Strain identifier

BacDive ID: 24516

Type strain: Yes

Species: Salinihabitans flavidus

Strain Designation: ISL-46

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 569882 (species)

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General

@ref: 21201

BacDive-ID: 24516

DSM-Number: 27842

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

description: Salinihabitans flavidus ISL-46 is an aerobe, Gram-negative, motile bacterium that was isolated from marine solar saltern.

NCBI tax id

  • NCBI tax id: 569882
  • Matching level: species

strain history

@refhistory
21201<- KCTC
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive24516.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Salinihabitans
  • species: Salinihabitans flavidus
  • full scientific name: Salinihabitans flavidus Yoon et al. 2009

@ref: 21201

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Salinihabitans

species: Salinihabitans flavidus

full scientific name: Salinihabitans flavidus Yoon et al. 2009

strain designation: ISL-46

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29235negative2.65 µm0.45 µmrod-shapedyes
67771negative
69480negative97.5

colony morphology

@refincubation period
212012-3 days
610803 days

pigmentation

  • @ref: 29235
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21201
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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

@refgrowthtypetemperature
21201positivegrowth30
29235positivegrowth04-37
29235positiveoptimum30
61080positivegrowth30
67771positivegrowth30

culture pH

@refabilitytypepH
29235positivegrowth5.5-6.0
29235positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29235aerobe
61080aerobe
67771aerobe

spore formation

@refspore formationconfidence
69480no91.334
69481no100

halophily

@refsaltgrowthtested relationconcentration
29235NaClpositivegrowth<18 %
29235NaClpositiveoptimum7 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2923530089acetate+carbon source
2923525115malate+carbon source
2923515361pyruvate+carbon source
2923530031succinate+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
21201catalase+1.11.1.6
29235alkaline phosphatase+3.1.3.1
29235catalase+1.11.1.6
29235cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21201--------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
21201marine solar salternYellow SeaRepublic of KoreaKORAsia
61080Marine solar saltern sedimentYellow SeaRepublic of KoreaKORAsia2006
67771From salten fieldRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Condition#Saline
#Engineered#Industrial#Industrial production
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_121887.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_47926;97_61610;98_82019;99_121887&stattab=map
  • Last taxonomy: Salinihabitans flavidus subclade
  • 16S sequence: FJ265707
  • Sequence Identity:
  • Total samples: 11
  • soil counts: 2
  • aquatic counts: 9

Safety information

risk assessment

  • @ref: 21201
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21201
  • description: Rhodobacteraceae bacterium ISL-46 16S ribosomal RNA gene, partial sequence
  • accession: FJ265707
  • length: 1421
  • database: nuccore
  • NCBI tax ID: 569882

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salinihabitans flavidus DSM 27842GCA_900110425scaffoldncbi569882
66792Salinihabitans flavidus strain DSM 27842569882.3wgspatric569882
66792Salinihabitans flavidus DSM 278422634166353draftimg569882

GC content

@refGC-contentmethod
2120163.5high performance liquid chromatography (HPLC)
2923563.5

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.5no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.869yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes77.653yes
69480spore-formingspore-formingAbility to form endo- or exosporesno91.334no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.159no
69480flagellatedmotile2+Ability to perform flagellated movementyes53.898no

External links

@ref: 21201

culture collection no.: DSM 27842, CCUG 56758, KCTC 22485, ISL -46

straininfo link

  • @ref: 88371
  • straininfo: 400206

literature

  • topic: Phylogeny
  • Pubmed-ID: 19622639
  • title: Salinihabitans flavidus gen. nov., sp. nov., isolated from a marine solar saltern.
  • authors: Yoon JH, Kang SJ, Lee SY, Oh TK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.009183-0
  • year: 2009
  • mesh: Alphaproteobacteria/classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/*metabolism
  • topic2: Metabolism

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
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
21201Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27842Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27842)
29235Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172565628776041
61080Curators of the CCUGhttps://www.ccug.se/strain?id=56758Culture Collection University of Gothenburg (CCUG) (CCUG 56758)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
88371Reimer, 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-ID400206.1