Strain identifier

BacDive ID: 5851

Type strain: Yes

Species: Hahella ganghwensis

Strain Designation: FR1050

Strain history: CIP <- 2005, JCM <- J. Chun, Seoul, Republic of Korea: strain FR1050

NCBI tax ID(s): 1121935 (strain), 286420 (species)

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General

@ref: 6706

BacDive-ID: 5851

DSM-Number: 17046

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

description: Hahella ganghwensis FR1050 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment of getbol, the Korean tidal flat.

NCBI tax id

NCBI tax idMatching level
1121935strain
286420species

strain history

@refhistory
6706<- J. Chun; FR1050
67770J. Chun FR1050.
67771<- J Chun, Seoul National Univ.
119528CIP <- 2005, JCM <- J. Chun, Seoul, Republic of Korea: strain FR1050

doi: 10.13145/bacdive5851.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Hahellaceae
  • genus: Hahella
  • species: Hahella ganghwensis
  • full scientific name: Hahella ganghwensis Baik et al. 2005

@ref: 6706

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Hahellaceae

genus: Hahella

species: Hahella ganghwensis

full scientific name: Hahella ganghwensis Baik et al. 2005

strain designation: FR1050

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31366negative1.25 µm0.45 µmrod-shaped
67771negative
69480yes97.428
69480negative99.984
119528negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6706BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
37638Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119528CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6706positivegrowth28mesophilic
31366positivegrowth15-40
31366positiveoptimum35mesophilic
37638positivegrowth25mesophilic
67770positivegrowth25mesophilic
67771positivegrowth25mesophilic
119528positivegrowth5-41

culture pH

@refabilitytypepHPH range
31366positivegrowth05-10alkaliphile
31366positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31366aerobe
67771aerobe
119528obligate aerobe

spore formation

@refspore formationconfidence
31366no
69481no100
69480no99.951

halophily

@refsaltgrowthtested relationconcentration
31366NaClpositivegrowth01-10 %
31366NaClpositiveoptimum5 %
119528NaClnogrowth0 %
119528NaClnogrowth2 %
119528NaClnogrowth4 %
119528NaClnogrowth6 %
119528NaClnogrowth8 %
119528NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3136625115malate+carbon source
31366506227N-acetylglucosamine+carbon source
11952816947citrate-carbon source
1195284853esculin-hydrolysis
11952817632nitrate+reduction
11952816301nitrite-reduction

metabolite production

  • @ref: 119528
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11952815688acetoin-
11952817234glucose-

enzymes

@refvalueactivityec
31366catalase+1.11.1.6
31366cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
119528oxidase+
119528beta-galactosidase-3.2.1.23
119528alcohol dehydrogenase-1.1.1.1
119528gelatinase+/-
119528amylase-
119528caseinase+3.4.21.50
119528catalase+1.11.1.6
119528tween esterase-
119528gamma-glutamyltransferase+2.3.2.2
119528lecithinase+
119528lipase+
119528lysine decarboxylase-4.1.1.18
119528ornithine decarboxylase-4.1.1.17
119528phenylalanine ammonia-lyase-4.3.1.24
119528tryptophan deaminase-
119528urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119528-++++++---++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119528---++-----------+-+------------+---------------------------++----------+---+-----------++--+-+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6706sediment of getbol, the Korean tidal flatGanghwa IslandRepublic of KoreaKORAsia
67770Sediment of getbol, the Korean tidal flatRepublic of KoreaKORAsia
67771From mud flat sedimentRepublic of KoreaKORAsia
119528Environment, Sediment sample of getbol (Korean tidal flat)Ganghwa IslandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_7571.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_643;96_3529;97_4334;98_5548;99_7571&stattab=map
  • Last taxonomy: Hahella ganghwensis subclade
  • 16S sequence: AY676463
  • Sequence Identity:
  • Total samples: 2442
  • soil counts: 373
  • aquatic counts: 1746
  • animal counts: 264
  • plant counts: 59

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67061Risk group (German classification)
1195281Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6706
  • description: Hahella ganghwensis 16S ribosomal RNA gene, partial sequence
  • accession: AY676463
  • length: 1454
  • database: ena
  • NCBI tax ID: 286420

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hahella ganghwensis DSM 170461121935.11wgspatric1121935
66792Hahella ganghwensis DSM 170462519899685draftimg1121935
67770Hahella ganghwensis DSM 17046GCA_000376785contigncbi1121935

GC content

@refGC-contentmethod
670644
6777044thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.589no
flagellatedyes93.354no
gram-positiveno99.053yes
anaerobicno94.866no
halophileyes56.185no
spore-formingno92.466no
thermophileno99.346yes
glucose-utilyes90.522no
aerobicyes91.066yes
glucose-fermentno87.51no

External links

@ref: 6706

culture collection no.: DSM 17046, JCM 12486, KCTC 12277, CIP 108747, IMSNU 60136

straininfo link

  • @ref: 75332
  • straininfo: 132253

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774643Hahella ganghwensis sp. nov., isolated from tidal flat sediment.Baik KS, Seong CN, Kim EM, Yi H, Bae KS, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.63411-02005Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Gammaproteobacteria/chemistry/*classification/genetics/isolation & purification, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny23979563Nonhongiella spirulinensis gen. nov., sp. nov., a bacterium isolated from a cultivation pond of Spirulina platensis in Sanya, China.Wang G, Fan J, Wu H, Zhang X, Li G, Zhang H, Yang X, Ye F, Xiang W, Li XAntonie Van Leeuwenhoek10.1007/s10482-013-0012-42013Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, *Water MicrobiologyGenetics
Phylogeny27216767Allohahella marinimesophila gen. nov., sp. nov., isolated from seawater and reclassification of Hahella antarctica as Allohahella antarctica comb. nov.Han Y, Zhao R, Yu T, Li Z, Zhang XHInt J Syst Evol Microbiol10.1099/ijsem.0.0011742016Antarctic Regions, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6706Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17046)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17046
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
31366Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2767928776041
37638Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6410
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
75332Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132253.1StrainInfo: A central database for resolving microbial strain identifiers
119528Curators of the CIPCollection of Institut Pasteur (CIP 108747)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108747