Strain identifier

BacDive ID: 13844

Type strain: Yes

Species: Albimonas donghaensis

Strain Designation: DS2

Strain history: <- CJ Kim, KRIBB

NCBI tax ID(s): 356660 (species)

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General

@ref: 7221

BacDive-ID: 13844

DSM-Number: 17890

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

description: Albimonas donghaensis DS2 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 356660
  • Matching level: species

strain history

@refhistory
7221<- C.-J. Kim, Korea Res. Inst. of Biosci. and Biotechnol. (KRIBB); DS2 <- J.-M. Lim
67771<- CJ Kim, KRIBB

doi: 10.13145/bacdive13844.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Albimonas
  • species: Albimonas donghaensis
  • full scientific name: Albimonas donghaensis Lim et al. 2008

@ref: 7221

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Albimonas

species: Albimonas donghaensis

full scientific name: Albimonas donghaensis Lim et al. 2008

strain designation: DS2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32395negative2.1 µm1.2 µmrod-shapedno
67771negative
69480negative98.5

Culture and growth conditions

culture medium

  • @ref: 7221
  • name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514a
  • composition: Name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a) Composition: Agar 15.0 g/l NaCl 9.725 g/l MgCl2 2.95 g/l Bacto peptone 2.5 g/l Na2SO4 1.62 g/l CaCl2 0.9 g/l Yeast extract 0.5 g/l KCl 0.275 g/l NaHCO3 0.08 g/l Fe(III) citrate 0.05 g/l KBr 0.04 g/l SrCl2 0.017 g/l H3BO3 0.011 g/l Na2HPO4 0.004 g/l Na-silicate 0.002 g/l NaF 0.0012 g/l (NH4)NO3 0.0008 g/l Distilled water

culture temp

@refgrowthtypetemperature
7221positivegrowth33
32395positivegrowth10-38
32395positiveoptimum29
67771positivegrowth30

culture pH

@refabilitytypepHPH range
32395positivegrowth6-9.5alkaliphile
32395positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32395aerobe
67771aerobe

spore formation

@refspore formationconfidence
32395no
69480no92.725
69481no100

halophily

@refsaltgrowthtested relationconcentration
32395NaClpositivegrowth0-14 %
32395NaClpositiveoptimum3.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3239522599arabinose+carbon source
3239518222xylose+carbon source

enzymes

@refvalueactivityec
32395acid phosphatase+3.1.3.2
32395alkaline phosphatase+3.1.3.1
32395catalase+1.11.1.6
32395gelatinase+
32395cytochrome oxidase+1.9.3.1
32395urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7221seawaterEast SeaRepublic of KoreaKORAsia
67771From seawater in the East SeaRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_30310.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_866;96_14848;97_18131;98_22552;99_30310&stattab=map
  • Last taxonomy: Albimonas donghaensis subclade
  • 16S sequence: DQ280370
  • Sequence Identity:
  • Total samples: 3284
  • soil counts: 54
  • aquatic counts: 2986
  • animal counts: 227
  • plant counts: 17

Safety information

risk assessment

  • @ref: 7221
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7221
  • description: Albimonas donghaensis strain DS2 16S ribosomal RNA gene, partial sequence
  • accession: DQ280370
  • length: 1383
  • database: nuccore
  • NCBI tax ID: 356660

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Albimonas donghaensis DSM 17890GCA_900106695contigncbi356660
66792Albimonas donghaensis strain DSM 17890356660.7wgspatric356660
66792Albimonas donghaensis DSM 178902693429856draftimg356660

GC content

@refGC-contentmethod
722172.0high performance liquid chromatography (HPLC)
3239572

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98.5yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.664yes
69480spore-formingspore-formingAbility to form endo- or exosporesno92.725yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes85.387yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.369yes
69480flagellatedmotile2+Ability to perform flagellated movementyes62.57no

External links

@ref: 7221

culture collection no.: DSM 17890, KCTC 12586

straininfo link

  • @ref: 83020
  • straininfo: 403174

literature

  • topic: Phylogeny
  • Pubmed-ID: 18175722
  • title: Albimonas donghaensis gen. nov., sp. nov., a non-photosynthetic member of the class Alphaproteobacteria isolated from seawater.
  • authors: Lim JM, Jeon CO, Jang HH, Park DJ, Shin YK, Yeo SH, Kim CJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65429-0
  • year: 2008
  • mesh: Alphaproteobacteria/*classification/genetics/isolation & purification/*physiology, Bacterial Typing Techniques, Base Composition, DNA Fingerprinting/methods, DNA, Bacterial/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7221Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17890)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17890
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
32395Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2861928776041
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
83020Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403174.1StrainInfo: A central database for resolving microbial strain identifiers