Strain identifier

BacDive ID: 6138

Type strain: Yes

Species: Tepidiphilus succinatimandens

Strain Designation: 4BON

Strain history: CIP <- 2002, B. Ollivier, IRD, Marseille, France: strain 4BON

NCBI tax ID(s): 224436 (species)

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General

@ref: 5970

BacDive-ID: 6138

DSM-Number: 15512

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

description: Tepidiphilus succinatimandens 4BON is an aerobe, thermophilic, Gram-negative bacterium that was isolated from oil field.

NCBI tax id

  • NCBI tax id: 224436
  • Matching level: species

strain history

@refhistory
5970<- B. Ollivier; 4BON
362042002, B. Ollivier, IRD, Marseille, France: strain 4BON
123363CIP <- 2002, B. Ollivier, IRD, Marseille, France: strain 4BON

doi: 10.13145/bacdive6138.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Hydrogenophilia
  • order: Hydrogenophilales
  • family: Hydrogenophilaceae
  • genus: Tepidiphilus
  • species: Tepidiphilus succinatimandens
  • full scientific name: Tepidiphilus succinatimandens (Bonilla Salinas et al. 2004) Poddar et al. 2014

  • synonyms

    • @ref: 20215
    • synonym: Petrobacter succinatimandens

@ref: 5970

domain: Bacteria

phylum: Proteobacteria

class: Hydrogenophilalia

order: Hydrogenophilales

family: Hydrogenophilaceae

genus: Tepidiphilus

species: Tepidiphilus succinatimandens

full scientific name: Tepidiphilus succinatimandens (Bonilla Salinas et al. 2004) Poddar et al. 2014

strain designation: 4BON

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29947negative2 µm0.35 µmrod-shapedyes
69480yes97.794
69480negative100
123363negativerod-shapedyes

colony morphology

  • @ref: 123363

pigmentation

  • @ref: 123363
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5970PETROBACTER SUCCINIMANDENS MEDIUM (DSMZ Medium 979)yeshttps://mediadive.dsmz.de/medium/979Name: PETROBACTER SUCCINIMANDENS MEDIUM (DSMZ Medium 979) Composition: Yeast extract 1.0 g/l NH4Cl 1.0 g/l K2HPO4 0.3 g/l KH2PO4 0.3 g/l MgCl2 x 6 H2O 0.2 g/l KCl 0.1 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l CaCl2 x 2 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l Pyridoxine hydrochloride 5e-05 g/l (DL)-alpha-Lipoic acid 2.5e-05 g/l p-Aminobenzoic acid 2.5e-05 g/l Calcium D-(+)-pantothenate 2.5e-05 g/l Nicotinic acid 2.5e-05 g/l Riboflavin 2.5e-05 g/l Thiamine HCl 2.5e-05 g/l Folic acid 1e-05 g/l Biotin 1e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Vitamin B12 5e-07 g/l Distilled water
36204MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123363CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5970positivegrowth55thermophilic
29947positivegrowth35-60
29947positiveoptimum55thermophilic
36204positivegrowth55thermophilic
123363positivegrowth37-45
123363nogrowth25mesophilic
123363nogrowth30mesophilic

culture pH

@refabilitytypepH
29947positivegrowth5.5-8
29947positiveoptimum6.9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
5970aerobe
5970anaerobe
29947aerobe
123363obligate aerobe

spore formation

@refspore formationconfidence
29947no
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
29947NaClpositivegrowth0-3 %
29947NaClpositiveoptimum0.5 %
123363NaClpositivegrowth0-2 %
123363NaClnogrowth4 %
123363NaClnogrowth6 %
123363NaClnogrowth8 %
123363NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2994716236ethanol+carbon source
2994715740formate+carbon source
2994715361pyruvate+carbon source
2994730031succinate+carbon source
2994717632nitrate+reduction
12336316947citrate-carbon source
1233634853esculin+hydrolysis
123363606565hippurate+hydrolysis
12336317632nitrate-builds gas from
12336317632nitrate+reduction
12336316301nitrite-builds gas from
12336316301nitrite-reduction
12336315792malonate-assimilation
12336317632nitrate-respiration

antibiotic resistance

  • @ref: 123363
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123363
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12336315688acetoin-
12336317234glucose-

enzymes

@refvalueactivityec
29947catalase+1.11.1.6
29947cytochrome oxidase+1.9.3.1
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
123363oxidase+
123363beta-galactosidase-3.2.1.23
123363alcohol dehydrogenase-1.1.1.1
123363gelatinase+/-
123363amylase-
123363DNase+
123363caseinase+3.4.21.50
123363catalase+1.11.1.6
123363tween esterase+
123363gamma-glutamyltransferase+2.3.2.2
123363lysine decarboxylase-4.1.1.18
123363ornithine decarboxylase-4.1.1.17
123363phenylalanine ammonia-lyase-4.3.1.24
123363tryptophan deaminase-
123363urease+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
123363--++-+----++----+---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123363------------------+------------------------------+-----------+--------------++-+++------+++-----+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5970oil fieldQueenslandAustraliaAUSAustralia and Oceania
123363Oil fieldAustraliaAUSAustralia and Oceania1989

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Oil reservoir
#Environmental#Terrestrial#Geologic

taxonmaps

  • @ref: 69479
  • File name: preview.99_27867.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16099;96_612;97_715;98_834;99_27867&stattab=map
  • Last taxonomy: Tepidiphilus
  • 16S sequence: AY219713
  • Sequence Identity:
  • Total samples: 1628
  • soil counts: 118
  • aquatic counts: 442
  • animal counts: 1041
  • plant counts: 27

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59701Risk group (German classification)
1233631Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5970
  • description: Petrobacter succinimandens BON4 16S ribosomal RNA gene, partial sequence
  • accession: AY219713
  • length: 1529
  • database: ena
  • NCBI tax ID: 224436

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tepidiphilus succinatimandens DSM 15512GCA_006503695scaffoldncbi224436
66792Tepidiphilus succinatimandens strain DSM 15512224436.3wgspatric224436

GC content

  • @ref: 5970
  • GC-content: 58.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.467yes
flagellatedyes78.347no
gram-positiveno98.99yes
anaerobicno88.954no
aerobicno54.91no
halophileno90.673no
spore-formingno95.792yes
glucose-utilno84.388no
thermophileyes98.804yes
glucose-fermentno87.062no

External links

@ref: 5970

culture collection no.: DSM 15512, CIP 107790

straininfo link

  • @ref: 75625
  • straininfo: 132024

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143002Petrobacter succinatimandens gen. nov., sp. nov., a moderately thermophilic, nitrate-reducing bacterium isolated from an Australian oil well.Salinas MB, Fardeau ML, Cayol JL, Casalot L, Patel BKC, Thomas P, Garcia JL, Ollivier BInt J Syst Evol Microbiol10.1099/ijs.0.02732-02004Australia, Base Composition, DNA, Bacterial/chemistry/genetics, Molecular Sequence Data, Nitrates/metabolism, Oxidation-Reduction, Petroleum/*microbiology, Phylogeny, Rhodocyclaceae/*classification/genetics/*isolation & purification/metabolism, TemperatureGenetics
Phylogeny24048864Taxonomic study of the genus Tepidiphilus: transfer of Petrobacter succinatimandens to the genus Tepidiphilus as Tepidiphilus succinatimandens comb. nov., emended description of the genus Tepidiphilus and description of Tepidiphilus thermophilus sp. nov., isolated from a terrestrial hot spring.Poddar A, Lepcha RT, Das SKInt J Syst Evol Microbiol10.1099/ijs.0.056424-02013Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/microbiology, Hot Springs/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny32579101Tepidiphilus olei sp. nov., isolated from the production water of a water-flooded oil reservoir in PR China.Wang XT, Shan JJ, Li XZ, Lin W, Xiu JL, Li DA, Zhang YZ, Wang LInt J Syst Evol Microbiol10.1099/ijsem.0.0042972020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrogenophilaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, Water/analysisTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
5970Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15512)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15512
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
29947Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2631628776041
36204Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5264
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)
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
75625Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132024.1StrainInfo: A central database for resolving microbial strain identifiers
123363Curators of the CIPCollection of Institut Pasteur (CIP 107790)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107790