Strain identifier

BacDive ID: 23259

Type strain: Yes

Species: Arcticibacter tournemirensis

Strain Designation: TF5-37.2-LB10

Strain history: CIP <- 2010, L. Urios, Pau Univ., Pau, France: strain TF5-37.2-LB10

NCBI tax ID(s): 699437 (species)

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General

@ref: 19206

BacDive-ID: 23259

DSM-Number: 23085

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

description: Arcticibacter tournemirensis TF5-37.2-LB10 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from fault water of a deep Toarcian argillite layer.

NCBI tax id

  • NCBI tax id: 699437
  • Matching level: species

strain history

@refhistory
19206<- L. Urios, Univ. Pau et Pays de l’Adour, UMR CNRS 5254, IPREM EEM, France; TF5-37.2-LB10
123565CIP <- 2010, L. Urios, Pau Univ., Pau, France: strain TF5-37.2-LB10

doi: 10.13145/bacdive23259.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Arcticibacter
  • species: Arcticibacter tournemirensis
  • full scientific name: Arcticibacter tournemirensis (Urios et al. 2013) García-López et al. 2020

  • synonyms

    @refsynonym
    20215Pedobacter tournemirensis
    20215Pararcticibacter tournemirensis

@ref: 19206

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Arcticibacter

species: Arcticibacter tournemirensis

full scientific name: Arcticibacter tournemirensis (Urios et al. 2013) García-López et al. 2020

strain designation: TF5-37.2-LB10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30569negative1.75 µm0.5 µmrod-shapedno
123565negativerod-shapedno
69480negative96.205

pigmentation

  • @ref: 30569
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33669MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
19206R2A MEDIUM (DSMZ Medium 830)yesName: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled waterhttps://mediadive.dsmz.de/medium/830
123565CIP Medium 368yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=368
123565CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
19206positivegrowth28
30569positivegrowth12-37
30569positiveoptimum30
33669positivegrowth30

culture pH

@refabilitytypepHPH range
30569positivegrowth06-09alkaliphile
30569positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30569aerobe
123565facultative anaerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
30569NaClpositivegrowth0-2 %
30569NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3056940585alpha-cyclodextrin+carbon source
3056922599arabinose+carbon source
3056917057cellobiose+carbon source
3056923652dextrin+carbon source
3056928757fructose+carbon source
3056928260galactose+carbon source
3056917234glucose+carbon source
3056917716lactose+carbon source
3056917306maltose+carbon source
3056937684mannose+carbon source
3056928053melibiose+carbon source
30569506227N-acetylglucosamine+carbon source
3056916634raffinose+carbon source
3056926546rhamnose+carbon source
3056917992sucrose+carbon source
3056927082trehalose+carbon source
3056918222xylose+carbon source
305694853esculin+hydrolysis
12356517632nitrate-reduction
12356516301nitrite+reduction

metabolite production

  • @ref: 123565
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
30569acid phosphatase+3.1.3.2
30569alkaline phosphatase+3.1.3.1
30569alpha-galactosidase+3.2.1.22
30569catalase+1.11.1.6
30569cytochrome oxidase+1.9.3.1
123565oxidase+
123565catalase-1.11.1.6
123565urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123565-++--+++--++++-++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
19206fault water of a deep Toarcian argillite layerAveyron, Tournemire (43° 58' 40'' N, 3° 00' 38'' E)FranceFRAEurope43.97783.0106
123565Environment, WaterPauFranceFRAEurope2009

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_145814.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_43800;97_56085;98_74264;99_145814&stattab=map
  • Last taxonomy: Arcticibacter tournemirensis subclade
  • 16S sequence: GU198945
  • Sequence Identity:
  • Total samples: 253
  • soil counts: 141
  • aquatic counts: 49
  • animal counts: 52
  • plant counts: 11

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
192061Risk group (German classification)
1235651Risk group (French classification)

Sequence information

16S sequences

  • @ref: 19206
  • description: Pedobacter tournemirensis strain TF5-37.2-LB10 16S ribosomal RNA gene, partial sequence
  • accession: GU198945
  • length: 1409
  • database: nuccore
  • NCBI tax ID: 699437

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arcticibacter tournemirensis DSM 23085GCA_006716645contigncbi699437
66792Arcticibacter tournemirensis TF5-37.2-LB10GCA_008690275scaffoldncbi699437
66792Pedobacter tournemirensis strain DSM 23085699437.5wgspatric699437
66792Pararcticibacter tournemirensis DSM 230852818991316draftimg699437

GC content

@refGC-contentmethod
1920646high performance liquid chromatography (HPLC)
3056946

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno96.205yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.848yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes58.908no
69480spore-formingspore-formingAbility to form endo- or exosporesno87.441no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.6yes
69480flagellatedmotile2+Ability to perform flagellated movementno85no

External links

@ref: 19206

culture collection no.: DSM 23085, CIP 110085, MOLA 820

straininfo link

  • @ref: 87482
  • straininfo: 386797

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22427449Pedobacter tournemirensis sp. nov., isolated from a fault water sample of a deep Toarcian argillite layer.Urios L, Intertaglia L, Magot MInt J Syst Evol Microbiol10.1099/ijs.0.038968-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, France, Molecular Sequence Data, Pedobacter/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, *Water MicrobiologyGenetics
Phylogeny29461180Pedobacter mongoliensis sp. nov., isolated from grassland soil.Yuan K, Cao M, Li J, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0026372018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Grassland, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31811376Pararcticibacter amylolyticus gen. nov., sp. nov., Isolated from a Rotten Hemp Rope, and Reclassification of Pedobacter tournemirensis as Pararcticibacter tournemirensis comb. nov.Cai YY, Dong WW, Hu YL, Jiang X, Wang YW, Zhou YQ, Peng N, Liang YX, Zhao SMCurr Microbiol10.1007/s00284-019-01828-z2019Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, Cannabis/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Pedobacter/*classification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19206Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23085)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23085
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
30569Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2690028776041
33669Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7905
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
87482Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID386797.1StrainInfo: A central database for resolving microbial strain identifiers
123565Curators of the CIPCollection of Institut Pasteur (CIP 110085)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110085