Strain identifier

BacDive ID: 130645

Type strain: Yes

Species: Litoreibacter ascidiaceicola

Strain Designation: RSS4-C1

Strain history: <- KCTC <- J. H. Yoon <- Y.-O. Kim; RSS4-C1

NCBI tax ID(s): 1486859 (species)

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General

@ref: 22081

BacDive-ID: 130645

DSM-Number: 100566

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

description: Litoreibacter ascidiaceicola RSS4-C1 is a mesophilic, Gram-negative bacterium that was isolated from golden sea squirt ( Halocynthia aurantium.

NCBI tax id

  • NCBI tax id: 1486859
  • Matching level: species

strain history

  • @ref: 22081
  • history: <- KCTC <- J. H. Yoon <- Y.-O. Kim; RSS4-C1

doi: 10.13145/bacdive130645.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Litoreibacter
  • species: Litoreibacter ascidiaceicola
  • full scientific name: Litoreibacter ascidiaceicola Kim et al. 2014

@ref: 22081

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Litoreibacter

species: Litoreibacter ascidiaceicola

full scientific name: Litoreibacter ascidiaceicola Kim et al. 2014

strain designation: RSS4-C1

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.995

colony morphology

  • @ref: 22081
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

  • @ref: 22081
  • 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

  • @ref: 22081
  • growth: positive
  • type: growth
  • temperature: 25
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-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
22081catalase+1.11.1.6
22081cytochrome-c oxidase+1.9.3.1
68369gelatinase-
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
22081+----+/--++-+/-+++---++/--

Isolation, sampling and environmental information

isolation

  • @ref: 22081
  • sample type: golden sea squirt ( Halocynthia aurantium
  • host species: Halocynthia aurantium
  • geographic location: Namhae, East sea
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Tunicata

taxonmaps

  • @ref: 69479
  • File name: preview.99_1305.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_572;97_665;98_1031;99_1305&stattab=map
  • Last taxonomy: Litoreibacter
  • 16S sequence: KJ410763
  • Sequence Identity:
  • Total samples: 1394
  • soil counts: 58
  • aquatic counts: 1213
  • animal counts: 106
  • plant counts: 17

Safety information

risk assessment

  • @ref: 22081
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22081
  • description: Litoreibacter ascidiaceicola strain RSS4-C1 16S ribosomal RNA gene, partial sequence
  • accession: KJ410763
  • length: 1389
  • database: ena
  • NCBI tax ID: 1486859

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Litoreibacter ascidiaceicola DSM 100566GCA_900129235contigncbi1486859
66792Litoreibacter ascidiaceicola strain DSM 1005661486859.3wgspatric1486859
66792Litoreibacter ascidiaceicola DSM 1005662695420937draftimg1486859

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno77.463no
gram-positiveno98.489no
anaerobicno97.621no
halophileyes76.862no
spore-formingno96.656no
glucose-utilyes64.253yes
flagellatedno91.61no
thermophileno95.534yes
aerobicyes92.185no
glucose-fermentno90.589no

External links

@ref: 22081

culture collection no.: DSM 100566, CECT 8539, KCTC 42050

straininfo link

  • @ref: 89156
  • straininfo: 396654

literature

  • topic: Phylogeny
  • Pubmed-ID: 24812362
  • title: Litoreibacter ascidiaceicola sp. nov., isolated from the golden sea squirt Halocynthia aurantium.
  • authors: Kim YO, Park S, Nam BH, Park JM, Kim DG, Yoon JH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.064196-0
  • year: 2014
  • mesh: Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistry, Urochordata/*microbiology
  • topic2: Genetics

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
22081Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100566Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100566)
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
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
89156Reimer, 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-ID396654.1