Strain identifier

BacDive ID: 5650

Type strain: Yes

Species: Tenacibaculum lutimaris

Strain Designation: TF-26

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 285258 (species)

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General

@ref: 6382

BacDive-ID: 5650

DSM-Number: 16505

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

description: Tenacibaculum lutimaris TF-26 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat.

NCBI tax id

  • NCBI tax id: 285258
  • Matching level: species

strain history

@refhistory
6382<- J.-H. Yoon; TF-26
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive5650.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Tenacibaculum
  • species: Tenacibaculum lutimaris
  • full scientific name: Tenacibaculum lutimaris Yoon et al. 2005

@ref: 6382

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Tenacibaculum

species: Tenacibaculum lutimaris

full scientific name: Tenacibaculum lutimaris Yoon et al. 2005

strain designation: TF-26

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
31371negative6 µm0.5 µmrod-shapedyesgliding
67771yesgliding
67771negative
69480negative99.987

pigmentation

  • @ref: 31371
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6382
  • 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
6382positivegrowth30mesophilic
31371positivegrowth10-39
31371positiveoptimum33.5mesophilic
67771positivegrowth30-37mesophilic

culture pH

@refabilitytypepH
31371positivegrowth07-08
31371positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
31371NaClpositivegrowth02-03 %
31371NaClpositiveoptimum2.5 %

observation

  • @ref: 67771
  • observation: quinones: MK-6

enzymes

@refvalueactivityec
31371catalase+1.11.1.6
31371cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6382tidal flatYellow Sea, Daepo BeachRepublic of KoreaKORAsia
67771From tidal flat; KoreaYellow Sea, Daepo BeachRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_7717.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_214;96_2278;97_2761;98_5642;99_7717&stattab=map
  • Last taxonomy: Tenacibaculum lutimaris
  • 16S sequence: AY661691
  • Sequence Identity:
  • Total samples: 34
  • aquatic counts: 27
  • animal counts: 7

Safety information

risk assessment

  • @ref: 6382
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6382
  • description: Tenacibaculum lutimaris strain TF-26 16S ribosomal RNA gene, partial sequence
  • accession: AY661691
  • length: 1473
  • database: ena
  • NCBI tax ID: 285258

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tenacibaculum lutimaris DSM 16505GCA_003610735scaffoldncbi285258
66792Tenacibaculum lutimaris strain DSM 16505285258.3wgspatric285258
66792Tenacibaculum lutimaris DSM 16505 (v2)2739368073draftimg285258

GC content

@refGC-content
3137132.6
6777132.3-32.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.386no
flagellatedno96.172yes
gram-positiveno98.676yes
anaerobicno99.56yes
aerobicyes93.343no
halophileno84.714no
spore-formingno96.464no
glucose-utilyes77.779no
thermophileno98.457yes
glucose-fermentno92.88no

External links

@ref: 6382

culture collection no.: DSM 16505, KCTC 12302, CIP 12302

straininfo link

  • @ref: 75133
  • straininfo: 138045

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774664Tenacibaculum lutimaris sp. nov., isolated from a tidal flat in the Yellow Sea, Korea.Yoon JH, Kang SJ, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.63416-02005Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification/physiology, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny18319452Tenacibaculum adriaticum sp. nov., from a bryozoan in the Adriatic Sea.Heindl H, Wiese J, Imhoff JFInt J Syst Evol Microbiol10.1099/ijs.0.65383-02008Animals, Bacterial Typing Techniques, Base Composition, Bryozoa/*microbiology, Croatia, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification/physiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny18398166Tenacibaculum aiptasiae sp. nov., isolated from a sea anemone Aiptasia pulchella.Wang JT, Chou YJ, Chou JH, Chen CA, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.65437-02008Animals, Base Composition, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Flavobacteriaceae/chemistry/classification/*genetics/*isolation & purification, Genes, Bacterial, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sea Anemones/*microbiology, Species Specificity, Terminology as TopicGenetics
Phylogeny23733002Tenacibaculum caenipelagi sp. nov., a member of the family Flavobacteriaceae isolated from tidal flat sediment.Park S, Yoon JHAntonie Van Leeuwenhoek10.1007/s10482-013-9941-12013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Tenacibaculum/*classification/genetics/*isolation & purificationEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6382Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16505)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16505
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
31371Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2768428776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75133Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138045.1StrainInfo: A central database for resolving microbial strain identifiers