Strain identifier

BacDive ID: 17796

Type strain: Yes

Species: Salinibacter ruber

Strain Designation: M31

Strain history: CIP <- 2002, CECT <- S. Benlloch <- J. Anton, Spain: strain M31

NCBI tax ID(s): 309807 (strain), 146919 (species)

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General

@ref: 5176

BacDive-ID: 17796

DSM-Number: 13855

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

description: Salinibacter ruber M31 is a mesophilic, Gram-negative bacterium that was isolated from solar saltern.

NCBI tax id

NCBI tax idMatching level
146919species
309807strain

strain history

@refhistory
5176<- J. Antón; M31
122278CIP <- 2002, CECT <- S. Benlloch <- J. Anton, Spain: strain M31

doi: 10.13145/bacdive17796.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/rhodothermota
  • domain: Bacteria
  • phylum: Rhodothermota
  • class: Rhodothermia
  • order: Rhodothermales
  • family: Salinibacteraceae
  • genus: Salinibacter
  • species: Salinibacter ruber
  • full scientific name: Salinibacter ruber Antón et al. 2002

@ref: 5176

domain: Bacteria

phylum: Rhodothermaeota

class: Rhodothermia

order: Cytophagales

family: Salinibacteraceae

genus: Salinibacter

species: Salinibacter ruber

full scientific name: Salinibacter ruber Antón et al. 2002 emend. Makhdoumi-Kakhki et al. 2012

strain designation: M31

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.978
122278negativerod-shapedno

pigmentation

  • @ref: 122278
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5176SALINIBACTER RUBER MEDIUM (DSMZ Medium 936)yeshttps://mediadive.dsmz.de/medium/936Name: SALINIBACTER RUBER MEDIUM (DSMZ Medium 936) Composition: NaCl 195.0 g/l MgSO4 x 7 H2O 49.5 g/l MgCl2 x 6 H2O 34.6 g/l Agar 20.0 g/l KCl 5.0 g/l CaCl2 x 2 H2O 1.25 g/l Yeast extract 1.0 g/l NaBr 0.625 g/l NaHCO3 0.25 g/l Distilled water
32764MEDIUM 429 - for Salinibacter ruberyesSodium hydrogen carbonate (0.250 g);Distilled water make up to (1000.000 ml);Sodium chloride (195.000 g);Potassium chloride (5.000 g);Magnesium chloride hexahydrate(34.600 g);Magnesium sulphate heptahydrate (49.500 g);Calcium chloride dihydrate (1.250 g);
122278CIP Medium 429yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=429
122278CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5176positivegrowth37mesophilic
32764positivegrowth37mesophilic
122278positivegrowth37-41
122278nogrowth5psychrophilic
122278nogrowth10psychrophilic
122278nogrowth25mesophilic
122278nogrowth30mesophilic
122278nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
122278NaClnogrowth6 %
122278NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1222784853esculin-hydrolysis
122278606565hippurate-hydrolysis
12227817632nitrate-reduction
12227816301nitrite-reduction
12227817632nitrate-respiration

metabolite production

  • @ref: 122278
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12227815688acetoin-
12227817234glucose-

enzymes

@refvalueactivityec
122278oxidase+
122278beta-galactosidase+3.2.1.23
122278alcohol dehydrogenase-1.1.1.1
122278gelatinase+/-
122278amylase+
122278caseinase+3.4.21.50
122278catalase+1.11.1.6
122278gamma-glutamyltransferase+2.3.2.2
122278lecithinase-
122278lipase-
122278lysine decarboxylase-4.1.1.18
122278ornithine decarboxylase-4.1.1.17
122278phenylalanine ammonia-lyase-4.3.1.24
122278protease+
122278urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122278-++--++-+-++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5176solar salternMallorcaSpainESPEurope
122278Environment, Solar saltern waterBalearic IslandsSpainESPEurope1999

isolation source categories

  • Cat1: #Condition
  • Cat2: #Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_7886.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_676;96_3658;97_4493;98_5763;99_7886&stattab=map
  • Last taxonomy: Salinibacter ruber subclade
  • 16S sequence: AF323500
  • Sequence Identity:
  • Total samples: 549
  • soil counts: 23
  • aquatic counts: 176
  • animal counts: 348
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51761Risk group (German classification)
1222781Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5176
  • description: Salinibacter ruber strain M31 16S ribosomal RNA gene, partial sequence
  • accession: AF323500
  • length: 1482
  • database: ena
  • NCBI tax ID: 309807

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salinibacter ruber DSM 13855 DSM 13855; M31GCA_000013045completencbi309807
66792Salinibacter ruber DSM 13855309807.25completepatric309807
66792Salinibacter ruber DSM 13855 strain DSM 13855; M31309807.35plasmidpatric309807
66792Salinibacter ruber M31, DSM 13855637000250completeimg309807

GC content

  • @ref: 5176
  • GC-content: 70

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes53.558no
flagellatedno88.862no
gram-positiveno97.12no
anaerobicno93.044no
halophileyes71.334no
spore-formingno88.186no
thermophileno69.646yes
glucose-utilyes85.583no
aerobicyes64.67no
glucose-fermentno75.737no

External links

@ref: 5176

culture collection no.: DSM 13855, CECT 5946, CIP 107417

straininfo link

  • @ref: 86788
  • straininfo: 100944

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11931160Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds.Anton J, Oren A, Benlloch S, Rodriguez-Valera F, Amann R, Rossello-Mora RInt J Syst Evol Microbiol10.1099/00207713-52-2-4852002Bacteria/*classification/genetics/isolation & purification, Bacterial Physiological Phenomena, Base Composition, DNA, Bacterial/chemistry, Fresh Water, Molecular Sequence Data, Phylogeny, Pigments, Biological, RNA, Ribosomal/chemistry, RNA, Ribosomal, 16S/chemistry, Sequence Homology, Nucleic Acid, Sodium Chloride, Spain, Species Specificity, TemperatureGenetics
Genetics19951421Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber.Pasic L, Rodriguez-Mueller B, Martin-Cuadrado AB, Mira A, Rohwer F, Rodriguez-Valera FBMC Genomics10.1186/1471-2164-10-5702009Bacteroidetes/*genetics, Base Composition, DNA, Bacterial/genetics, *Genome, Bacterial, *Genomic Islands, Genomic Library, *Metagenomics, Molecular Sequence Data, Phylogeny, Pseudogenes, Sequence Analysis, DNAPhylogeny
Phylogeny21856978Salinibacter iranicus sp. nov. and Salinibacter luteus sp. nov., isolated from a salt lake, and emended descriptions of the genus Salinibacter and of Salinibacter ruber.Makhdoumi-Kakhki A, Amoozegar MA, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.031971-02011Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Iran, Microscopy, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, *Water MicrobiologyGenetics
Genetics31071110A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber.Bagheri M, Marashi SA, Amoozegar MAPLoS One10.1371/journal.pone.02163362019Autotrophic Processes/*physiology, *Bacteroidetes/genetics/metabolism, Gene Regulatory Networks/*physiology, Genome, Bacterial/*physiology, Metabolic Networks and Pathways/*physiology, *Models, BiologicalMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5176Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13855)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13855
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
32764Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4851
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
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
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
86788Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100944.1StrainInfo: A central database for resolving microbial strain identifiers
122278Curators of the CIPCollection of Institut Pasteur (CIP 107417)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107417