Strain identifier

BacDive ID: 23232

Type strain: Yes

Species: Shimia marina

Strain Designation: CL-TA03

Strain history: D. H. Choi CL-TA03.

NCBI tax ID(s): 321267 (species)

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

@ref: 19053

BacDive-ID: 23232

DSM-Number: 26895

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

description: Shimia marina CL-TA03 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from from biofilm in a coastal fish farm.

NCBI tax id

  • NCBI tax id: 321267
  • Matching level: species

strain history

@refhistory
19053<- JCM <- D. H. Choi; CL-TA03
67770D. H. Choi CL-TA03.

doi: 10.13145/bacdive23232.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Shimia
  • species: Shimia marina
  • full scientific name: Shimia marina Choi and Cho 2006

@ref: 19053

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Shimia

species: Shimia marina

full scientific name: Shimia marina Choi and Cho 2006

strain designation: CL-TA03

type strain: yes

Morphology

cell morphology

  • @ref: 31768
  • gram stain: negative
  • cell length: 0.8-3.6 µm
  • cell width: 0.3-0.6 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 19053
  • incubation period: 1-2 days

pigmentation

  • @ref: 31768
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19053
  • 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
19053positivegrowth30mesophilic
31768positivegrowth15-35
31768positiveoptimum30-35mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31768positivegrowth06-10alkaliphile
31768positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31768
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31768
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31768NaClpositivegrowth03-07 %
31768NaClpositiveoptimum03-07 %

observation

@refobservation
31768aggregates in chains
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3176816947citrate+carbon source
3176816236ethanol+carbon source
3176815428glycine+carbon source
3176828087glycogen+carbon source
3176825017leucine+carbon source
3176818257ornithine+carbon source
3176815361pyruvate+carbon source
3176816634raffinose+carbon source
3176830031succinate+carbon source
3176817632nitrate+reduction
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
19053catalase+1.11.1.6
19053cytochrome-c oxidase+1.9.3.1
31768alkaline phosphatase+3.1.3.1
31768catalase+1.11.1.6
31768gelatinase+
31768cytochrome 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
19053--------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19053from biofilm in a coastal fish farmTongyeongRepublic of KoreaKORAsia
67770Biofilm in a coastal fish farm in TongyeongRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Aquaculture
#Environmental#Biofilm
#Host#Fishes

taxonmaps

  • @ref: 69479
  • File name: preview.99_8298.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2271;97_2752;98_6038;99_8298&stattab=map
  • Last taxonomy: Shimia marina
  • 16S sequence: AY962292
  • Sequence Identity:
  • Total samples: 1630
  • soil counts: 16
  • aquatic counts: 1469
  • animal counts: 141
  • plant counts: 4

Safety information

risk assessment

  • @ref: 19053
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19053
  • description: Shimia marina strain CL-TA03 16S ribosomal RNA gene, partial sequence
  • accession: AY962292
  • length: 1382
  • database: ena
  • NCBI tax ID: 321267

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shimia marina DSM 26895GCA_900112745scaffoldncbi321267
66792Shimia marina strain DSM 26895321267.13wgspatric321267
66792Shimia marina DSM 268952619618961draftimg321267

GC content

@refGC-contentmethod
1905357.2high performance liquid chromatography (HPLC)
3176857.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes60.951no
flagellatedno74.263no
gram-positiveno98.797no
anaerobicno98.182no
aerobicyes88.616yes
halophileyes80.063no
spore-formingno97.215yes
glucose-fermentno91.876yes
thermophileno98.577yes
glucose-utilyes55.884yes

External links

@ref: 19053

culture collection no.: DSM 26895, JCM 13038, KCCM 42117, BCRC 80068, CIP 109331, NCIMB 14294

straininfo link

  • @ref: 87458
  • straininfo: 292325

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16902023Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm.Choi DH, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.64235-02006Agar, Aquaculture, Base Composition, *Biofilms, Culture Media, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Locomotion, *Marine Biology, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Roseobacter/chemistry/*classification/isolation & purification/physiology, Salts, Sequence Homology, Nucleic Acid, Species Specificity, TemperatureCultivation
Phylogeny20453104Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera.Chen MH, Sheu SY, Chen CA, Wang JT, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.022848-02010Aerobiosis, Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella/physiology, Locomotion, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TaiwanGenetics
Phylogeny23907225Shimia biformata sp. nov., isolated from surface seawater, and emended description of the genus Shimia Choi and Cho 2006.Hameed A, Shahina M, Lin SY, Lai WA, Hsu YH, Liu YC, Huang YM, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.053553-02013Bacterial Typing Techniques, Base Composition, Cadaverine/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistryGenetics
Genetics26852259Draft genome sequence of Shimia marina CECT 7688(T).Rodrigo-Torres L, Pujalte MJ, Arahal DRMar Genomics10.1016/j.margen.2016.01.0062016Base Composition, *Genome, Bacterial, Molecular Sequence Annotation, Republic of Korea, Rhodobacteraceae/*genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19053Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26895)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26895
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
31768Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2804128776041
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
87458Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292325.1StrainInfo: A central database for resolving microbial strain identifiers