Strain identifier

BacDive ID: 158792

Type strain: Yes

Species: Tenacibaculum todarodis

Strain Designation: LPB0136

Strain history: H. Yi; Korea Univ., South Korea; LPB0136.

NCBI tax ID(s): 1850252 (species)

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General

@ref: 65551

BacDive-ID: 158792

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

description: Tenacibaculum todarodis LPB0136 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from isolated from a squid, Todarodes pacificus.

NCBI tax id

  • NCBI tax id: 1850252
  • Matching level: species

strain history

  • @ref: 67770
  • history: H. Yi; Korea Univ., South Korea; LPB0136.

doi: 10.13145/bacdive158792.20230509.8.1

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 todarodis
  • full scientific name: Tenacibaculum todarodis Shin et al. 2018

@ref: 65551

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Tenacibaculum

species: Tenacibaculum todarodis

strain designation: LPB0136

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
65551negative1.5-2.3 µm0.5-0.6 µmrod-shapedyesgliding
69480negative99.972

colony morphology

  • @ref: 65551
  • colony size: 0.5-1.5 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA

pigmentation

  • @ref: 65551
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

  • @ref: 65551
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65551positivegrowth4-25
65551positiveoptimum25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
65551positivegrowth5.0-9.0alkaliphile
65551positiveoptimum7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 65551
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
65551no
69480no99.983
69481no100

halophily

  • @ref: 65551
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 2-4 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6555117128adipate-carbon source
6555127689decanoate-carbon source
6555185146carboxymethylcellulose-hydrolysis
65551casein+hydrolysis
6555117029chitin-hydrolysis
6555116947citrate-carbon source
6555117634D-glucose-carbon source
6555116899D-mannitol-carbon source
6555116024D-mannose-carbon source
6555116991dna+hydrolysis
655515291gelatin+hydrolysis
6555124265gluconate-carbon source
6555117234glucose-fermentation
6555117368hypoxanthine-hydrolysis
6555130849L-arabinose-carbon source
6555117895L-tyrosine+hydrolysis
6555125115malate-carbon source
6555117306maltose-carbon source
65551506227N-acetylglucosamine-carbon source
6555117632nitrate-reduction
6555118401phenylacetate-carbon source
6555153311sodium alginate-hydrolysis
6555128017starch-hydrolysis
6555153424tween 20-hydrolysis
6555153423tween 40-hydrolysis
6555153425tween 60-hydrolysis
6555153426tween 80+hydrolysis
6555115318xanthine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6555116136hydrogen sulfideno
6555135581indoleno

enzymes

@refvalueactivityec
65551catalase+1.11.1.6
65551cytochrome oxidase+1.9.3.1
65551alkaline phosphatase+3.1.3.1
65551leucine arylamidase+3.4.11.1
65551valine arylamidase+
65551cystine arylamidase+3.4.11.3
65551trypsin+3.4.21.4
65551acid phosphatase+3.1.3.2
65551naphthol-AS-BI-phosphohydrolase+
65551urease-3.5.1.5
65551arginine dihydrolase-3.5.3.6
65551esterase (C 4)-
65551esterase Lipase (C 8)-
65551lipase (C 14)-
65551alpha-chymotrypsin-3.4.21.1
65551alpha-galactosidase-3.2.1.22
65551beta-galactosidase-3.2.1.23
65551beta-glucuronidase-3.2.1.31
65551alpha-glucosidase-3.2.1.20
65551beta-glucosidase-3.2.1.21
65551N-acetyl-beta-glucosaminidase-3.2.1.52
65551alpha-mannosidase-3.2.1.24
65551alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65551C13:00.6
    65551C14:00.3
    65551C13:0 iso2.6
    65551C14:0 iso2.8
    65551C15:0 iso16.9
    65551C16:0 iso1
    65551C15:1ω6c5.3
    65551C17:1ω6c0.9
    65551C15:0 anteiso0.4
    65551C15:0 2OH0.6
    65551C15:0 3OH6.6
    65551C16:0 3OH1.1
    65551C15:0 iso 3OH18.8
    65551C16:0 iso 3OH7.5
    65551C17:0 iso 3OH5.9
    65551C15:1 iso G14.6
    65551C16:1 iso H1.3
    65551C16:1ω6c / C16:1ω7c6.8
    65551iso-C17:1ω9c / iso-C16:0 10-methyl0.5
  • type of FA analysis: whole cell analysis
  • incubation medium: MA
  • incubation temperature: 25
  • incubation time: 3
  • library/peak naming table: TSBA6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment culturehost species
65551isolated from a squid, Todarodes pacificusEast SeaRepublic of KoreaKORAsia37.8908128.829MA
67770Squid Todarodes pacificusTodarodes pacificus

isolation source categories

  • Cat1: #Host
  • Cat2: #Reptilia

taxonmaps

  • @ref: 69479
  • File name: preview.99_4739.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_214;96_2345;97_2855;98_3552;99_4739&stattab=map
  • Last taxonomy: Tenacibaculum todarodis subclade
  • 16S sequence: KX066858
  • Sequence Identity:
  • Total samples: 3627
  • soil counts: 104
  • aquatic counts: 2941
  • animal counts: 550
  • plant counts: 32

Sequence information

16S sequences

  • @ref: 65551
  • description: 16S rRNA gene sequence
  • accession: KX066858
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tenacibaculum todarodis LPB0136GCA_001889045completencbi1850252
66792Tenacibaculum todarodis LPB01362728369366completeimg1850252

GC content

  • @ref: 65551
  • GC-content: 30.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.225yes
gram-positiveno97.681yes
anaerobicno99.575yes
halophileno70.17no
spore-formingno96.776yes
glucose-utilyes74.179yes
aerobicyes92.596yes
thermophileno99.572no
motileno88.565no
glucose-fermentno91.784no

External links

@ref: 65551

culture collection no.: KACC 18887, JCM 31564

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29521615Tenacibaculum todarodis sp. nov., isolated from a squid.Shin SK, Kim E, Yi HInt J Syst Evol Microbiol10.1099/ijsem.0.0026922018Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Decapodiformes/*microbiology, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Tenacibaculum/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny35943445Tenacibaculum aquimarinum sp. nov., isolated from a marine alga and seawater.Kristyanto S, Kim KR, Jung J, Kim HM, Kim K, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0054772022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, *TenacibaculumTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
65551Su-Kyoung Shin, Eunji Kim and Hana YiTenacibaculum todarodis sp. nov., isolated from a squid10.1099/ijsem.0.002692IJSEM 68: 1479-1483 201829521615
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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