Strain identifier

BacDive ID: 130638

Type strain: Yes

Species: Lutimaribacter litoralis

Strain Designation: KU5D5

Strain history: <- H Iwaki, Kansai Univ., Japan

NCBI tax ID(s): 1010611 (species)

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General

@ref: 22066

BacDive-ID: 130638

DSM-Number: 29506

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

description: Lutimaribacter litoralis KU5D5 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 1010611
  • Matching level: species

strain history

@refhistory
22066<- KCTC <- H. Iwaki, Kansai University, Osaka, Japan; KU5D5
67770H. Iwaki KU5D5.
67771<- H Iwaki, Kansai Univ., Japan

doi: 10.13145/bacdive130638.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Lutimaribacter
  • species: Lutimaribacter litoralis
  • full scientific name: Lutimaribacter litoralis Iwaki et al. 2013

  • synonyms

    @refsynonym
    20215Thalassovita litoralis
    20215Thalassobius litoralis

@ref: 22066

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Thalassobius

species: Thalassobius litoralis

full scientific name: Thalassobius litoralis (Iwaki et al. 2013) Hördt et al. 2020

strain designation: KU5D5

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
67771negative
69480negative99.997

colony morphology

  • @ref: 22066
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

  • @ref: 22066
  • 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
22066positivegrowth25mesophilic
67770positivegrowth25mesophilic
67771positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.956

observation

@refobservation
67770quinones: Q-10
67771quinones: Q-10

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
22066catalase+1.11.1.6
22066cytochrome-c 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
22066----------------++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
22066seawatercoastal region of Goto IslandsJapanJPNAsia
67770Seawater obtained from the coastal region of the Goto IslandsJapanJPNAsia
67771From seawaterGoto IslandsJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_174902.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_6918;97_84394;98_114456;99_174902&stattab=map
  • Last taxonomy: Lutimaribacter litoralis subclade
  • 16S sequence: AB627076
  • Sequence Identity:
  • Total samples: 380
  • soil counts: 7
  • aquatic counts: 302
  • animal counts: 54
  • plant counts: 17

Safety information

risk assessment

  • @ref: 22066
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22066
  • description: Lutimaribacter litoralis gene for 16S rRNA, partial sequence
  • accession: AB627076
  • length: 1425
  • database: ena
  • NCBI tax ID: 1010611

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thalassovita litoralis DSM 29506GCA_900182725contigncbi1010611
66792Lutimaribacter litoralis strain DSM 295061010611.6wgspatric1010611
66792Lutimaribacter litoralis DSM 295062724679730draftimg1010611

GC content

@refGC-contentmethod
6777158.9
6777058.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno78.437no
flagellatedno92.087no
gram-positiveno98.416no
anaerobicno98.987yes
aerobicyes83.169yes
halophileyes72.341no
spore-formingno96.412no
thermophileno97.936yes
glucose-utilno66.99yes
glucose-fermentno89.417yes

External links

@ref: 22066

culture collection no.: DSM 29506, JCM 17792, KCTC 23660

straininfo link

  • @ref: 89149
  • straininfo: 405226

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23370733Isolation and characterization of a marine cyclohexylacetate-degrading bacterium Lutimaribacter litoralis sp. nov., and reclassification of Oceanicola pacificus as Lutimaribacter pacificus comb. nov.Iwaki H, Yasukawa N, Fujioka M, Takada K, Hasegawa YCurr Microbiol10.1007/s00284-013-0321-x2013Acetates/*metabolism, Bacterial Typing Techniques, Base Composition, Cyclohexanes/*metabolism, DNA, Bacterial/genetics, Environmental Restoration and Remediation, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification, Seawater/*microbiologyMetabolism
Phylogeny27334981Lutimaribacter marinistellae sp. nov., isolated from a starfish.Zhang Y, Tang P, Xu Y, Fang W, Wang X, Fang Z, Xiao YInt J Syst Evol Microbiol10.1099/ijsem.0.0012512016Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Starfish/*microbiology, Ubiquinone/chemistryTranscriptome

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
22066Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29506Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29506)
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
89149Reimer, 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-ID405226.1