Strain identifier

BacDive ID: 5964

Type strain: Yes

Species: Natronobacterium gregoryi

Strain Designation: SP2

Strain history: CIP <- 1996, ATCC <- NCIMB <- D. Grant <- B.J. Tindall: strain SP2

NCBI tax ID(s): 797304 (strain), 44930 (species)

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General

@ref: 1374

BacDive-ID: 5964

DSM-Number: 3393

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

description: Natronobacterium gregoryi SP2 is a mesophilic, Gram-negative archaeon that was isolated from solar salt works liquor.

NCBI tax id

NCBI tax idMatching level
44930species
797304strain

strain history

@refhistory
1374<- B.J. Tindall, SP2
67770NCIMB 2189 <-- W. D. Grant <-- B. J. Tindall SP2.
119736CIP <- 1996, ATCC <- NCIMB <- D. Grant <- B.J. Tindall: strain SP2

doi: 10.13145/bacdive5964.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Natrialbales
  • family: Natrialbaceae
  • genus: Natronobacterium
  • species: Natronobacterium gregoryi
  • full scientific name: Natronobacterium gregoryi Tindall et al. 1984

@ref: 1374

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Natrialbaceae

genus: Natronobacterium

species: Natronobacterium gregoryi

full scientific name: Natronobacterium gregoryi Tindall et al. 1984

strain designation: SP2

type strain: yes

Morphology

cell morphology

  • @ref: 119736
  • gram stain: negative
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1374NATRONOBACTERIA 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
38516MEDIUM 172 - for NatronorubrumyesDistilled water make up to (1000.000 ml);Sodium chloride (200.000 g);Potassium chloride (0.500 g);Magnesium sulphate heptahydrate (0.240 g);Agar (20.000 g);Yeastextract (5.000 g);Ammonium chloride (0.250 g);Sodium glutamate (1.000 g);Calcium sulphate dihy
119736CIP Medium 172yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=172

culture temp

@refgrowthtypetemperaturerange
1374positivegrowth37mesophilic
38516positivegrowth37mesophilic
67770positivegrowth37mesophilic
119736positivegrowth25-45
119736nogrowth5psychrophilic
119736nogrowth15psychrophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: MK-8, MK-8(H2), MMK-8, MMK-8(H2), DMK-8, DMK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1197364853esculin-hydrolysis
119736606565hippurate-hydrolysis
11973617632nitrate-reduction
11973616301nitrite-reduction
11973615792malonate-assimilation
6837717634D-glucose+builds acid from
6837715824D-fructose+builds acid from
6837717306maltose+builds acid from
6837717992sucrose+builds acid from
6837718257ornithine-degradation
6837716199urea+hydrolysis
6837727897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
11973635581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837735581indole-
11973615688acetoin-
11973617234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)-
68382esterase lipase (C 8)-
68377tryptophan deaminase-4.1.99.1
68377gamma-glutamyltransferase+2.3.2.2
68377proline-arylamidase-3.4.11.5
68377beta-galactosidase+3.2.1.23
68377alkaline phosphatase+3.1.3.1
68377lipase-
68377urease+3.5.1.5
68377ornithine decarboxylase-4.1.1.17
68377beta-lactamase-3.5.2.6
119736oxidase+
119736beta-galactosidase+3.2.1.23
119736alcohol dehydrogenase-1.1.1.1
119736gelatinase-
119736catalase+1.11.1.6
119736gamma-glutamyltransferase-2.3.2.2
119736lysine decarboxylase-4.1.1.18
119736ornithine decarboxylase-4.1.1.17
119736phenylalanine ammonia-lyase-4.3.1.24
119736tryptophan deaminase-
119736urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
49222-+---+----++-+------
119736--+-----++----------

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
49222-++++-+-++-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1374solar salt works liquorMagadi LakeKenyaKENAfrica
49222Pig lung,pleuropneumoniaSwitzerlandCHEEurope
67770Lake MagadiKenyaKENAfrica
119736Environment, Water, Magadi lakeMagadi LakeKenyaKENAfrica

isolation source categories

Cat1Cat2
#Environmental#Aquatic
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_187257.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17652;96_68892;97_89541;98_121827;99_187257&stattab=map
  • Last taxonomy: Natronobacterium gregoryi subclade
  • 16S sequence: D87970
  • Sequence Identity:
  • Total samples: 4
  • aquatic counts: 4

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
13741Risk group (German classification)
1197361Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Natronobacterium gregoryi gene for 16S rRNA, complete sequence, strain: JCM 8860AB6634671472ena797304
20218Natronobacterium gregoryi DNA for 16S rRNAD879701467ena797304

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Natronobacterium gregoryi SP2GCA_000230715completencbi797304
66792Natronobacterium gregoryi SP2GCA_002855455contigncbi797304
66792Natronobacterium gregoryi SP2GCA_900114025contigncbi44930
66792Natronobacterium gregoryi SP22811995171draftimg797304
66792Natronobacterium gregoryi SP22529293212draftimg797304
66792Natronobacterium gregoryi SP22510461022completeimg797304
66792Natronobacterium gregoryi DSM 33932693429900draftimg797304
67770Natronobacterium gregoryi SP2GCA_000337655contigncbi797304
66792Natronobacterium gregoryi strain SP244930.7wgspatric44930
66792Natronobacterium gregoryi SP2797304.7wgspatric797304
66792Natronobacterium gregoryi SP2797304.6completepatric797304
66792Natronobacterium gregoryi SP2797304.15patric797304

GC content

@refGC-contentmethod
137465.0
6777065Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno82.056no
flagellatedno97.079no
gram-positiveno98.527no
anaerobicno90.207no
aerobicyes64.057no
halophileyes85.999no
spore-formingno92.557no
glucose-utilyes87.668no
thermophileno85.453yes
glucose-fermentno84.63no

External links

@ref: 1374

culture collection no.: DSM 3393, ATCC 43098, CCM 3738, NCMB 2189, CCUG 28374, JCM 17874, CIP 104747, IAM 13177, JCM 8860, NBRC 102187, NCIMB 14426, VKM B-1750, NCIMB 2189

straininfo link

  • @ref: 75453
  • straininfo: 92979

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism20437233Identification of polyhydroxyalkanoates in Halococcus and other haloarchaeal species.Legat A, Gruber C, Zangger K, Wanner G, Stan-Lotter HAppl Microbiol Biotechnol10.1007/s00253-010-2611-62010Australia, Geologic Sediments/microbiology, Halobacteriaceae/*chemistry/isolation & purification/metabolism/ultrastructure, Halococcus/*chemistry/isolation & purification/metabolism/ultrastructure, Hydroxybutyrates/*chemistry/metabolism, Magnetic Resonance Spectroscopy, Microscopy, Electron, Transmission, Polyesters/*chemistry/metabolismEnzymology
Phylogeny23749283Natronobacterium texcoconense sp. nov., a haloalkaliphilic archaeon isolated from soil of a former lake.Ruiz-Romero E, Sanchez-Lopez KB, Coutino-Coutino MLA, Gonzalez-Pozos S, Bello-Lopez JM, Lopez-Ramirez MP, Ramirez-Villanueva DA, Dendooven LInt J Syst Evol Microbiol10.1099/ijs.0.053629-02013Base Composition, DNA, Archaeal/genetics, Hydrogen-Ion Concentration, Lakes, Mexico, Molecular Sequence Data, Natronobacterium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1374Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3393)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3393
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
38516Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16690
49222Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28374)https://www.ccug.se/strain?id=28374
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/
68377Automatically annotated from API NH
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
75453Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92979.1StrainInfo: A central database for resolving microbial strain identifiers
119736Curators of the CIPCollection of Institut Pasteur (CIP 104747)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104747