Strain identifier

BacDive ID: 130648

Type strain: Yes

Species: Halocynthiibacter namhaensis

Strain Designation: RA2-3, RA2-3(T)

Strain history: <- JH Yoon, Sungkyunkwan Univ.

NCBI tax ID(s): 1290553 (species)

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General

@ref: 22120

BacDive-ID: 130648

DSM-Number: 100421

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

description: Halocynthiibacter namhaensis RA2-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea squirt Halocynthia roretzi.

NCBI tax id

  • NCBI tax id: 1290553
  • Matching level: species

strain history

@refhistory
22120<- KCTC <- J. H. Yoon; RA2-3
67771<- JH Yoon, Sungkyunkwan Univ.

doi: 10.13145/bacdive130648.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Halocynthiibacter
  • species: Halocynthiibacter namhaensis
  • full scientific name: Halocynthiibacter namhaensis Kim et al. 2014

@ref: 22120

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Halocynthiibacter

species: Halocynthiibacter namhaensis

full scientific name: Halocynthiibacter namhaensis Kim et al. 2014

strain designation: RA2-3, RA2-3(T)

type strain: yes

Morphology

cell morphology

  • @ref: 67771
  • gram stain: negative

colony morphology

  • @ref: 22120
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

  • @ref: 22120
  • 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
22120positivegrowth25mesophilic
67771positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

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
22120catalase+1.11.1.6
22120cytochrome-c 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
22120------------------+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
22120sea squirt Halocynthia roretziHalocynthia roretziSouth SeaRepublic of KoreaKORAsia
67771From sea squirtthe South SeaRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Tunicata

taxonmaps

  • @ref: 69479
  • File name: preview.99_5645.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2657;97_3338;98_4207;99_5645&stattab=map
  • Last taxonomy: Halocynthiibacter namhaensis subclade
  • 16S sequence: KC416645
  • Sequence Identity:
  • Total samples: 884
  • soil counts: 29
  • aquatic counts: 810
  • animal counts: 44
  • plant counts: 1

Safety information

risk assessment

  • @ref: 22120
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22120
  • description: Halocynthiibacter namhaensis strain RA2-3 16S ribosomal RNA gene, partial sequence
  • accession: KC416645
  • length: 1391
  • database: ena
  • NCBI tax ID: 1290553

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halocynthiibacter namhaensis RA2-3GCA_000812685contigncbi1290553
66792Halocynthiibacter namhaensis RA2-32636415494draftimg1290553

External links

@ref: 22120

culture collection no.: DSM 100421, KCTC 32362, NBRC 109999

straininfo link

  • @ref: 89159
  • straininfo: 396584

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24573327Halocynthiibacter namhaensis gen. nov., sp. nov., a novel alphaproteobacterium isolated from sea squirt Halocynthia roretzi.Kim YO, Park S, Kim H, Park DS, Nam BH, Kim DG, Yoon JHAntonie Van Leeuwenhoek10.1007/s10482-014-0142-32014Animals, Aquatic Organisms/microbiology, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Urochordata/*microbiologyGenetics
Phylogeny25713042Pseudohalocynthiibacter aestuariivivens gen. nov., sp. nov., isolated from a tidal flat.Won SM, Park S, Park JM, Kim BC, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.0001282015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryGenetics
Phylogeny26243211Halocynthiibacter arcticus sp. nov., isolated from Arctic marine sediment.Baek K, Lee YM, Shin SC, Hwang K, Hwang CY, Hong SG, Lee HKInt J Syst Evol Microbiol10.1099/ijsem.0.0005072015

Reference

@idauthorstitledoi/urlcatalogue
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
22120Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100421Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100421)
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
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/
89159Reimer, 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-ID396584.1