Strain identifier

BacDive ID: 2970

Type strain: Yes

Species: Hydrogenophaga defluvii

Strain history: CIP <- 2003, DSMZ <- P. Kämpfer, Giessen Univ., Giessen, Germany <- R. Schulze, Germany: strain BSB 9.5

NCBI tax ID(s): 249410 (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: 5856

BacDive-ID: 2970

DSM-Number: 15341

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

description: Hydrogenophaga defluvii DSM 15341 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 249410
  • Matching level: species

strain history

@refhistory
5856<- P. Kämpfer; BSB 9.5 <- R. Schulze
118869CIP <- 2003, DSMZ <- P. Kämpfer, Giessen Univ., Giessen, Germany <- R. Schulze, Germany: strain BSB 9.5

doi: 10.13145/bacdive2970.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Hydrogenophaga
  • species: Hydrogenophaga defluvii
  • full scientific name: Hydrogenophaga defluvii Kämpfer et al. 2005

@ref: 5856

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Hydrogenophaga

species: Hydrogenophaga defluvii

full scientific name: Hydrogenophaga defluvii Kämpfer et al. 2005

type strain: yes

Morphology

cell morphology

  • @ref: 118869
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5856HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428)yeshttps://mediadive.dsmz.de/medium/428Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water
5856MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)yeshttps://mediadive.dsmz.de/medium/81Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
5856NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
32885MEDIUM 9 - Brain heart infusion BHIyesDistilled water make up to (1000.000 ml);Brain heart infusion (37.000 g)
118869CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328
118869CIP Medium 9yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=9

culture temp

@refgrowthtypetemperaturerange
5856positivegrowth28mesophilic
32885positivegrowth30mesophilic
60071positivegrowth30mesophilic
118869positivegrowth25-30mesophilic
118869nogrowth5psychrophilic
118869nogrowth10psychrophilic
118869nogrowth37mesophilic
118869nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60071aerobe
118869obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
118869NaClpositivegrowth0 %
118869NaClnogrowth2 %
118869NaClnogrowth4 %
118869NaClnogrowth6 %
118869NaClnogrowth8 %
118869NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11886916947citrate-carbon source
1188694853esculin-hydrolysis
11886917632nitrate+reduction
11886916301nitrite-reduction
11886917632nitrate-respiration

antibiotic resistance

  • @ref: 118869
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118869
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
118869oxidase+
118869beta-galactosidase-3.2.1.23
118869alcohol dehydrogenase-1.1.1.1
118869gelatinase-
118869amylase-
118869DNase-
118869caseinase-3.4.21.50
118869catalase+1.11.1.6
118869tween esterase+
118869lecithinase-
118869lipase-
118869lysine decarboxylase-4.1.1.18
118869ornithine decarboxylase-4.1.1.17
118869protease-
118869tryptophan deaminase-
118869urease-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
118869-+++-+-----+--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118869-------------------------------+----------------------++--+-+---+--------+----+----+----+-++-+---+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
5856activated sludgeMunichGermanyDEUEurope
60071Activated sludgeMünchenGermanyDEUEurope1995
118869Environment, Activated sludgeMünchenGermanyDEUEurope1995

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_14636.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_872;97_2609;98_11081;99_14636&stattab=map
  • Last taxonomy: Hydrogenophaga
  • 16S sequence: AJ585993
  • Sequence Identity:
  • Total samples: 46
  • soil counts: 2
  • aquatic counts: 41
  • animal counts: 1
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
58561Risk group (German classification)
1188691Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5856
  • description: Hydrogenophaga defluvii partial 16S rRNA gene, type strain BSB 9.5T
  • accession: AJ585993
  • length: 1502
  • database: ena
  • NCBI tax ID: 249410

External links

@ref: 5856

culture collection no.: DSM 15341, CCUG 53903, CIP 108119, BSB 9.5

straininfo link

  • @ref: 72492
  • straininfo: 135115

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653898Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge.Kampfer P, Schulze R, Jackel U, Malik KA, Amann R, Spring SInt J Syst Evol Microbiol10.1099/ijs.0.03041-02005Comamonadaceae/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Sewage/*microbiology, Waste Disposal, Fluid/*methodsGenetics
Phylogeny21282897Hydrogenophaga temperata sp. nov., a betaproteobacterium isolated from compost in Korea.Kim YJ, Kim MK, Weon HY, Kim HB, Yang DCJ Gen Appl Microbiol10.2323/jgam.56.4192010*Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny28920826Hydrogenophaga soli sp. nov., isolated from rice field soil.Yang D, Cha S, Choi J, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0022772017Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Oryza, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny31661044Hydrogenophaga borbori sp. nov., isolated from activated sludge.Choi GM, Lee SY, Kim SY, Wee JH, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0037872020Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/*microbiology, UbiquinoneTranscriptome

Reference

@idauthorscataloguedoi/urltitle
5856Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15341)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15341
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
32885Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5706
60071Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53903)https://www.ccug.se/strain?id=53903
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
72492Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135115.1StrainInfo: A central database for resolving microbial strain identifiers
118869Curators of the CIPCollection of Institut Pasteur (CIP 108119)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108119