Strain identifier

BacDive ID: 24542

Type strain: Yes

Species: Saccharospirillum salsuginis

Strain Designation: YIM-Y25

Variant: Isotype of BacDive ID 131172

Strain history: Cui X., YIM; YIM-y25 < Li H.-M., Cui X.L. and Chen G. College of Bio-resources and Environmental Science/ Yunnan University

NCBI tax ID(s): 418750 (species)

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General

@ref: 20799

BacDive-ID: 24542

DSM-Number: 19800

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, spiral-shaped

description: Saccharospirillum salsuginis YIM-Y25 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Yipinglang salt mine.

NCBI tax id

  • NCBI tax id: 418750
  • Matching level: species

strain history

@refhistory
20799<- S.-K. Tang, YIM; YIM-Y25
67772Cui X., YIM; YIM-y25 < Li H.-M., Cui X.L. and Chen G. College of Bio-resources and Environmental Science/ Yunnan University

doi: 10.13145/bacdive24542.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Saccharospirillaceae
  • genus: Saccharospirillum
  • species: Saccharospirillum salsuginis
  • full scientific name: Saccharospirillum salsuginis Chen et al. 2009

@ref: 20799

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Saccharospirillaceae

genus: Saccharospirillum

species: Saccharospirillum salsuginis

full scientific name: Saccharospirillum salsuginis Chen et al. 2009

strain designation: YIM-Y25

variant: Isotype of BacDive ID 131172

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29006negative5.5 µm0.6 µmspiral-shapedyes
69480yes90.601
69480negative99.881

pigmentation

  • @ref: 29006
  • production: no

Culture and growth conditions

culture medium

  • @ref: 20799
  • name: MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514b
  • composition: Name: MEDIUM 514 plus additional salt (DSMZ Medium 514b; with strain-specific modifications) Composition: NaCl 80.0 g/l Agar 17.5 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20799positivegrowth28mesophilic
29006positivegrowth15-50
29006positiveoptimum37mesophilic
67772positiveminimum15psychrophilic
67772positiveoptimum37mesophilic
67772positivemaximum50thermophilic

culture pH

@refabilitytypepHPH range
29006positivegrowth6.0-10.0alkaliphile
29006positiveoptimum8
67772positivemaximum10.0
67772positiveoptimum8.0
67772positiveminimum6.0

Physiology and metabolism

oxygen tolerance

  • @ref: 29006
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29006no
69481no99
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
29006NaClpositivegrowth01-15 %
29006NaClpositiveoptimum5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2900630089acetate+carbon source
2900616449alanine+carbon source
2900622599arabinose+carbon source
2900622653asparagine+carbon source
2900617057cellobiose+carbon source
2900628757fructose+carbon source
2900628260galactose+carbon source
2900617234glucose+carbon source
2900617716lactose+carbon source
2900625115malate+carbon source
2900617306maltose+carbon source
2900629864mannitol+carbon source
2900637684mannose+carbon source
2900617268myo-inositol+carbon source
2900628044phenylalanine+carbon source
2900626271proline+carbon source
2900615361pyruvate+carbon source
2900616634raffinose+carbon source
2900626546rhamnose+carbon source
2900633942ribose+carbon source
2900630911sorbitol+carbon source
2900617992sucrose+carbon source
2900627082trehalose+carbon source
2900616296D-tryptophan+carbon source
2900653426tween 80+carbon source
290064853esculin+hydrolysis
2900617632nitrate+reduction

metabolite production

  • @ref: 29006
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 29006
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29006acid phosphatase+3.1.3.2
29006alkaline phosphatase+3.1.3.1
29006catalase+1.11.1.6
29006cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
20799Yipinglang salt mineYunnanChinaCHNAsia
67772Subterranean brine sample from the Yipinglang salt mineYunnanChinaCHNAsia25.3101.9

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Condition#Saline

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
207991Risk group (German classification)
677721

Sequence information

16S sequences

  • @ref: 20799
  • description: Saccharospirillum salsuginis strain YIM-Y25 16S ribosomal RNA gene, partial sequence
  • accession: EF177670
  • length: 1416
  • database: ena
  • NCBI tax ID: 418750

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharospirillum salsuginis KCTC 22169GCA_014651855scaffoldncbi418750
66792Saccharospirillum salsuginis strain KCTC 22169418750.3wgspatric418750

GC content

  • @ref: 29006
  • GC-content: 58.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
flagellatedyes82.455no
gram-positiveno98.53no
anaerobicno97.741yes
aerobicyes90.134yes
halophileno59.232no
spore-formingno94.939yes
glucose-utilyes91.928yes
thermophileno98.324no
motileyes89.113yes
glucose-fermentno81.736no

External links

@ref: 20799

culture collection no.: DSM 19800, KCTC 22169, CCTCC AA 207033, UCCCB26

straininfo link

  • @ref: 88397
  • straininfo: 401933

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19502320Saccharospirillum salsuginis sp. nov., a gammaproteobacterium from a subterranean brine.Chen YG, Cui XL, Li QY, Wang YX, Tang SK, Liu ZX, Wen ML, Peng Q, Xu LHInt J Syst Evol Microbiol10.1099/ijs.0.003616-02009Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, *Soil Microbiology, Species SpecificityGenetics
Phylogeny20363931Saccharospirillum aestuarii sp. nov., isolated from tidal flat sediment, and an emended description of the genus Saccharospirillum.Choi A, Oh HM, Cho JCInt J Syst Evol Microbiol10.1099/ijs.0.022996-02010Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny28675353Saccharospirillum correiae sp. nov., an endophytic bacterium isolated from the halophyte Halimione portulacoides.Fidalgo C, Rocha J, Proenca DN, Morais PV, Alves A, Henriques IInt J Syst Evol Microbiol10.1099/ijsem.0.0019142017Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, WetlandsTranscriptome
Phylogeny30016235Saccharospirillum mangrovi sp. nov., a bacterium isolated from mangrove sediment.Zhang W, Yuan Y, Su D, Ding L, Yan X, Wu M, Epstein SS, He SInt J Syst Evol Microbiol10.1099/ijsem.0.0028992018Avicennia, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny31671052Saccharospirillum alexandrii sp. nov., isolated from the toxigenic marine dinoflagellate Alexandrium catenella LZT09.Yang Q, Jiang Z, Zhou X, Xie Z, Wang Y, Wang D, Feng L, Yang G, Ge Y, Zhang XInt J Syst Evol Microbiol10.1099/ijsem.0.0038322020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Dinoflagellida/*microbiology, Eutrophication, Fatty Acids/chemistry, Gammaproteobacteria/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20799Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-19800Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19800)
29006Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172543928776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67772Curators of the UCCCBhttps://ucccb.uc.pt/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88397Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID401933.1