Strain identifier
BacDive ID: 5896
Type strain:
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)
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 id | Matching level |
---|---|
348780 | strain |
2257 | species |
strain history
@ref | history |
---|---|
985 | <- H.G. Trüper, strain Gabara |
67770 | IFO 14720 <-- DSM 2160 <-- H. G. Trüper strain Gabara. |
121792 | CIP <- 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
@ref synonym 20215 Natronobacterium pharaonis 20215 Halobacterium 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
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.989 | ||
121792 | negative | rod-shaped | yes |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
985 | NATRONOBACTERIA MEDIUM (DSMZ Medium 371) | yes | https://mediadive.dsmz.de/medium/371 | Name: 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 |
985 | NATRONOBACTERIUM MEDIUM (DSMZ Medium 205) | yes | https://mediadive.dsmz.de/medium/205 | Name: 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 |
40918 | MEDIUM 47 - for Natronomonas pharaonis | yes | Sodium 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 | |
121792 | CIP Medium 47 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=47 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
985 | positive | growth | 37 | mesophilic |
40918 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
121792 | positive | growth | 30-37 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.979 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
121792 | NaCl | positive | growth | 0-6 % |
121792 | NaCl | no | growth | 8 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
121792 | 17632 | nitrate | - | reduction |
121792 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 121792
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
121792 | beta-galactosidase | + | 3.2.1.23 |
121792 | alcohol dehydrogenase | - | 1.1.1.1 |
121792 | gelatinase | + | |
121792 | catalase | + | 1.11.1.6 |
121792 | lysine decarboxylase | - | 4.1.1.18 |
121792 | ornithine decarboxylase | - | 4.1.1.17 |
121792 | urease | - | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
985 | water sample | Wadi Natrun | Egypt | EGY | Africa |
67770 | Alkaline brines of eutrophic desert lakes of Wadi Natrun | Egypt | EGY | Africa | |
121792 | Environment, Alkaline brine in lakes of Wadi Natrum | Egypt | EGY | Africa |
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
@ref | biosafety level | biosafety level comment |
---|---|---|
985 | 1 | Risk group (German classification) |
121792 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
985 | Natronomonas pharaonis strain Gabara 16S ribosomal RNA, complete sequence | NR_074179 | 1466 | nuccore | 2257 |
67770 | Natronobacterium pharaonis DNA for 16S rRNA | D87971 | 1465 | ena | 348780 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Natronomonas pharaonis DSM 2160 Gabara | GCA_000026045 | complete | ncbi | 348780 |
66792 | Natronomonas pharaonis Gabara, DSM 2160 | 637000187 | complete | img | 348780 |
66792 | Natronomonas pharaonis DSM 2160 strain Gabara | 348780.21 | plasmid | patric | 348780 |
66792 | Natronomonas pharaonis DSM 2160 strain Gabara | 348780.20 | plasmid | patric | 348780 |
66792 | Natronomonas pharaonis DSM 2160 | 348780.14 | complete | patric | 348780 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 62.6 | thermal denaturation, midpoint method (Tm) |
67770 | 64.3 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 78.641 | no |
flagellated | no | 97.366 | no |
gram-positive | no | 98.137 | no |
anaerobic | no | 95.261 | no |
aerobic | yes | 76.959 | no |
halophile | yes | 91.508 | no |
spore-forming | no | 94.587 | no |
thermophile | no | 79.047 | no |
glucose-util | yes | 83.877 | no |
glucose-ferment | no | 80.639 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12201058 | Radiation sensitivity of N. pharaonis in comparison with E. coli K12 strains. | Quint RM, Solar S, Stan-Lotter H | Radiat Environ Biophys | 10.1007/s00411-002-0146-7 | 2002 | Cell 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 Specificity | Metabolism |
Metabolism | 18671971 | A halorhodopsin-overproducing mutant isolated from an extremely haloalkaliphilic archaeon Natronomonas pharaonis. | Ihara K, Narusawa A, Maruyama K, Takeguchi M, Kouyama T | FEBS Lett | 10.1016/j.febslet.2008.07.030 | 2008 | Amino 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, Mutation | Enzymology |
Phylogeny | 19667395 | Natronomonas 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 ML | Int J Syst Evol Microbiol | 10.1099/ijs.0.010132-0 | 2009 | Crystallization, 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 Specificity | Genetics |
Phylogeny | 20495022 | Halomarina oriensis gen. nov., sp. nov., a halophilic archaeon isolated from a seawater aquarium. | Inoue K, Itoh T, Ohkuma M, Kogure K | Int J Syst Evol Microbiol | 10.1099/ijs.0.020677-0 | 2010 | Aerobiosis, 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, Temperature | Metabolism |
23100763 | An evidence of laccases in archaea. | Sharma KK, Kuhad RC | Indian J Microbiol | 10.1007/s12088-009-0039-4 | 2009 | |||
Phylogeny | 23851717 | Natronomonas 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 SK | Antonie Van Leeuwenhoek | 10.1007/s10482-013-9970-9 | 2013 | Bacterial 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, Temperature | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
985 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2160) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2160 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
40918 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15856 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
75376 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID41222.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121792 | Curators of the CIP | Collection of Institut Pasteur (CIP 103997) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103997 |