Strain identifier

BacDive ID: 5891

Type strain: Yes

Species: Natrinema pellirubrum

Strain Designation: 157

Strain history: CIP <- 1999, NCIMB, Halobacterium salinarium <- M. Formisano: strain 157

NCBI tax ID(s): 797303 (strain), 69525 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 5915

BacDive-ID: 5891

DSM-Number: 15624

keywords: genome sequence, 16S sequence, Archaea, obligate aerobe, mesophilic

description: Natrinema pellirubrum 157 is an obligate aerobe, mesophilic archaeon that was isolated from "Red heat" in salted hides.

NCBI tax id

NCBI tax idMatching level
797303strain
69525species

strain history

@refhistory
5915<- NCIMB <- M. Formisano, Univ. Naples, Italy
67770NCIMB 786 <-- M. Formisano.
121656CIP <- 1999, NCIMB, Halobacterium salinarium <- M. Formisano: strain 157

doi: 10.13145/bacdive5891.20230509.8.1

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 pellirubrum
  • full scientific name: Natrinema pellirubrum McGenity et al. 1998

@ref: 5915

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Natrialbaceae

genus: Natrinema

species: Natrinema pellirubrum

full scientific name: Natrinema pellirubrum McGenity et al. 1998

strain designation: 157

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.26
6948099.961negative
121656nonegativeoval-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5915HALOBACTERIA MEDIUM (DSMZ Medium 372)yeshttps://mediadive.dsmz.de/medium/372Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water
5915PAYNE, SEGHAL & GIBBONS MEDIUM (DSMZ Medium 1160)yeshttps://mediadive.dsmz.de/medium/1160Name: PAYNE, SEGHAL & GIBBONS MEDIUM (DSMZ Medium 1160) Composition: NaCl 250.0 g/l Agar 20.0 g/l MgSO4 x 7 H2O 20.0 g/l Yeast extract 10.0 g/l Casamino acids 7.5 g/l Trisodium citrate 3.0 g/l KCl 2.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water
39832MEDIUM 330 - for Natrinema pallidumyesDistilled water make up to (1000.000 ml);Sodium chloride (200.000 g);Potassium chloride (2.000 g);ManganeseII chloride tetrahydrate (0.360 mg);Magnesium sulphate heptahydrate (20.000 g);Agar (20.000 g);Yeast extract (5.000 g);Ferrous chloride tetrahydrate
121656CIP Medium 330yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=330

culture temp

@refgrowthtypetemperaturerange
5915positivegrowth37mesophilic
39832positivegrowth37mesophilic
67770positivegrowth37mesophilic
121656positivegrowth25-45
121656nogrowth5psychrophilic
121656nogrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121656
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no97
69480no99.853

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
121656606565hippurate-hydrolysis
12165617632nitrate-builds gas from
12165617632nitrate+reduction
12165616301nitrite-builds gas from
12165616301nitrite-reduction
12165617632nitrate-respiration

antibiotic resistance

  • @ref: 121656
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 121656
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
121656oxidase+
121656beta-galactosidase-3.2.1.23
121656alcohol dehydrogenase-1.1.1.1
121656gelatinase-
121656catalase+1.11.1.6
121656gamma-glutamyltransferase+2.3.2.2
121656lysine decarboxylase-4.1.1.18
121656ornithine decarboxylase-4.1.1.17
121656tryptophan deaminase-
121656urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
5915"Red heat" in salted hides
1216561962

isolation source categories

  • Cat1: #Condition
  • Cat2: #Saline

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59151Risk group (German classification)
1216561Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Natrinema pellirubrum gene for 16S ribosomal RNA, partial sequence, strain: JCM 10476AB4772311433ena797303
20218Natrinema pellirubrum gene for 16S rRNA, complete sequence, strain: JCM 10476AB6634641473ena797303
5915Halobacterium salinarium NCIMB 786 16S rRNA geneAJ0029471458ena797303

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Natrinema pellirubrum DSM 15624GCA_000230735completencbi797303
66792Natrinema pellirubrum 1572537562080draftimg797303
66792Natrinema pellirubrum 1572509601048completeimg797303
67770Natrinema pellirubrum DSM 15624GCA_000337635contigncbi797303
66792Natrinema pellirubrum DSM 15624797303.10plasmidpatric797303
66792Natrinema pellirubrum DSM 15624797303.11plasmidpatric797303
66792Natrinema pellirubrum DSM 15624797303.5wgspatric797303
66792Natrinema pellirubrum DSM 15624797303.4completepatric797303

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileno83.548no
flagellatedno96.369no
gram-positiveno96.895no
anaerobicno95.707no
aerobicyes85.261no
halophileyes88.559no
spore-formingno92.714no
glucose-utilyes89.313no
thermophileno92.064yes
glucose-fermentno84.189no

External links

@ref: 5915

culture collection no.: DSM 15624, CIP 106293, JCM 10476, NCIMB 786, CGMCC 1.3708, CGMCC 1.6174, IAM 13169

straininfo link

@refstraininfo
7537158839
75372312365

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9828420Proposal of a new halobacterial genus Natrinema gen. nov., with two species Natrinema pellirubrum nom. nov. and Natrinema pallidum nom. nov.McGenity TJ, Gemmell RT, Grant WDInt J Syst Bacteriol10.1099/00207713-48-4-11871998DNA, Archaeal/chemistry, DNA, Ribosomal/chemistry, Genes, rRNA, Halobacteriaceae/*classification/isolation & purification/physiology, Halobacterium/*classification/isolation & purification/physiology, Halobacterium salinarum/classification/isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Species Specificity, Terminology as Topic, *Water MicrobiologyEnzymology
Phylogeny17082411Natrinema ejinorense sp. nov., isolated from a saline lake in Inner Mongolia, China.Castillo AM, Gutierrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.64421-02006Base Composition, Carbohydrate Metabolism, China, DNA, Archaeal/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Gelatin/metabolism, Genes, rRNA, Halobacteriaceae/*classification/cytology/*isolation & purification/physiology, Hydrogen Sulfide/metabolism, Hydrogen-Ion Concentration, Lipids/analysis, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Starch/metabolism, Temperature, *Water MicrobiologyMetabolism
Phylogeny28905703Saliphagus infecundisoli gen. nov., sp. nov., an extremely halophilic archaeon isolated from a saline soil.Yin XQ, Liu BB, Chu X, Salam N, Li X, Yang ZW, Zhang Y, Xiao M, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0022702017China, DNA, Archaeal/genetics, Genes, Archaeal, Glycolipids/chemistry, Halobacteriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5915Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15624)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15624
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
39832Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18407
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/
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
75371Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID58839.1StrainInfo: A central database for resolving microbial strain identifiers
75372Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312365.1StrainInfo: A central database for resolving microbial strain identifiers
121656Curators of the CIPCollection of Institut Pasteur (CIP 106293)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106293