Strain identifier

BacDive ID: 7764

Type strain: Yes

Species: Nesterenkonia halotolerans

Strain history: KCTC 19014 <-- W.-J. Li YIM 70084.

NCBI tax ID(s): 225325 (species)

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General

@ref: 5944

BacDive-ID: 7764

DSM-Number: 15474

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

description: Nesterenkonia halotolerans DSM 15474 is a mesophilic, Gram-positive, motile bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 225325
  • Matching level: species

strain history

@refhistory
5944<- W.-J. Li <- CCTCC <- YIM
67770KCTC 19014 <-- W.-J. Li YIM 70084.

doi: 10.13145/bacdive7764.20230509.8.1

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 halotolerans
  • full scientific name: Nesterenkonia halotolerans Li et al. 2004

@ref: 5944

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Nesterenkonia

species: Nesterenkonia halotolerans

full scientific name: Nesterenkonia halotolerans Li et al. 2004

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30096positivecoccus-shapedyes
69480positive100

pigmentation

  • @ref: 30096
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 5944
  • name: NESTERENKONIA MODIFIED MEDIUM (DSMZ Medium 993a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/993a
  • composition: Name: NESTERENKONIA MODIFIED MEDIUM (DSMZ Medium 993a) Composition: MgCl2 x 6 H2O 100.0 g/l Agar 20.0 g/l Glycerol 10.0 g/l Yeast extract 5.0 g/l L-Asparagine 1.0 g/l K2HPO4 1.0 g/l MnCl2 x 4 H2O 0.001 g/l ZnSO4 x 7 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
5944positivegrowth28mesophilic
30096positivegrowth04-40
30096positiveoptimum28mesophilic
67770positivegrowth28mesophilic

culture pH

  • @ref: 30096
  • ability: positive
  • type: growth
  • pH: 07-09
  • PH range: alkaliphile

Physiology and metabolism

spore formation

@refspore formationconfidence
30096no
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
30096NaClpositivegrowth0-25 %
30096NaClpositiveoptimum10 %

murein

  • @ref: 5944
  • murein short key: A11.42
  • type: A4alpha L-Lys-Gly-D-Asp

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3009623652dextrin+carbon source
3009628757fructose+carbon source
3009628260galactose+carbon source
300965291gelatin+carbon source
3009617234glucose+carbon source
3009617716lactose+carbon source
3009617306maltose+carbon source
3009637684mannose+carbon source
3009617992sucrose+carbon source
3009616199urea+carbon source

enzymes

@refvalueactivityec
30096gelatinase+
30096urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5944soilXijiangChinaCHNAsia
67770Hypersaline soilXinjang ProvinceChinaCHNAsia

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: AY226508
  • Sequence Identity:
  • Total samples: 3970
  • soil counts: 791
  • aquatic counts: 600
  • animal counts: 2130
  • plant counts: 449

Safety information

risk assessment

  • @ref: 5944
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5944
  • description: Nesterenkonia sp. YIM 70084 16S ribosomal RNA gene, partial sequence
  • accession: AY226508
  • length: 1490
  • database: ena
  • NCBI tax ID: 225325

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nesterenkonia halotolerans DSM 15474GCA_014874065contigncbi225325
66792Nesterenkonia halotolerans strain DSM 15474225325.3wgspatric225325
66792Nesterenkonia halotolerans DSM 154742870876733draftimg225325

GC content

@refGC-contentmethod
3009664.4
6777064.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes60.929yes
gram-positiveyes92.823yes
anaerobicno99.427no
aerobicyes95.02no
halophileyes71.661no
spore-formingno92.34yes
glucose-utilyes91.515yes
flagellatedno90.746no
thermophileno97.31yes
glucose-fermentno90.39no

External links

@ref: 5944

culture collection no.: DSM 15474, CCTCC AA 001022, YIM 70084, JCM 13018, KCTC 19014

straininfo link

  • @ref: 77207
  • straininfo: 132022

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143032Nesterenkonia halotolerans sp. nov. and Nesterenkonia xinjiangensis sp. nov., actinobacteria from saline soils in the west of China.Li WJ, Chen HH, Zhang YQ, Schumann P, Stackebrandt E, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.02935-02004Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Micrococcaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sodium Chloride, Soil MicrobiologyGenetics
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
5944Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15474)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15474
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
30096Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2645228776041
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/
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
77207Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132022.1StrainInfo: A central database for resolving microbial strain identifiers