Strain identifier

BacDive ID: 5896

Type strain: Yes

Species: Natronomonas pharaonis

Strain Designation: Gabara

Strain history: CIP <- 1994, IFO <- 1988, DSMZ, Halobacterium pharaonis <- H.G. Trüper: strain Gabara <- G.S.H. Soliman

NCBI tax ID(s): 348780 (strain), 2257 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 985

BacDive-ID: 5896

DSM-Number: 2160

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

description: Natronomonas pharaonis Gabara is a mesophilic, Gram-negative archaeon that was isolated from water sample.

NCBI tax id

NCBI tax idMatching level
348780strain
2257species

strain history

@refhistory
985<- H.G. Trüper, strain Gabara
67770IFO 14720 <-- DSM 2160 <-- H. G. Trüper strain Gabara.
121792CIP <- 1994, IFO <- 1988, DSMZ, Halobacterium pharaonis <- H.G. Trüper: strain Gabara <- G.S.H. Soliman

doi: 10.13145/bacdive5896.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Halobacteriales
  • family: Halobacteriaceae
  • genus: Natronomonas
  • species: Natronomonas pharaonis
  • full scientific name: Natronomonas pharaonis (Soliman and Trüper 1983) Kamekura et al. 1997
  • synonyms

    @refsynonym
    20215Natronobacterium pharaonis
    20215Halobacterium pharaonis

@ref: 985

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Halobacteriaceae

genus: Natronomonas

species: Natronomonas pharaonis

full scientific name: Natronomonas pharaonis (Soliman and Trüper 1983) Kamekura et al. 1997

strain designation: Gabara

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.989
121792negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
985NATRONOBACTERIA MEDIUM (DSMZ Medium 371)yeshttps://mediadive.dsmz.de/medium/371Name: NATRONOBACTERIA MEDIUM (DSMZ Medium 371) Composition: NaCl 200.0 g/l Agar 20.0 g/l Casamino acids 5.0 g/l Yeast extract 5.0 g/l Na2CO3 5.0 g/l Na2-glutamate 1.0 g/l KH2PO4 1.0 g/l KCl 1.0 g/l NH4Cl 1.0 g/l MgSO4 x 7 H2O 0.24 g/l CaSO4 x 2 H2O 0.17 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
985NATRONOBACTERIUM MEDIUM (DSMZ Medium 205)yeshttps://mediadive.dsmz.de/medium/205Name: NATRONOBACTERIUM MEDIUM (DSMZ Medium 205) Composition: NaCl 250.0 g/l Agar 20.0 g/l Casamino acids 15.0 g/l Trisodium citrate x 2 H2O 3.0 g/l MgSO4 x 7 H2O 2.5 g/l Glutamic acid 2.5 g/l KCl 2.0 g/l Distilled water
40918MEDIUM 47 - for Natronomonas pharaonisyesSodium carbonate decahydrate (5.000 g);Distilled water make up to (1000.000ml);Sodium chloride (250.000 g);Potassium chloride (1.000 g);Magnesium sulphate heptahydrate (0.240 g);Agar (20.000 g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (1.00
121792CIP Medium 47yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=47

culture temp

@refgrowthtypetemperaturerange
985positivegrowth37mesophilic
40918positivegrowth37mesophilic
67770positivegrowth37mesophilic
121792positivegrowth30-37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.979

halophily

@refsaltgrowthtested relationconcentration
121792NaClpositivegrowth0-6 %
121792NaClnogrowth8 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12179217632nitrate-reduction
12179216301nitrite-reduction

metabolite production

  • @ref: 121792
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
121792beta-galactosidase+3.2.1.23
121792alcohol dehydrogenase-1.1.1.1
121792gelatinase+
121792catalase+1.11.1.6
121792lysine decarboxylase-4.1.1.18
121792ornithine decarboxylase-4.1.1.17
121792urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
985water sampleWadi NatrunEgyptEGYAfrica
67770Alkaline brines of eutrophic desert lakes of Wadi NatrunEgyptEGYAfrica
121792Environment, Alkaline brine in lakes of Wadi NatrumEgyptEGYAfrica

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_187090.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17906;96_68778;97_89420;98_121689;99_187090&stattab=map
  • Last taxonomy: Natronomonas pharaonis subclade
  • 16S sequence: NR_074179
  • Sequence Identity:
  • Total samples: 33
  • soil counts: 8
  • aquatic counts: 25

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
9851Risk group (German classification)
1217921Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
985Natronomonas pharaonis strain Gabara 16S ribosomal RNA, complete sequenceNR_0741791466nuccore2257
67770Natronobacterium pharaonis DNA for 16S rRNAD879711465ena348780

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Natronomonas pharaonis DSM 2160 GabaraGCA_000026045completencbi348780
66792Natronomonas pharaonis Gabara, DSM 2160637000187completeimg348780
66792Natronomonas pharaonis DSM 2160 strain Gabara348780.21plasmidpatric348780
66792Natronomonas pharaonis DSM 2160 strain Gabara348780.20plasmidpatric348780
66792Natronomonas pharaonis DSM 2160348780.14completepatric348780

GC content

@refGC-contentmethod
6777062.6thermal denaturation, midpoint method (Tm)
6777064.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno78.641no
flagellatedno97.366no
gram-positiveno98.137no
anaerobicno95.261no
aerobicyes76.959no
halophileyes91.508no
spore-formingno94.587no
thermophileno79.047no
glucose-utilyes83.877no
glucose-fermentno80.639no

External links

@ref: 985

culture collection no.: DSM 2160, ATCC 35678, JCM 8858, CCM 3872, CIP 103997, IFO 14720, NBRC 14720, NCIMB 2260, VKM B-1749

straininfo link

  • @ref: 75376
  • straininfo: 41222

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12201058Radiation sensitivity of N. pharaonis in comparison with E. coli K12 strains.Quint RM, Solar S, Stan-Lotter HRadiat Environ Biophys10.1007/s00411-002-0146-72002Cell Line, Cobalt Radioisotopes, Dose-Response Relationship, Radiation, Escherichia coli/classification/*metabolism/*radiation effects, *Gamma Rays, Natronobacterium/classification/*metabolism/*radiation effects, Oxygen/*metabolism, Radiation Dosage, Reproducibility of Results, Sensitivity and Specificity, Species SpecificityMetabolism
Metabolism18671971A halorhodopsin-overproducing mutant isolated from an extremely haloalkaliphilic archaeon Natronomonas pharaonis.Ihara K, Narusawa A, Maruyama K, Takeguchi M, Kouyama TFEBS Lett10.1016/j.febslet.2008.07.0302008Amino Acid Substitution, Asparagine/genetics/metabolism, Aspartic Acid/genetics/metabolism, Cell Membrane/chemistry/metabolism, Gene Expression Regulation, Archaeal, Halobacteriaceae/genetics/isolation & purification/*metabolism, Halorhodopsins/*biosynthesis/chemistry/genetics, MutationEnzymology
Phylogeny19667395Natronomonas moolapensis sp. nov., non-alkaliphilic isolates recovered from a solar saltern crystallizer pond, and emended description of the genus Natronomonas.Burns DG, Janssen PH, Itoh T, Minegishi H, Usami R, Kamekura M, Dyall-Smith MLInt J Syst Evol Microbiol10.1099/ijs.0.010132-02009Crystallization, DNA, Archaeal/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Halobacteriaceae/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityGenetics
Phylogeny20495022Halomarina oriensis gen. nov., sp. nov., a halophilic archaeon isolated from a seawater aquarium.Inoue K, Itoh T, Ohkuma M, Kogure KInt J Syst Evol Microbiol10.1099/ijs.0.020677-02010Aerobiosis, Base Composition, Cluster Analysis, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Glycolipids/analysis, Halobacteriaceae/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Japan, Magnesium/metabolism, Molecular Sequence Data, Organic Chemicals/metabolism, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureMetabolism
23100763An evidence of laccases in archaea.Sharma KK, Kuhad RCIndian J Microbiol10.1007/s12088-009-0039-42009
Phylogeny23851717Natronomonas gomsonensis sp. nov., isolated from a solar saltern.Kim TY, Kim SJ, Park SJ, Kim JG, Cha IT, Jung MY, Lee SA, Roh SW, Yim KJ, Itoh T, Rhee SKAntonie Van Leeuwenhoek10.1007/s10482-013-9970-92013Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Geologic Sediments/microbiology, Halobacteriaceae/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Korea, Magnesium Chloride/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
985Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2160)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2160
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
40918Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15856
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
75376Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41222.1StrainInfo: A central database for resolving microbial strain identifiers
121792Curators of the CIPCollection of Institut Pasteur (CIP 103997)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103997