Strain identifier

BacDive ID: 3021

Type strain: Yes

Species: Tepidicella xavieri

Strain Designation: TU-16

Strain history: CIP <- 2005, M. Da Costa, Coimbra Univ., Coimbra, Portugal: strain TU-16

NCBI tax ID(s): 360241 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8122

BacDive-ID: 3021

DSM-Number: 19605

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

description: Tepidicella xavieri TU-16 is an aerobe, thermophilic, Gram-negative bacterium that was isolated from hot spring run offs.

NCBI tax id

  • NCBI tax id: 360241
  • Matching level: species

strain history

@refhistory
8122<- M. S. da Costa, Univ. Coimbra; TU-16
123971CIP <- 2005, M. Da Costa, Coimbra Univ., Coimbra, Portugal: strain TU-16

doi: 10.13145/bacdive3021.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Tepidicella
  • species: Tepidicella xavieri
  • full scientific name: Tepidicella xavieri França et al. 2006

@ref: 8122

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Tepidicella

species: Tepidicella xavieri

full scientific name: Tepidicella xavieri França et al. 2006

strain designation: TU-16

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31754negative01-02 µm0.5-1 µmrod-shapedyes
69480negative99.999
123971negativerod-shapedyes

pigmentation

  • @ref: 31754
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8122REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)yeshttps://mediadive.dsmz.de/medium/830cName: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
38303MEDIUM 572 - for Pseudoxantomonas taiwanensisyesDistilled water make up to (1000.000 ml);Sodium chloride (8.000 mg);Zincsulphate heptahydrate (0.500 mg);Boric acid (0.500 mg);Sodium nitrate (689.000 mg);Manganese II sulphate monohydrate (2.200 mg);Magnesium sulphate heptahydrate (100.000 mg);Nitrilotri
123971CIP Medium 572yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=572

culture temp

@refgrowthtypetemperaturerange
8122positivegrowth45thermophilic
31754positivegrowth25-55
31754positiveoptimum45thermophilic
38303positivegrowth45thermophilic
123971positivegrowth25-55
123971nogrowth15psychrophilic

culture pH

@refabilitytypepHPH range
31754positivegrowth6.5-10.5alkaliphile
31754positiveoptimum8.5-9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31754aerobe
123971obligate aerobe

spore formation

@refspore formationconfidence
31754no
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
31754NaClpositivegrowth0-2 %
31754NaClpositiveoptimum0-2 %
123971NaClnogrowth0 %
123971NaClnogrowth2 %
123971NaClnogrowth4 %
123971NaClnogrowth6 %
123971NaClnogrowth8 %
123971NaClnogrowth10 %

observation

  • @ref: 31754
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3175435391aspartate+carbon source
3175416947citrate+carbon source
3175427570histidine+carbon source
3175425017leucine+carbon source
3175425115malate+carbon source
3175428044phenylalanine+carbon source
3175417822serine+carbon source
3175416296D-tryptophan+carbon source
317544853esculin+hydrolysis
12397116947citrate-carbon source
1239714853esculin-hydrolysis
123971606565hippurate+hydrolysis
12397117632nitrate-reduction
12397116301nitrite-reduction

metabolite production

  • @ref: 123971
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12397115688acetoin-
12397117234glucose-

enzymes

@refvalueactivityec
31754catalase+1.11.1.6
31754cytochrome oxidase+1.9.3.1
31754urease+3.5.1.5
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
123971oxidase+
123971beta-galactosidase-3.2.1.23
123971alcohol dehydrogenase-1.1.1.1
123971gelatinase+/-
123971amylase-
123971DNase+
123971caseinase+3.4.21.50
123971catalase+1.11.1.6
123971tween esterase-
123971gamma-glutamyltransferase-2.3.2.2
123971lecithinase-
123971lipase-
123971lysine decarboxylase-4.1.1.18
123971ornithine decarboxylase-4.1.1.17
123971phenylalanine ammonia-lyase-4.3.1.24
123971tryptophan deaminase-
123971urease-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
123971-+++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
8122hot spring run offsAzores, Island of Sao MiguelPortugalPRTEurope
123971Environment, Hot spring runoffsSao Miguel Island, AzoresPortugalPRTEurope2004

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Thermal spring
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_33024.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_15945;97_19550;98_24427;99_33024&stattab=map
  • Last taxonomy: Tepidicella xavieri subclade
  • 16S sequence: DQ295805
  • Sequence Identity:
  • Total samples: 3126
  • soil counts: 187
  • aquatic counts: 1595
  • animal counts: 1262
  • plant counts: 82

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
81221Risk group (German classification)
1239711Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8122
  • description: Tepidicella xavieri strain TU-16 16S ribosomal RNA gene, partial sequence
  • accession: DQ295805
  • length: 1480
  • database: ena
  • NCBI tax ID: 360241

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tepidicella xavieri DSM 19605GCA_004363315scaffoldncbi360241
66792Tepidicella xavieri strain DSM 19605360241.4wgspatric360241
66792Tepidicella xavieri DSM 196052770939514draftimg360241

GC content

  • @ref: 31754
  • GC-content: 64.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes94.442yes
flagellatedyes86.739no
gram-positiveno99.026yes
anaerobicno96.598no
aerobicyes80.598yes
halophileno75.445no
spore-formingno93.401no
glucose-utilno76.075no
thermophileyes76.927yes
glucose-fermentno89.724no

External links

@ref: 8122

culture collection no.: DSM 19605, CIP 108724, LMG 23030

straininfo link

  • @ref: 72543
  • straininfo: 138401

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585714Tepidicella xavieri gen. nov., sp. nov., a betaproteobacterium isolated from a hot spring runoff.Franca L, Rainey FA, Nobre MF, da Costa MSInt J Syst Evol Microbiol10.1099/ijs.0.64193-02006Betaproteobacteria/*classification/cytology/*isolation & purification/physiology, Hot Springs, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/analysis/genetics, Temperature, *Water MicrobiologyGenetics
Phylogeny30741332Tepidicella baoligensis sp. nov., A Novel Member of Betaproteobacterium Isolated from an Oil Reservoir.You J, Li Y, Hong S, Wang J, Yu J, Mu B, Ma X, Xue YCurr Microbiol10.1007/s00284-018-1604-z2019Base Composition, Burkholderiales/*classification/cytology/*physiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flagella, Hydrogen-Ion Concentration, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, Species Specificity, Temperature, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8122Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19605)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19605
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
31754Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2802728776041
38303Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6385
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
72543Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138401.1StrainInfo: A central database for resolving microbial strain identifiers
123971Curators of the CIPCollection of Institut Pasteur (CIP 108724)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108724