Strain identifier

BacDive ID: 24508

Type strain: Yes

Species: Shimia haliotis

Strain Designation: WM35

Strain history: J.-W. Bae WM35.

NCBI tax ID(s): 1280847 (species)

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General

@ref: 21101

BacDive-ID: 24508

DSM-Number: 28453

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

description: Shimia haliotis WM35 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from intestinal tract of an abalone Haliotis discus hannai.

NCBI tax id

  • NCBI tax id: 1280847
  • Matching level: species

strain history

@refhistory
21101<- KACC <- J.-W. Bae; WM35
67770J.-W. Bae WM35.

doi: 10.13145/bacdive24508.20230509.8.1

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 haliotis
  • full scientific name: Shimia haliotis Hyun et al. 2013

@ref: 21101

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Shimia

species: Shimia haliotis

full scientific name: Shimia haliotis Hyun et al. 2013

strain designation: WM35

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31134negative2 µm0.8 µmrod-shapedyes
69480negative99.998

colony morphology

  • @ref: 21101
  • incubation period: 2-3 days

pigmentation

  • @ref: 31134
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21101
  • 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
21101positivegrowth30mesophilic
31134positivegrowth15-37
31134positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31134positivegrowth06-09alkaliphile
31134positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31134
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
31134NaClpositivegrowth0-5 %
31134NaClpositiveoptimum3 %

observation

@refobservation
31134aggregates in clumps
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3113430089acetate+carbon source
3113421217L-alaninamide+carbon source
3113416449alanine+carbon source
3113422653asparagine+carbon source
3113416947citrate+carbon source
3113417234glucose+carbon source
3113429987glutamate+carbon source
3113424996lactate+carbon source
3113428053melibiose+carbon source
3113418257ornithine+carbon source
3113426271proline+carbon source
3113417272propionate+carbon source
3113451850methyl pyruvate+carbon source
3113417822serine+carbon source
3113430031succinate+carbon source
3113417748thymidine+carbon source
3113417632nitrate+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
21101catalase+1.11.1.6
21101cytochrome-c oxidase+1.9.3.1
31134acid phosphatase+3.1.3.2
31134alkaline phosphatase+3.1.3.1
31134alpha-galactosidase+3.2.1.22
31134catalase+1.11.1.6
31134gelatinase+
31134cytochrome 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
21101------++------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
21101intestinal tract of an abalone Haliotis discus hannaiHaliotis discus hannaiJeju, northern coastRepublic of KoreaKORAsia
67770Intestinal tract of an abalone, Haliotis discus hannai, which was collected from the northern coast of JejuHaliotis discus hannaiRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Mollusca
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_94795.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2271;97_2752;98_3418;99_94795&stattab=map
  • Last taxonomy: Shimia haliotis
  • 16S sequence: KC196071
  • Sequence Identity:
  • Total samples: 1019
  • soil counts: 4
  • aquatic counts: 982
  • animal counts: 23
  • plant counts: 10

Safety information

risk assessment

  • @ref: 21101
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21101
  • description: Shimia haliotis strain WM35 16S ribosomal RNA gene, partial sequence
  • accession: KC196071
  • length: 1386
  • database: ena
  • NCBI tax ID: 1280847

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shimia haliotis strain DSM 284531280847.3wgspatric1280847
66792Shimia haliotis DSM 284532619619046draftimg1280847
67770Shimia haliotis DSM 28453GCA_900114415contigncbi1280847

GC content

@refGC-contentmethod
2110153.8
6777053.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes64.803yes
gram-positiveno98.661no
anaerobicno98.129yes
aerobicyes92.343no
halophileyes80.291no
spore-formingno97.093no
thermophileno96.956yes
glucose-utilyes61.623no
flagellatedno72.933no
glucose-fermentno86.786yes

External links

@ref: 21101

culture collection no.: DSM 28453, JCM 18870, KACC 17212

straininfo link

  • @ref: 88366
  • straininfo: 400689

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23811138Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai.Hyun DW, Kim MS, Shin NR, Kim JY, Kim PS, Whon TW, Yun JH, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.053140-02013Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Gastropoda/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny31274408Ruegeria lutea sp. nov., isolated from marine sediment, Masan Bay, South Korea.Kim J, Kim DY, Yang KH, Kim S, Lee SSInt J Syst Evol Microbiol10.1099/ijsem.0.0035682019Bacterial Typing Techniques, Base Composition, Bays, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21101Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28453Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28453)
31134Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172746228776041
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
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.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
88366Reimer, 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-ID400689.1