Strain identifier

BacDive ID: 13861

Type strain: Yes

Species: Celeribacter halophilus

Strain Designation: ZXM137

Strain history: <- LMG <- X.-H. Zhang, Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao

NCBI tax ID(s): 576117 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 18180

BacDive-ID: 13861

DSM-Number: 26270

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

description: Celeribacter halophilus ZXM137 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater collected from a coastal region.

NCBI tax id

  • NCBI tax id: 576117
  • Matching level: species

strain history

  • @ref: 18180
  • history: <- LMG <- X.-H. Zhang, Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao

doi: 10.13145/bacdive13861.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Celeribacter
  • species: Celeribacter halophilus
  • full scientific name: Celeribacter halophilus (Wang et al. 2012) Lai et al. 2014
  • synonyms

    • @ref: 20215
    • synonym: Huaishuia halophila

@ref: 18180

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Celeribacter

species: Celeribacter halophilus

full scientific name: Celeribacter halophilus (Wang et al. 2012) Lai et al. 2014

strain designation: ZXM137

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29904negative0.8 µm0.3 µmrod-shapedno
69480negative99.997

pigmentation

  • @ref: 29904
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 18180
  • 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

@refgrowthtypetemperaturerange
18180positivegrowth28mesophilic
29904positivegrowth04-45
29904positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
29904positivegrowth06-09alkaliphile
29904positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29904
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.969

halophily

  • @ref: 29904
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.5-11 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2990428757fructose+carbon source
2990428260galactose+carbon source
2990417234glucose+carbon source
2990429864mannitol+carbon source
2990437684mannose+carbon source
299044853esculin+hydrolysis
6836817632nitrate-reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836830911sorbitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

  • @ref: 68368
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
29904catalase+1.11.1.6
29904cytochrome oxidase+1.9.3.1
29904urease+3.5.1.5
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368beta-galactosidase+3.2.1.23
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
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
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
18180-+---+/-----------+/----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARANO2N2OX
18180+---------------------
18180+++++-+--+---+-+++--+
18180++----+-----+/-+---+/----

Isolation, sampling and environmental information

isolation

  • @ref: 18180
  • sample type: seawater collected from a coastal region
  • geographic location: Qingdao
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 36.027
  • longitude: 120.184

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_2675.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1423;97_1699;98_2073;99_2675&stattab=map
  • Last taxonomy: Celeribacter halophilus
  • 16S sequence: FJ436725
  • Sequence Identity:
  • Total samples: 1758
  • soil counts: 95
  • aquatic counts: 1574
  • animal counts: 82
  • plant counts: 7

Safety information

risk assessment

  • @ref: 18180
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18180
  • description: Celeribacter halophilus strain ZXM137 16S ribosomal RNA gene, partial sequence
  • accession: FJ436725
  • length: 1370
  • database: ena
  • NCBI tax ID: 576117

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Celeribacter halophilus DSM 26270GCA_003254175scaffoldncbi576117
66792Celeribacter halophilus CGMCC 1.8891GCA_900114135scaffoldncbi576117
66792Celeribacter halophilus ZXM137GCA_001550085scaffoldncbi576117
66792Celeribacter halophilus strain CGMCC 1.8891576117.6wgspatric576117
66792Celeribacter halophilus strain DSM 26270576117.7wgspatric576117
66792Celeribacter halophilus CGMCC 1.88912617270905draftimg576117
66792Celeribacter halophilus ZXM1372728369168draftimg576117
66792Celeribacter halophilus DSM 262702593339274draftimg576117

GC content

@refGC-contentmethod
1818060.1high performance liquid chromatography (HPLC)
2990460.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno85.399no
gram-positiveno98.971no
anaerobicno96.576yes
halophileyes67.675no
spore-formingno97.768no
aerobicyes68.008no
glucose-utilyes88.574no
thermophileno97.188no
motileno65.693no
glucose-fermentno88.064yes

External links

@ref: 18180

culture collection no.: DSM 26270, CGMCC 1.8891, LMG 24854

straininfo link

  • @ref: 83037
  • straininfo: 360660

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21398505Huaishuia halophila gen. nov., sp. nov., isolated from coastal seawater.Wang H, Zhang X, Yan S, Qi Z, Yu Y, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.025536-02011Aerobiosis, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Hydroxybutyrates/metabolism, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Polyesters/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Roseobacter/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureMetabolism
Phylogeny25256706Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov.Lai Q, Cao J, Yuan J, Li F, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.069039-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Phosphatidylglycerols/chemistry, *Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny26297231Celeribacter naphthalenivorans sp. nov., a naphthalene-degrading bacterium from tidal flat sediment.Taek Oh Y, Avedoza C, Lee SS, Jeong SE, Jia B, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.0003812015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Molecular Sequence Data, Naphthalenes, Phospholipids/chemistry, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhodobacteraceae/classification, Seawater/*microbiology, Sequence Analysis, DNA, UbiquinoneGenetics
Phylogeny26303941Celeribacter manganoxidans sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediment of a polymetallic nodule province.Wang L, Liu Y, Wang Y, Dai X, Zhang XHInt J Syst Evol Microbiol10.1099/ijsem.0.0005582015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Manganese/*metabolism, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny29388535Marivivens niveibacter sp. nov., isolated from the seawater of tropical mangrove.Hu D, Wang L, Lai Q, Sun F, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0025442018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*chemistry, Sequence Analysis, DNA, Ubiquinone/chemistry, *WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
18180Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26270)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26270
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
29904Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2627628776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
68368Automatically annotated from API 20E
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
83037Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360660.1StrainInfo: A central database for resolving microbial strain identifiers