Strain identifier

BacDive ID: 2972

Type strain: Yes

Species: Hydrogenophaga caeni

Strain Designation: EMB71

Strain history: <- C. O. Jeon, Gyeongsang Nat. Univ. (GSNU), Jinju, Korea; EMB71

NCBI tax ID(s): 370976 (species)

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

@ref: 7294

BacDive-ID: 2972

DSM-Number: 17962

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

description: Hydrogenophaga caeni EMB71 is a facultative aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 370976
  • Matching level: species

strain history

  • @ref: 7294
  • history: <- C. O. Jeon, Gyeongsang Nat. Univ. (GSNU), Jinju, Korea; EMB71

doi: 10.13145/bacdive2972.20230509.8.1

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 caeni
  • full scientific name: Hydrogenophaga caeni Chung et al. 2007

@ref: 7294

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Hydrogenophaga

species: Hydrogenophaga caeni

full scientific name: Hydrogenophaga caeni Chung et al. 2007

strain designation: EMB71

type strain: yes

Morphology

cell morphology

  • @ref: 23087
  • gram stain: negative
  • cell length: 1.4-2.0 µm
  • cell width: 0.8-1.2 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: monotrichous, polar

colony morphology

  • @ref: 23087
  • colony color: white
  • colony shape: circular
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7294R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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 water
23087Reasoner's 2A agar (R2A)yes

culture temp

@refgrowthtypetemperaturerange
7294positivegrowth25mesophilic
23087positivegrowth15.0-35.0
23087positiveoptimum30.0mesophilic

culture pH

@refabilitytypepHPH range
23087positiveoptimum7.0-8.0
23087positivegrowth6.0-9.0alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 23087
  • oxygen tolerance: facultative aerobe

spore formation

  • @ref: 23087
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2308727613amygdalin-builds acid from
2308718305arbutin-builds acid from
2308715824D-fructose-builds acid from
2308712936D-galactose-builds acid from
2308717634D-glucose-builds acid from
2308717716lactose-builds acid from
2308716899D-mannitol-builds acid from
2308716024D-mannose-builds acid from
2308730849L-arabinose-builds acid from
2308728053melibiose-builds acid from
2308726546rhamnose-builds acid from
2308717814salicin-builds acid from
2308730911sorbitol-builds acid from
2308717992sucrose-builds acid from
2308730849L-arabinose-growth
2308729864mannitol-growth
23087casein-hydrolysis
230874853esculin-hydrolysis
230875291gelatin-hydrolysis
2308728017starch-hydrolysis
2308753424tween 20-hydrolysis
2308718186tyrosine-hydrolysis
2308716199urea-hydrolysis
2308717521(-)-quinic acid-oxidation
23087167632-oxobutanoate-oxidation
23087286442-oxopentanoate-oxidation
23087167244-hydroxybutyrate-oxidation
23087181014-hydroxyphenylacetic acid-oxidation
2308730089acetate-oxidation
2308740585alpha-cyclodextrin-oxidation
2308773706bromosuccinate-oxidation
2308716947citrate-oxidation
2308718333D-arabitol-oxidation
2308717057cellobiose-oxidation
2308715824D-fructose-oxidation
2308712936D-galactose-oxidation
2308718024D-galacturonic acid-oxidation
2308730612D-glucarate-oxidation
230878391D-gluconate-oxidation
2308717784D-glucosaminic acid-oxidation
2308714314D-glucose 6-phosphate-oxidation
2308715748D-glucuronate-oxidation
2308716899D-mannitol-oxidation
2308716024D-mannose-oxidation
2308727605D-psicose-oxidation
2308716523D-serine-oxidation
2308723652dextrin-oxidation
2308717126DL-carnitine-oxidation
2308717113erythritol-oxidation
2308716000ethanolamine-oxidation
2308728066gentiobiose-oxidation
2308729042glucose 1-phosphate-oxidation
2308732323glucuronamide-oxidation
2308717754glycerol-oxidation
2308714336glycerol 1-phosphate-oxidation
2308728087glycogen-oxidation
2308773804glycyl L-aspartic acid-oxidation
2308717596inosine-oxidation
2308717240itaconate-oxidation
2308716977L-alanine-oxidation
2308730849L-arabinose-oxidation
2308718287L-fucose-oxidation
2308729985L-glutamate-oxidation
2308715603L-leucine-oxidation
2308715729L-ornithine-oxidation
2308717295L-phenylalanine-oxidation
2308718183L-pyroglutamic acid-oxidation
2308717115L-serine-oxidation
230876359lactulose-oxidation
2308715792malonate-oxidation
2308728053melibiose-oxidation
23087320055methyl beta-D-glucopyranoside-oxidation
2308751850methyl pyruvate-oxidation
2308773784glycyl-l-glutamate-oxidation
2308717272propionate-oxidation
2308716634raffinose-oxidation
2308741865sebacic acid-oxidation
23087143136succinamate-oxidation
2308717992sucrose-oxidation
2308717748thymidine-oxidation
2308727082trehalose-oxidation
2308732528turanose-oxidation
2308716704uridine-oxidation
2308727248urocanic acid-oxidation
2308717151xylitol-oxidation
2308716634raffinose+builds acid from
2308717268myo-inositol+builds acid from
2308715971L-histidine+growth
2308717306maltose+growth
2308730911sorbitol+growth
2308753426tween 80+hydrolysis
23087645522-hydroxybutyrate+oxidation
23087309162-oxoglutarate+oxidation
23087620642,3-butanediol+oxidation
23087370543-hydroxybutyrate+oxidation
23087182404-hydroxy-L-proline+oxidation
2308715963ribitol+oxidation
2308717925alpha-D-glucose+oxidation
2308736219alpha-lactose+oxidation
2308716383cis-aconitate+oxidation
2308715570D-alanine+oxidation
2308715895D-galactonic acid lactone+oxidation
2308717924D-sorbitol+oxidation
2308724996lactate+oxidation
2308715740formate+oxidation
2308716865gamma-aminobutyric acid+oxidation
2308721217L-alaninamide+oxidation
2308773786L-alanylglycine+oxidation
2308717196L-asparagine+oxidation
2308715971L-histidine+oxidation
2308717203L-proline+oxidation
2308762345L-rhamnose+oxidation
2308716857L-threonine+oxidation
2308717306maltose+oxidation
2308775146monomethyl succinate+oxidation
2308717268myo-inositol+oxidation
2308728037N-acetylgalactosamine+oxidation
23087506227N-acetylglucosamine+oxidation
2308750048phenylethylamine+oxidation
2308717148putrescine+oxidation
2308730031succinate+oxidation
2308716094thiosulfate+oxidation
2308753423tween 40+oxidation
2308753426tween 80+oxidation
2308717632nitrate+reduction

enzymes

@refvalueactivityec
23087acid phosphatase-3.1.3.2
23087alkaline phosphatase+3.1.3.1
23087alpha-chymotrypsin-3.4.21.1
23087alpha-fucosidase-3.2.1.51
23087alpha-galactosidase-3.2.1.22
23087alpha-glucosidase-3.2.1.20
23087alpha-mannosidase-3.2.1.24
23087beta-galactosidase-3.2.1.23
23087beta-glucosidase-3.2.1.21
23087beta-glucuronidase-3.2.1.31
23087catalase+1.11.1.6
23087cystine arylamidase-3.4.11.3
23087cytochrome oxidase+1.9.3.1
23087esterase (C 4)-
23087esterase lipase (C 8)+
23087leucine arylamidase+3.4.11.1
23087lipase (C 14)-
23087N-acetyl-beta-glucosaminidase-3.2.1.52
23087naphthol-AS-BI-phosphohydrolase-
23087trypsin-3.4.21.4

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
7294activated sludgePohangRepublic of KoreaKORAsia
23087R2A agar7 days20.0

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_146866.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_3877;97_6591;98_8192;99_146866&stattab=map
  • Last taxonomy: Hydrogenophaga caeni
  • 16S sequence: DQ372983
  • Sequence Identity:
  • Total samples: 19
  • aquatic counts: 17
  • animal counts: 1
  • plant counts: 1

Safety information

risk assessment

  • @ref: 7294
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7294
  • description: Hydrogenophaga caeni strain EMB71 16S ribosomal RNA gene, partial sequence
  • accession: DQ372983
  • length: 1446
  • database: ena
  • NCBI tax ID: 370976

GC content

  • @ref: 7294
  • GC-content: 61.6
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 7294

culture collection no.: DSM 17962, KCTC 12613

straininfo link

  • @ref: 72494
  • straininfo: 408351

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17473270Hydrogenophaga caeni sp. nov., isolated from activated sludge.Chung BS, Ryu SH, Park M, Jeon Y, Chung YR, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.64629-02007Bacterial Typing Techniques, Base Composition, Carbon/metabolism, Comamonadaceae/chemistry/*classification/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Molecular Sequence Data, Movement, Nitrogen/metabolism, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sewage/*microbiology, Temperature, Water MicrobiologyMetabolism
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7294Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17962)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17962
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
23087Bok Sil Chung,Seung Hyun Ryu,Minjeong Park,Yeji Jeon,Young Ryun Chung,Che Ok Jeon10.1099/ijs.0.64629-0Hydrogenophaga caeni sp. nov., isolated from activated sludgeIJSEM 57: 1126-1130 200717473270
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
72494Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408351.1StrainInfo: A central database for resolving microbial strain identifiers