Strain identifier

BacDive ID: 7767

Type strain: Yes

Species: Nesterenkonia sandarakina

Strain history: CIP <- 2005, DSMZ <- W.L. Li

NCBI tax ID(s): 272918 (species)

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General

@ref: 6019

BacDive-ID: 7767

DSM-Number: 15664

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

description: Nesterenkonia sandarakina DSM 15664 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 272918
  • Matching level: species

strain history

@refhistory
6019<- W.-J. Li
67770KCTC 19011 <-- W.-J. Li YIM 70009.
67771<- W. J. Li
122412CIP <- 2005, DSMZ <- W.L. Li

doi: 10.13145/bacdive7767.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Nesterenkonia
  • species: Nesterenkonia sandarakina
  • full scientific name: Nesterenkonia sandarakina Li et al. 2005

@ref: 6019

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Nesterenkonia

species: Nesterenkonia sandarakina

full scientific name: Nesterenkonia sandarakina Li et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31313positivecoccus-shapedno
67771positive
122412negativeoval-shapedyes

colony morphology

  • @ref: 122412

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6019ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
42043Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122412CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6019positivegrowth28mesophilic
42043positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
122412positivegrowth10-30
122412nogrowth37mesophilic
122412nogrowth41thermophilic

culture pH

@refabilitytypepHPH range
31313positivegrowth05-12alkaliphile
31313positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
122412obligate aerobe

spore formation

  • @ref: 31313
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31313NaClpositivegrowth01-15 %
31313NaClpositiveoptimum5 %

murein

  • @ref: 6019
  • murein short key: A11.42
  • type: A4alpha L-Lys-Gly-D-Asp

observation

@refobservation
67770quinones: MK-7, MK-8
67771quinones: MK-7, MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3131322599arabinose+carbon source
3131317057cellobiose+carbon source
3131323652dextrin+carbon source
3131328757fructose+carbon source
3131328260galactose+carbon source
3131317234glucose+carbon source
3131317306maltose+carbon source
3131329864mannitol+carbon source
3131337684mannose+carbon source
3131333942ribose+carbon source
3131317814salicin+carbon source
3131317992sucrose+carbon source
3131327082trehalose+carbon source
3131318222xylose+carbon source
122412606565hippurate-hydrolysis
12241217632nitrate-reduction
12241216301nitrite-reduction

metabolite production

  • @ref: 122412
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 122412
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
31313catalase+1.11.1.6
122412oxidase-
122412beta-galactosidase+3.2.1.23
122412alcohol dehydrogenase-1.1.1.1
122412gelatinase+/-
122412amylase-
122412DNase-
122412caseinase+3.4.21.50
122412catalase+1.11.1.6
122412coagulase-
122412tween esterase-
122412gamma-glutamyltransferase-2.3.2.2
122412lecithinase-
122412lipase-
122412lysine decarboxylase-4.1.1.18
122412ornithine decarboxylase-4.1.1.17
122412phenylalanine ammonia-lyase-4.3.1.24
122412urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122412--++-++-+--+---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6019soileastern desertEgyptEGYAfrica
67770Desert soilEgyptEGYAfrica
67771Desert soilEgyptEGYAfrica
122412Environment, Soil sampleEastern desertEgyptEGYAfrica

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2896.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1530;97_1826;98_2239;99_2896&stattab=map
  • Last taxonomy: Nesterenkonia
  • 16S sequence: AY588277
  • Sequence Identity:
  • Total samples: 3970
  • soil counts: 791
  • aquatic counts: 600
  • animal counts: 2130
  • plant counts: 449

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
60191Risk group (German classification)
1224121Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6019
  • description: Nesterenkonia sandarakina strain YIM 70009 16S ribosomal RNA gene, partial sequence
  • accession: AY588277
  • length: 1461
  • database: ena
  • NCBI tax ID: 272918

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nesterenkonia sandarakina strain DSM 15664272918.6wgspatric272918
66792Nesterenkonia sandarakina DSM 156642856487714draftimg272918
67770Nesterenkonia sandarakina DSM 15664GCA_013410215contigncbi272918

GC content

@refGC-contentmethod
601964
6777064thermal denaturation, midpoint method (Tm)
6777164.0thermal denaturation, midpoint method (Tm)

External links

@ref: 6019

culture collection no.: DSM 15664, CCTCC AA 203007, CIP 108680, KCTC 19011, YIM 70009, JCM 13020

straininfo link

  • @ref: 77210
  • straininfo: 265479

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653919Nesterenkonia sandarakina sp. nov. and Nesterenkonia lutea sp. nov., novel actinobacteria, and emended description of the genus Nesterenkonia.Li WJ, Chen HH, Kim CJ, Zhang YQ, Park DJ, Lee JC, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63281-02005Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Micrococcaceae/chemistry/*classification/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny26813578Nesterenkonia aurantiaca sp. nov., an alkaliphilic actinobacterium isolated from Antarctica.Finore I, Orlando P, Di Donato P, Leone L, Nicolaus B, Poli AInt J Syst Evol Microbiol10.1099/ijsem.0.0009172016

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6019Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15664)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15664
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
31313Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2762828776041
42043Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6335
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
77210Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265479.1StrainInfo: A central database for resolving microbial strain identifiers
122412Curators of the CIPCollection of Institut Pasteur (CIP 108680)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108680