Strain identifier

BacDive ID: 134184

Type strain: Yes

Species: Lutibacter litoralis

Strain Designation: CL-TF09

Strain history: D. H. Choi CL-TF09.

NCBI tax ID(s): 321268 (species)

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General

@ref: 31734

BacDive-ID: 134184

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

description: Lutibacter litoralis CL-TF09 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from tidal flat sediment.

NCBI tax id

  • NCBI tax id: 321268
  • Matching level: species

strain history

  • @ref: 67770
  • history: D. H. Choi CL-TF09.

doi: 10.13145/bacdive134184.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Lutibacter
  • species: Lutibacter litoralis
  • full scientific name: Lutibacter litoralis Choi and Cho 2006

@ref: 31734

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Lutibacter

species: Lutibacter litoralis

strain designation: CL-TF09

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31734negative1-5.7 µm0.3-0.8 µmrod-shapedno
69480negative99.995

pigmentation

  • @ref: 31734
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
31734positivegrowth05-30
31734positiveoptimum25-30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
31734positivegrowth07-08
31734positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

  • @ref: 31734
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31734no
69481no100
69480no99.981

halophily

@refsaltgrowthtested relationconcentration
31734NaClpositivegrowth01-05 %
31734NaClpositiveoptimum01-05 %

observation

@refobservation
31734aggregates in chains
67770quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3173429016arginine+carbon source
3173416947citrate+carbon source
3173428757fructose+carbon source
3173415428glycine+carbon source
3173428087glycogen+carbon source
3173418257ornithine+carbon source
3173415361pyruvate+carbon source
3173416634raffinose+carbon source
3173417814salicin+carbon source
3173430911sorbitol+carbon source
3173430031succinate+carbon source
317344853esculin+hydrolysis

enzymes

@refvalueactivityec
31734catalase+1.11.1.6
31734gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
31734tidal flat sediment
67770Tidal flat sediment in GanghwaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Tidal flat
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_66396.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_333;96_2985;97_10235;98_12563;99_66396&stattab=map
  • Last taxonomy: Lutibacter
  • 16S sequence: AY962293
  • Sequence Identity:
  • Total samples: 2355
  • soil counts: 89
  • aquatic counts: 2223
  • animal counts: 38
  • plant counts: 5

Sequence information

16S sequences

  • @ref: 31734
  • description: Lutibacter litoralis strain CL-TF09 16S ribosomal RNA gene, partial sequence
  • accession: AY962293
  • length: 1444
  • database: nuccore
  • NCBI tax ID: 321268

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lutibacter litoralis JCM 13034GCA_014646675scaffoldncbi321268
66792Lutibacter litoralis strain JCM 13034321268.3wgspatric321268

GC content

@refGC-contentmethod
3173433.9
6777033.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.643yes
gram-positiveno98.46yes
anaerobicno96.575yes
aerobicyes73.102yes
halophileno83.978no
spore-formingno95.74yes
thermophileno93.993yes
glucose-utilyes82.107no
motileno91.691no
glucose-fermentno88.463no

External links

@ref: 31734

culture collection no.: KCCM 42118, JCM 13034, CIP 109245

straininfo link

  • @ref: 91781
  • straininfo: 290981

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585692Lutibacter litoralis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment.Choi DH, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.64146-02006Fatty Acids/analysis, Flavobacteriaceae/chemistry/*classification/genetics/*isolation & purification/ultrastructure, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Seawater/microbiologyGenetics
Phylogeny19654353Lutibacter maritimus sp. nov., isolated from a tidal flat sediment.Park S, Kang SJ, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.012401-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Flavobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny21091530Marinitalea sucinacia gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment.Kim KY, Park SJ, Hahm YT, Cha CJFEMS Microbiol Lett10.1111/j.1574-6968.2010.02147.x2010DNA, Bacterial/genetics, Fatty Acids/metabolism, Flavobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny21460139Lutibacter aestuarii sp. nov., isolated from a tidal flat sediment, and emended description of the genus Lutibacter Choi and Cho 2006.Lee SY, Lee MH, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.030320-02011Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Flavobacteriaceae/chemistry/*classification/genetics/*isolation & purification, Genes, rRNA, Geologic Sediments/*microbiology, Lipids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny22659501Lutibacter flavus sp. nov., a marine bacterium isolated from a tidal flat sediment.Choi A, Yang SJ, Cho JCInt J Syst Evol Microbiol10.1099/ijs.0.043471-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny24842302Ochrovirga pacifica gen. nov., sp. nov., a novel agar-lytic marine bacterium of the family Flavobacteriaceae isolated from a seaweed.Kwon YK, Kim JH, Kim JJ, Yang SH, Ye BR, Heo SJ, Hyun JH, Qian ZJ, Park HS, Kang DH, Oh CCurr Microbiol10.1007/s00284-014-0598-42014Agar/metabolism, Base Composition, Fatty Acids/metabolism, Flavobacteriaceae/classification/genetics/immunology/*isolation & purification/metabolism, Micronesia, Molecular Sequence Data, Phylogeny, Seawater/*microbiology, Seaweed/*microbiologyMetabolism
Phylogeny26275791Lutibacter holmesii sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius, and emended description of the genus Lutibacter.Nedashkovskaya OI, Van Trappen S, Zhukova NV, De Vos PInt J Syst Evol Microbiol10.1099/ijsem.0.0005252015Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Japan, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Strongylocentrotus/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_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
31734Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172801028776041
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/
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
91781Reimer, 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-ID290981.1