Strain identifier

BacDive ID: 5647

Type strain: Yes

Species: Tenacibaculum mesophilum

Strain Designation: KK10306

Strain history: CIP <- 2001, IFO

NCBI tax ID(s): 104268 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 5154

BacDive-ID: 5647

DSM-Number: 13764

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

description: Tenacibaculum mesophilum KK10306 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from sponge .

NCBI tax id

  • NCBI tax id: 104268
  • Matching level: species

strain history

@refhistory
5154<- M. Suzuki <- A. Yokoyama; MBIC 1140
328592001, IFO
120913CIP <- 2001, IFO

doi: 10.13145/bacdive5647.20230509.8.1

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 mesophilum
  • full scientific name: Tenacibaculum mesophilum Suzuki et al. 2001

@ref: 5154

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Tenacibaculum

species: Tenacibaculum mesophilum

full scientific name: Tenacibaculum mesophilum Suzuki et al. 2001

strain designation: KK10306

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.962
120913negativerod-shapedyes

pigmentation

  • @ref: 120913
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5154BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
5154MARINE AGAR (DSMZ Medium 123)yeshttps://mediadive.dsmz.de/medium/123Name: MARINE AGAR (DSMZ Medium 123) Composition: NaCl 24.0 g/l Agar 15.0 g/l MgCl2 x 6 H2O 11.0 g/l Bacto peptone 5.0 g/l Na2SO4 4.0 g/l CaCl2 x 6 H2O 2.0 g/l Yeast extract 1.0 g/l KCl 0.7 g/l KBr 0.1 g/l SrCl2 x 6 H2O 0.04 g/l H3BO3 0.03 g/l NaSiO3 x 9 H2O 0.005 g/l NaF 0.003 g/l NH4NO3 0.002 g/l Fe(III)PO4 x 4 H2O 0.001 g/l Distilled water
32859Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120913CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5154positivegrowth30mesophilic
32859positivegrowth25mesophilic
120913positivegrowth15-41
120913nogrowth5psychrophilic
120913nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120913
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
120913NaClnogrowth0 %
120913NaClnogrowth2 %
120913NaClnogrowth4 %
120913NaClnogrowth6 %
120913NaClnogrowth8 %
120913NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1209134853esculin-hydrolysis
120913606565hippurate+hydrolysis
12091317632nitrate-reduction
12091316301nitrite+reduction
12091315792malonate-assimilation
12091317632nitrate-respiration

antibiotic resistance

  • @ref: 120913
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120913
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12091315688acetoin-
12091317234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
120913oxidase+
120913beta-galactosidase-3.2.1.23
120913alcohol dehydrogenase-1.1.1.1
120913gelatinase+
120913amylase-
120913DNase+
120913caseinase+3.4.21.50
120913catalase+1.11.1.6
120913tween esterase+
120913gamma-glutamyltransferase+2.3.2.2
120913lecithinase+
120913lipase-
120913lysine decarboxylase-4.1.1.18
120913ornithine decarboxylase-4.1.1.17
120913phenylalanine ammonia-lyase-4.3.1.24
120913protease+
120913tryptophan deaminase-
120913urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120913-+++-+++++++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120913--------------------------------------------------------------+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic locationisolation date
5154sponge (Halichondria okadai)Halichondria okadaiJapanJPNAsia
120913SpongeJapanJPNAsiaNumazu1997

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Porifera (Sponges)

taxonmaps

  • @ref: 69479
  • File name: preview.99_4564.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_214;96_2278;97_2761;98_3429;99_4564&stattab=map
  • Last taxonomy: Tenacibaculum mesophilum subclade
  • 16S sequence: AB032501
  • Sequence Identity:
  • Total samples: 2147
  • soil counts: 112
  • aquatic counts: 787
  • animal counts: 1209
  • plant counts: 39

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51541Risk group (German classification)
1209131Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Tenacibaculum mesophilum gene for 16S rRNA, partial sequence, strain: NBRC 16307AB6810581447ena104268
5154Tenacibaculum mesophilum gene for 16S rRNA, partial sequence, strain:MBIC1140AB0325011444ena104268

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tenacibaculum mesophilum DSM 13764GCA_003867075chromosomencbi104268
66792Tenacibaculum mesophilum DSM 13764GCA_009362255completencbi104268
66792Tenacibaculum mesophilum DSM 13764GCA_900129475contigncbi104268
66792Tenacibaculum mesophilum strain DSM 13764104268.6wgspatric104268
66792Tenacibaculum mesophilum strain DSM 13764104268.20completepatric104268
66792Tenacibaculum mesophilum strain DSM 13764104268.24completepatric104268
66792Tenacibaculum mesophilum DSM 137642840679509completeimg104268
66792Tenacibaculum mesophilum DSM 137642695420951draftimg104268

GC content

  • @ref: 5154
  • GC-content: 31.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno83.482no
flagellatedno95.71no
gram-positiveno97.948no
anaerobicno99.451no
aerobicyes89.141no
halophileno72.448no
spore-formingno95.844no
thermophileno98.819no
glucose-utilyes81.368no
glucose-fermentno92.022no

External links

@ref: 5154

culture collection no.: DSM 13764, IFO 16307, NBRC 16307, MBIC 1140, CIP 107215

straininfo link

  • @ref: 75130
  • straininfo: 49516

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11594591Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov.Suzuki M, Nakagawa Y, Harayama S, Yamamoto SInt J Syst Evol Microbiol10.1099/00207713-51-5-16392001Animals, Chlorophyta/microbiology, Cytophaga/chemistry/classification/genetics, DNA Gyrase/genetics, DNA, Ribosomal/analysis/genetics, Genotype, Gram-Negative Aerobic Rods and Cocci/*classification/genetics, Nucleic Acid Hybridization, Phenotype, *Phylogeny, Porifera/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
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
Genetics31776213Complete Genome Sequence of Sponge-Associated Tenacibaculum mesophilum DSM 13764(T).Miyake S, Soh M, Ding Y, Seedorf HMicrobiol Resour Announc10.1128/MRA.00517-192019
Phylogeny32080799Insights into the microbiome of farmed Asian sea bass (Lates calcarifer) with symptoms of tenacibaculosis and description of Tenacibaculum singaporense sp. nov.Miyake S, Soh M, Azman MN, Ngoh SY, Orban L, Seedorf HAntonie Van Leeuwenhoek10.1007/s10482-020-01391-92020Animals, Aquaculture, Bass/*microbiology, Fish Diseases/*microbiology, Fishes, Flavobacteriaceae/classification, Flavobacteriaceae Infections/microbiology/pathology, Genes, Bacterial, Genome, Bacterial, *Microbiota, Perciformes/microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Tenacibaculum/classification/genetics/growth & development/isolation & purificationGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5154Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13764)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13764
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
32859Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4626
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68382Automatically annotated from API zym
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
75130Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49516.1StrainInfo: A central database for resolving microbial strain identifiers
120913Curators of the CIPCollection of Institut Pasteur (CIP 107215)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107215