Strain identifier

BacDive ID: 24085

Type strain: Yes

Species: Natrinema salifodinae

Strain Designation: KCY07-B2

Strain history: W. Zhang KCY07-B2.

NCBI tax ID(s): 1202768 (species)

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General

@ref: 21174

BacDive-ID: 24085

DSM-Number: 26231

keywords: genome sequence, 16S sequence, Archaea, aerobe, mesophilic, Gram-negative, rod-shaped

description: Natrinema salifodinae KCY07-B2 is an aerobe, mesophilic, Gram-negative archaeon that was isolated from salt mine.

NCBI tax id

  • NCBI tax id: 1202768
  • Matching level: species

strain history

@refhistory
21174<- Z. Weiyan, Zhejiang Univ., Hangzhou, China; KCY07-B2
67770W. Zhang KCY07-B2.

doi: 10.13145/bacdive24085.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Natrialbales
  • family: Natrialbaceae
  • genus: Natrinema
  • species: Natrinema salifodinae
  • full scientific name: Natrinema salifodinae (Zhang et al. 2013) de la Haba et al. 2022

  • synonyms

    • @ref: 20215
    • synonym: Halopiger salifodinae

@ref: 21174

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Natrialbaceae

genus: Halopiger

species: Halopiger salifodinae

full scientific name: Halopiger salifodinae Zhang et al. 2013

strain designation: KCY07-B2

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31060negativerod-shapedno
69480negative99.903

pigmentation

  • @ref: 31060
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21174
  • name: HALOLAMINA MEDIUM (NOM-3) (DSMZ Medium 1528)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1528
  • composition: Name: HALOLAMINA MEDIUM (NOM-3) (DSMZ Medium 1528) Composition: NaCl 184.0 g/l MgSO4 x 7 H2O 26.8 g/l MgCl2 x 6 H2O 23.0 g/l Agar 20.0 g/l KCl 5.4 g/l Yeast extract 1.0 g/l Bacto peptone 0.5 g/l K2HPO4 0.3 g/l NH4Cl 0.25 g/l CaCl2 x 2 H2O 0.25 g/l Sodium formate 0.25 g/l Sodium lactate 0.25 g/l Sodium acetate 0.25 g/l Sodium pyruvate 0.25 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21174positivegrowth37mesophilic
31060positivegrowth25-50
31060positiveoptimum41thermophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
31060positivegrowth6.0-8.0
31060positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31060
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no92
69480no99.962

halophily

@refsaltgrowthtested relationconcentration
31060NaClpositivegrowth11.02-31.32 %
31060NaClpositiveoptimum18.27 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3106030089acetate+carbon source
3106022653asparagine+carbon source
3106016947citrate+carbon source
3106017234glucose+carbon source
3106029987glutamate+carbon source
3106015428glycine+carbon source
3106025115malate+carbon source
3106037684mannose+carbon source
3106017822serine+carbon source
3106030911sorbitol+carbon source
3106030031succinate+carbon source
3106026986threonine+carbon source
310604853esculin+hydrolysis

metabolite production

  • @ref: 31060
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
31060acid phosphatase+3.1.3.2
31060catalase+1.11.1.6
31060cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21174salt mineXinjiang Province, Akesu area, Kuche countyChinaCHNAsia
67770Salt mine in Kuche countyXinjiangChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_188074.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17652;96_69346;97_90067;98_122437;99_188074&stattab=map
  • Last taxonomy: Halopiger salifodinae subclade
  • 16S sequence: JX014296
  • Sequence Identity:
  • Total samples: 8
  • soil counts: 4
  • aquatic counts: 1
  • plant counts: 3

Safety information

risk assessment

  • @ref: 21174
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21174
  • description: Halopiger salifodinae strain KCY07-B2 16S ribosomal RNA gene, partial sequence
  • accession: JX014296
  • length: 1472
  • database: ena
  • NCBI tax ID: 1202768

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Natrinema salifodinae CGMCC 1.12284GCA_900110455scaffoldncbi1202768
66792Halopiger salifodinae KCY07-B22645727804draftimg1202768
66792Halopiger salifodinae CGMCC 1.122842671180170draftimg1202768
67770Natrinema salifodinae KCY07-B2GCA_000784335scaffoldncbi1202768
66792Halopiger salifodinae strain CGMCC 1.122841202768.6wgspatric1202768

GC content

@refGC-contentmethod
2117462.5high performance liquid chromatography (HPLC)
3106062.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
glucose-fermentno80.559no
motileno81.171yes
flagellatedno95.532no
gram-positiveno96.889yes
anaerobicno94.895yes
aerobicyes84.68no
halophileyes91.267yes
spore-formingno94.833no
thermophileno77.362no
glucose-utilyes89.721no

External links

@ref: 21174

culture collection no.: DSM 26231, CGMCC 1.12284, JCM 18547

straininfo link

  • @ref: 88050
  • straininfo: 397477

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23563233Halopiger salifodinae sp. nov., an extremely halophilic archaeon isolated from a salt mine.Zhang WY, Meng Y, Zhu XF, Wu MInt J Syst Evol Microbiol10.1099/ijs.0.050971-02013Base Composition, China, DNA, Archaeal/genetics, Glycolipids/analysis, Halobacteriaceae/*classification/genetics/isolation & purification, *Mining, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Sodium ChlorideGenetics
Genetics26664653Draft genome sequence of Halopiger salifodinae KCY07-B2(T), an extremly halophilic archaeon isolated from a salt mine.Zhang WY, Hu J, Pan J, Sun C, Wu M, Xu XWStand Genomic Sci10.1186/s40793-015-0113-y2015

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21174Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26231Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26231)
31060Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172738928776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88050Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID397477.1