacter kerguelensis
  • full scientific name: Paeniglutamicibacter kerguelensis (Gupta et al. 2004) Busse 2016

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter kerguelensis

@ref: 6109

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Paeniglutamicibacter

species: Paeniglutamicibacter kerguelensis

full scientific name: Paeniglutamicibacter kerguelensis (Gupta et al. 2004) Busse 2016

strain designation: KGN15

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31239positiverod-shapedno
69480positive100
120405positiverod-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
18397Zinc yellow (1018)10-14 daysISP 2
18397Zinc yellow (1018)10-14 daysISP 3
18397Zinc yellow (1018)10-14 daysISP 4
18397Zinc yellow (1018)10-14 daysISP 5
18397Zinc yellow (1018)10-14 daysISP 6
18397Zinc yellow (1018)10-14 daysISP 7
120405

multicellular morphology

@refforms multicellular complexmedium name
18397noISP 2
18397noISP 3
18397noISP 4
18397noISP 5
18397noISP 6
18397noISP 7

pigmentation

  • @ref: 31239
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6109TRYPTICASE 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
18397ISP 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
18397ISP 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:
18397ISP 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
18397ISP 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
18397ISP 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
18397ISP 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
39773MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120405CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120405CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338

culture temp

@refgrowthtypetemperaturerange
18397positiveoptimum28mesophilic
6109positivegrowth22psychrophilic
31239positivegrowth04-30
31239positiveoptimum22psychrophilic
39773positivegrowth22psychrophilic
67770positivegrowth22psychrophilic
120405positivegrowth10-25psychrophilic
120405nogrowth37mesophilic
120405nogrowth41thermophilic
120405nogrowth45thermophilic

culture pH

  • @ref: 31239
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31239aerobe
120405obligate aerobe

spore formation

@refspore formationconfidence
31239no
69481no95
69480no99.974

halophily

  • @ref: 120405
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9, MK-8, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1839717234glucose+
1839722599arabinose+
1839717992sucrose+
1839718222xylose-
1839717268myo-inositol+
1839729864mannitol-
1839728757fructose+
1839726546rhamnose+
1839716634raffinose+
1839762968cellulose-
3123922599arabinose+carbon source
3123929016arginine+carbon source
3123922653asparagine+carbon source
3123928757fructose+carbon source
3123928260galactose+carbon source
3123929987glutamate+carbon source
3123927570histidine+carbon source
3123937684mannose+carbon source
3123928053melibiose+carbon source
3123915361pyruvate+carbon source
3123926546rhamnose+carbon source
3123930911sorbitol+carbon source
3123917992sucrose+carbon source
3123927082trehalose+carbon source
3123917151xylitol+carbon source
3123918222xylose+carbon source
312394853esculin+hydrolysis
12040516947citrate+carbon source
1204054853esculin+hydrolysis
120405606565hippurate+hydrolysis
12040517632nitrate-reduction
12040516301nitrite-reduction
12040517632nitrate-respiration
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917992sucrose-fermentation

antibiotic resistance

  • @ref: 120405
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120405
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12040515688acetoin-
12040517234glucose-

enzymes

@refvalueactivityec
31239catalase+1.11.1.6
31239gelatinase+
31239cytochrome oxidase+1.9.3.1
31239urease+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
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
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
120405oxidase-
120405beta-galactosidase+3.2.1.23
120405alcohol dehydrogenase-1.1.1.1
120405gelatinase-
120405amylase-
120405DNase-
120405caseinase-3.4.21.50
120405catalase+1.11.1.6
120405tween esterase-
120405gamma-glutamyltransferase+2.3.2.2
120405lecithinase-
120405lipase-
120405lysine decarboxylase-4.1.1.18
120405ornithine decarboxylase-4.1.1.17
120405phenylalanine ammonia-lyase-4.3.1.24
120405tryptophan deaminase-
120405urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18397++--++-+++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18397-++-++++---++-++-+-
120405++++++++-++++-++-+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120405-++---+-+++---------------+----+-----------------+---+---+++++++--+----+++-+--+++--------++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
6109sea waterKerguelenAustralia and Oceania
67770Seawater at a site located 110 km south-west of the Kerguelen IslandAntarcticaAntarcticaATA
120405Environment, Sea waterAntarcticaAntarcticaATA

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_56645.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_158;97_169;98_188;99_56645&stattab=map
  • Last taxonomy: Paeniglutamicibacter
  • 16S sequence: AJ606062
  • Sequence Identity:
  • Total samples: 724
  • soil counts: 390
  • aquatic counts: 83
  • animal counts: 196
  • plant counts: 55

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61091Risk group (German classification)
183971
1204051Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6109
  • description: Arthrobacter kerguelensis 16S rRNA gene, type strain KGN15
  • accession: AJ606062
  • length: 1482
  • database: ena
  • NCBI tax ID: 254788

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paeniglutamicibacter kerguelensis DSM 15797GCA_017876535contigncbi254788
66792Paeniglutamicibacter kerguelensis strain DSM 15797254788.3wgspatric254788
66792Paeniglutamicibacter kerguelensis DSM 157972918371629draftimg254788

GC content

@refGC-content
610956
3123958

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileno68.997yes
gram-positiveyes86.867yes
anaerobicno99.547yes
aerobicyes93.574yes
halophileno77.793no
spore-formingno84.069yes
glucose-utilyes84.458yes
flagellatedno90.99no
thermophileno98.849yes
glucose-fermentno84.179no

External links

@ref: 6109

culture collection no.: DSM 15797, CIP 108629, JCM 12165

straininfo link

  • @ref: 77053
  • straininfo: 134412

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545486Arthrobacter gangotriensis sp. nov. and Arthrobacter kerguelensis sp. nov. from Antarctica.Gupta P, Reddy GSN, Delille D, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.63110-02004Antarctic Regions, Arthrobacter/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Cell Wall/chemistry, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/chemistry/isolation & purification, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry/isolation & purification, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysis/chemistry/isolation & purification, Water MicrobiologyEnzymology
Phylogeny33555249Paeniglutamicibacter terrestris sp. nov., isolated from phenanthrene-degrading consortium enriched from Antarctic soil.Sakdapetsiri C, Kuntaveesuk A, Ngaemthao W, Suriyachadkun C, Muangchinda C, Chavanich S, Viyakarn V, Chen B, Pinyakong OInt J Syst Evol Microbiol10.1099/ijsem.0.0046892021

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6109Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15797)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15797
18397Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM15797.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
31239Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2756328776041
39773Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6279
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/
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
77053Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134412.1StrainInfo: A central database for resolving microbial strain identifiers
120405Curators of the CIPCollection of Institut Pasteur (CIP 108629)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108629