Strain identifier

BacDive ID: 130812

Type strain: Yes

Species: Simiduia litorea

Strain history: NRIC 0917 <-- L. A. Romanenko KMM 9504.

NCBI tax ID(s): 1435348 (species)

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General

@ref: 22064

BacDive-ID: 130812

DSM-Number: 29670

keywords: 16S sequence, Bacteria, mesophilic

description: Simiduia litorea DSM 29670 is a mesophilic bacterium that was isolated from seashore sediment, water depth 0.5 m.

NCBI tax id

  • NCBI tax id: 1435348
  • Matching level: species

strain history

@refhistory
22064<- N. Tanaka, NODAI Culture Collection Centre, Tokyo University of Agriculture <- L. A. Romanenko, G.B. Eliakov Pacific Institute of Bioorganic Chemistry, Vladivostoc
67770NRIC 0917 <-- L. A. Romanenko KMM 9504.

doi: 10.13145/bacdive130812.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Cellvibrionales
  • family: Cellvibrionaceae
  • genus: Simiduia
  • species: Simiduia litorea
  • full scientific name: Simiduia litorea Tanaka et al. 2014

@ref: 22064

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Cellvibrionaceae, not assigned to order

family: Cellvibrionaceae

genus: Simiduia

species: Simiduia litorea

full scientific name: Simiduia litorea Tanaka et al. 2014

type strain: yes

Morphology

multimedia

  • @ref: 22064
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_29670.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 22064
  • 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
22064positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

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
68369cytochrome 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_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
22064-----+--++-+++------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
22064seashore sediment, water depth 0.5 mSea of JapanRussiaRUSAsia
67770Sediment from the seashore of the Sea of Japan, at a water depth of 0.5 mRussiaRUS

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_98015.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_235;96_2150;97_2596;98_27831;99_98015&stattab=map
  • Last taxonomy: Simiduia
  • 16S sequence: AB894237
  • Sequence Identity:
  • Total samples: 1693
  • soil counts: 40
  • aquatic counts: 1602
  • animal counts: 45
  • plant counts: 6

Safety information

risk assessment

  • @ref: 22064
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22064
  • description: Simiduia litorea gene for 16S ribosomal RNA, partial sequence
  • accession: AB894237
  • length: 1506
  • database: ena
  • NCBI tax ID: 1435348

External links

@ref: 22064

culture collection no.: DSM 29670, JCM 19759, KMM 9504, NRIC 0917

straininfo link

  • @ref: 89300
  • straininfo: 407029

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24827709Simiduia litorea sp. nov., isolated from seashore sediments of the Sea of Japan.Tanaka N, Romanenko LA, Svetashev VI, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.061846-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny25106923Simiduia curdlanivorans sp. nov., a curdlan-degrading bacterium isolated from the junction between the ocean and a freshwater spring, and emended description of the genus Simiduia.Park S, Kim SI, Jung YT, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.065334-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Gammaproteobacteria/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, beta-Glucans/*metabolismGenetics
29597058Structure of 3,6-dideoxy-3-[(R)-2-hydroxypropanoylamino]-D-galactose-containing O-polysaccharide from marine bacterium Simiduia litorea KMM 9504(T).Kokoulin MS, Romanenko LA, Mikhailov VVCarbohydr Res10.1016/j.carres.2018.03.0102018Gammaproteobacteria/*chemistry, Lipopolysaccharides/*chemistry, Magnetic Resonance Spectroscopy, O Antigens/chemistry

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
22064Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29670Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29670)
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/
89300Reimer, 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-ID407029.1