Strain identifier

BacDive ID: 13832

Type strain: Yes

Species: Pseudodonghicola xiamenensis

Strain Designation: Y-2

Strain history: <- Z. Shao, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China; Y-2 <- T. Tan

NCBI tax ID(s): 1121479 (strain), 337702 (species)

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General

@ref: 7513

BacDive-ID: 13832

DSM-Number: 18339

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

description: Pseudodonghicola xiamenensis Y-2 is a mesophilic, Gram-negative, ovoid-shaped bacterium that was isolated from surface seawater.

NCBI tax id

NCBI tax idMatching level
337702species
1121479strain

strain history

  • @ref: 7513
  • history: <- Z. Shao, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China; Y-2 <- T. Tan

doi: 10.13145/bacdive13832.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Pseudodonghicola
  • species: Pseudodonghicola xiamenensis
  • full scientific name: Pseudodonghicola xiamenensis (Tan et al. 2009) Hameed et al. 2014

  • synonyms

    • @ref: 20215
    • synonym: Donghicola xiamenensis

@ref: 7513

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Pseudodonghicola

species: Pseudodonghicola xiamenensis

full scientific name: Pseudodonghicola xiamenensis (Tan et al. 2009) Hameed et al. 2014

strain designation: Y-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
28899negative1.5 µm0.85 µmovoid-shaped
69480negative99.993

Culture and growth conditions

culture medium

  • @ref: 7513
  • name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/381
  • composition: Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381; with strain-specific modifications) Composition: NaCl 30.0 g/l Agar 20.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7513positivegrowth28mesophilic
28899positivegrowth18-37
28899positiveoptimum25mesophilic

culture pH

  • @ref: 28899
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

spore formation

@refspore formationconfidence
28899no
69481no93
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
28899NaClpositivegrowth0-12 %
28899NaClpositiveoptimum2 %

observation

  • @ref: 28899
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
28899620642,3-butanediol+carbon source
2889930089acetate+carbon source
2889921217L-alaninamide+carbon source
2889922599arabinose+carbon source
2889929987glutamate+carbon source
2889928087glycogen+carbon source
2889927570histidine+carbon source
2889924996lactate+carbon source
2889928044phenylalanine+carbon source
2889926271proline+carbon source
2889917272propionate+carbon source
2889951850methyl pyruvate+carbon source
2889930031succinate+carbon source
2889953426tween 80+carbon source
2889917632nitrate+reduction

enzymes

@refvalueactivityec
28899catalase+1.11.1.6
28899cytochrome oxidase+1.9.3.1
28899urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 7513
  • sample type: surface seawater
  • geographic location: Fujian, near Haitian Dock of Xiamen island at the west bank of the Taiwan Strait
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_10829.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_5364;97_6477;98_8062;99_10829&stattab=map
  • Last taxonomy: Pseudodonghicola xiamenensis subclade
  • 16S sequence: DQ120728
  • Sequence Identity:
  • Total samples: 38
  • soil counts: 1
  • aquatic counts: 29
  • animal counts: 8

Safety information

risk assessment

  • @ref: 7513
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7513
  • description: Donghicola xiamenensis strain Y-2 16S ribosomal RNA gene, partial sequence
  • accession: DQ120728
  • length: 1424
  • database: ena
  • NCBI tax ID: 1121479

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudodonghicola xiamenensis DSM 18339GCA_000429365scaffoldncbi1121479
66792Pseudodonghicola xiamenensis CGMCC 1.7081GCA_014653505contigncbi337702
66792Donghicola xiamenensis DSM 183391121479.3wgspatric1121479
66792Pseudodonghicola xiamenensis strain CGMCC 1.7081337702.5wgspatric337702
66792Pseudodonghicola xiamenensis DSM 183392524023213draftimg1121479

GC content

@refGC-contentmethod
751362.4high performance liquid chromatography (HPLC)
2889962.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
motileyes61.803no
flagellatedno82.676no
gram-positiveno98.427yes
anaerobicno97.448no
aerobicyes84.006no
halophileyes64.321no
spore-formingno96.161yes
thermophileno98.312yes
glucose-utilyes67.987no
glucose-fermentno90.825no

External links

@ref: 7513

culture collection no.: DSM 18339, CGMCC 1.7081, LMG 24574, MCCC 1A00107

straininfo link

  • @ref: 83008
  • straininfo: 343987

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406808Donghicola xiamenensis sp. nov., a marine bacterium isolated from seawater of the Taiwan Strait in China.Tan T, Wang B, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.000901-02009Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny24844264Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the genus Donghicola Yoon et al. 2007.Hameed A, Shahina M, Lin SY, Nakayan P, Liu YC, Lai WA, Hsu YHInt J Syst Evol Microbiol10.1099/ijs.0.060962-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistryGenetics
Phylogeny25589735Salipiger nanhaiensis sp. nov., a bacterium isolated from deep sea water.Dai X, Shi X, Gao X, Liang J, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.0000662015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7513Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18339)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18339
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
28899Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2533928776041
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)
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
83008Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343987.1StrainInfo: A central database for resolving microbial strain identifiers