Strain identifier

BacDive ID: 5972

Type strain: Yes

Species: Haladaptatus cibarius

Strain Designation: D43

Strain history: J.-W. Bae D43.

NCBI tax ID(s): 1455608 (strain), 453847 (species)

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General

@ref: 8136

BacDive-ID: 5972

DSM-Number: 19505

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

description: Haladaptatus cibarius D43 is an aerobe, mesophilic, Gram-negative archaeon that was isolated from salt-fermented seafood.

NCBI tax id

NCBI tax idMatching level
1455608strain
453847species

strain history

@refhistory
8136<- S. W. Roh, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; D43
67770J.-W. Bae D43.

doi: 10.13145/bacdive5972.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Halobacteriales
  • family: Halobacteriaceae
  • genus: Haladaptatus
  • species: Haladaptatus cibarius
  • full scientific name: Haladaptatus cibarius Roh et al. 2010

@ref: 8136

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Halobacteriaceae

genus: Haladaptatus

species: Haladaptatus cibarius

full scientific name: Haladaptatus cibarius Roh et al. 2010

strain designation: D43

type strain: yes

Morphology

cell morphology

  • @ref: 29432
  • gram stain: negative
  • cell width: 1 µm
  • cell shape: coccus-shaped
  • motility: yes

pigmentation

  • @ref: 29432
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8136
  • name: MEDIUM FOR H. DOMBROWSKII (DSMZ Medium 954)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/954
  • composition: Name: MEDIUM FOR H. DOMBROWSKII (DSMZ Medium 954) Composition: NaCl 200.0 g/l MgCl2 x 6 H2O 20.0 g/l Agar 20.0 g/l Tris 12.1 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l KCl 2.0 g/l CaCl2 x 2 H2O 0.2 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8136positivegrowth37mesophilic
29432positivegrowth15-50
29432positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
29432positivegrowth06-08
29432positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29432
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
29432NaClpositivegrowth10-30 %
29432NaClpositiveoptimum15 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2943230089acetate+carbon source
2943215740formate+carbon source
2943228757fructose+carbon source
2943217234glucose+carbon source
2943217716lactose+carbon source
2943217992sucrose+carbon source

metabolite production

  • @ref: 29432
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 29432
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29432catalase+1.11.1.6
29432gelatinase+
29432cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8136salt-fermented seafoodRepublic of KoreaKORAsia
67770Jeotgal, traditional Korean fermented seafoodRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Seafood
#Condition#Saline
#Engineered#Food production#Fermented

Safety information

risk assessment

  • @ref: 8136
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Haladaptatus cibarius gene for 16S rRNA, complete sequence, strain: JCM 15962AB6633451471ena1455608
8136Haladaptatus cibarius D43 16S ribosomal RNA gene, partial sequenceEF6607471405ena1455608

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Haladaptatus cibarius D432582580505draftimg1455608
67770Haladaptatus cibarius D43GCA_000710615contigncbi1455608
66792Haladaptatus cibarius D431455608.3wgspatric1455608

GC content

@refGC-contentmethod
813656.5fluorimetric
2943256.5
6777056.5thermal denaturation, midpoint method (Tm)

External links

@ref: 8136

culture collection no.: DSM 19505, JCM 15962, KCTC 4055

straininfo link

  • @ref: 75461
  • straininfo: 399544

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19667394Haladaptatus cibarius sp. nov., an extremely halophilic archaeon from seafood, and emended description of the genus Haladaptatus.Roh SW, Lee ML, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.013037-02009Animals, Base Composition, DNA, Archaeal/analysis, DNA, Ribosomal/analysis, Fermentation, Genes, rRNA, Genotype, Halobacteriaceae/*classification/genetics/*isolation & purification/physiology, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seafood/*microbiology, Sequence Analysis, DNA, Shellfish/*microbiology, *Sodium Chloride, Species SpecificityGenetics
Phylogeny25190334Haladaptatus pallidirubidus sp. nov., a halophilic archaeon isolated from saline soil samples in Yunnan and Xinjiang, China.Liu BB, Zhao WY, Chu X, Hozzein WN, Prabhu DM, Wadaan MA, Tang SK, Zhang LL, Li WJAntonie Van Leeuwenhoek10.1007/s10482-014-0259-42014Aerobiosis, Archaea/chemistry/*classification/genetics/*isolation & purification, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Glycolipids/analysis, Hydrogen-Ion Concentration, Microbiological Techniques, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
8136Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19505)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19505
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
29432Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125838
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/
75461Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399544.1StrainInfo: A central database for resolving microbial strain identifiers