Strain identifier

BacDive ID: 130642

Type strain: Yes

Species: Celeribacter indicus

Strain Designation: P73

Strain history: <- Q. Lai, Xiamen Univ., China; P73

NCBI tax ID(s): 1208324 (species)

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General

@ref: 22077

BacDive-ID: 130642

DSM-Number: 27257

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

description: Celeribacter indicus P73 is a mesophilic, Gram-negative bacterium that was isolated from deep sea sediment.

NCBI tax id

  • NCBI tax id: 1208324
  • Matching level: species

strain history

  • @ref: 22077
  • history: <- Q. Lai, Xiamen Univ., China; P73

doi: 10.13145/bacdive130642.20230509.8.1

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 indicus
  • full scientific name: Celeribacter indicus Lai et al. 2014

@ref: 22077

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Celeribacter

species: Celeribacter indicus

full scientific name: Celeribacter indicus Lai et al. 2014

strain designation: P73

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.996

colony morphology

  • @ref: 22077
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

  • @ref: 22077
  • 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

  • @ref: 22077
  • growth: positive
  • type: growth
  • temperature: 25
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.996

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
22077catalase+1.11.1.6
22077cytochrome-c oxidase+1.9.3.1
68369cytochrome 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_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
22077----++-++--+-----+--+

Isolation, sampling and environmental information

isolation

  • @ref: 22077
  • sample type: deep sea sediment
  • geographic location: south-west Indian Ocean Ridge (63.93° E 27.85° S at a depth of 2946 m)
  • latitude: -27.85
  • longitude: 63.93

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4141.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1423;97_2529;98_3128;99_4141&stattab=map
  • Last taxonomy: Celeribacter indicus
  • 16S sequence: EU440950
  • Sequence Identity:
  • Total samples: 450
  • soil counts: 30
  • aquatic counts: 410
  • animal counts: 9
  • plant counts: 1

Safety information

risk assessment

  • @ref: 22077
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22077
  • description: Celeribacter indicus strain P73 16S ribosomal RNA gene, partial sequence
  • accession: EU440950
  • length: 1428
  • database: ena
  • NCBI tax ID: 1208324

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Celeribacter indicus P73GCA_000819565completencbi1208324
66792Celeribacter indicus P73GCA_900106965contigncbi1208324
66792Celeribacter indicus P731208324.3completepatric1208324
66792Celeribacter indicus strain P731208324.11wgspatric1208324
66792Celeribacter indicus DSM 272572693429899draftimg1208324
66792Celeribacter indicus P732528768207draftimg1208324

GC content

  • @ref: 22077
  • GC-content: 66.0
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno57.024no
flagellatedno83.682no
gram-positiveno98.231no
anaerobicno98.152no
aerobicyes84.843no
halophileyes56.966no
spore-formingno96.271no
glucose-utilyes92.092yes
thermophileno98.831yes
glucose-fermentno90.639yes

External links

@ref: 22077

culture collection no.: DSM 27257, LMG 27600, MCCC 1A01112

straininfo link

  • @ref: 89153
  • straininfo: 388574

literature

  • topic: Phylogeny
  • Pubmed-ID: 25256706
  • title: Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov.
  • authors: Lai Q, Cao J, Yuan J, Li F, Shao Z
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.069039-0
  • year: 2014
  • mesh: Bacterial 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/chemistry
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
22077Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27257Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27257)
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/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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
89153Reimer, 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-ID388574.1