Strain identifier
BacDive ID: 2972
Type strain:
Species: Hydrogenophaga caeni
Strain Designation: EMB71
Strain history: <- C. O. Jeon, Gyeongsang Nat. Univ. (GSNU), Jinju, Korea; EMB71
NCBI tax ID(s): 370976 (species)
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
@ref | name | growth | link | composition |
---|---|---|---|---|
7294 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: 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 |
23087 | Reasoner's 2A agar (R2A) | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7294 | positive | growth | 25 | mesophilic |
23087 | positive | growth | 15.0-35.0 | |
23087 | positive | optimum | 30.0 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
23087 | positive | optimum | 7.0-8.0 | |
23087 | positive | growth | 6.0-9.0 | alkaliphile |
Physiology and metabolism
oxygen tolerance
- @ref: 23087
- oxygen tolerance: facultative aerobe
spore formation
- @ref: 23087
- spore formation: no
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23087 | 27613 | amygdalin | - | builds acid from |
23087 | 18305 | arbutin | - | builds acid from |
23087 | 15824 | D-fructose | - | builds acid from |
23087 | 12936 | D-galactose | - | builds acid from |
23087 | 17634 | D-glucose | - | builds acid from |
23087 | 17716 | lactose | - | builds acid from |
23087 | 16899 | D-mannitol | - | builds acid from |
23087 | 16024 | D-mannose | - | builds acid from |
23087 | 30849 | L-arabinose | - | builds acid from |
23087 | 28053 | melibiose | - | builds acid from |
23087 | 26546 | rhamnose | - | builds acid from |
23087 | 17814 | salicin | - | builds acid from |
23087 | 30911 | sorbitol | - | builds acid from |
23087 | 17992 | sucrose | - | builds acid from |
23087 | 30849 | L-arabinose | - | growth |
23087 | 29864 | mannitol | - | growth |
23087 | casein | - | hydrolysis | |
23087 | 4853 | esculin | - | hydrolysis |
23087 | 5291 | gelatin | - | hydrolysis |
23087 | 28017 | starch | - | hydrolysis |
23087 | 53424 | tween 20 | - | hydrolysis |
23087 | 18186 | tyrosine | - | hydrolysis |
23087 | 16199 | urea | - | hydrolysis |
23087 | 17521 | (-)-quinic acid | - | oxidation |
23087 | 16763 | 2-oxobutanoate | - | oxidation |
23087 | 28644 | 2-oxopentanoate | - | oxidation |
23087 | 16724 | 4-hydroxybutyrate | - | oxidation |
23087 | 18101 | 4-hydroxyphenylacetic acid | - | oxidation |
23087 | 30089 | acetate | - | oxidation |
23087 | 40585 | alpha-cyclodextrin | - | oxidation |
23087 | 73706 | bromosuccinate | - | oxidation |
23087 | 16947 | citrate | - | oxidation |
23087 | 18333 | D-arabitol | - | oxidation |
23087 | 17057 | cellobiose | - | oxidation |
23087 | 15824 | D-fructose | - | oxidation |
23087 | 12936 | D-galactose | - | oxidation |
23087 | 18024 | D-galacturonic acid | - | oxidation |
23087 | 30612 | D-glucarate | - | oxidation |
23087 | 8391 | D-gluconate | - | oxidation |
23087 | 17784 | D-glucosaminic acid | - | oxidation |
23087 | 14314 | D-glucose 6-phosphate | - | oxidation |
23087 | 15748 | D-glucuronate | - | oxidation |
23087 | 16899 | D-mannitol | - | oxidation |
23087 | 16024 | D-mannose | - | oxidation |
23087 | 27605 | D-psicose | - | oxidation |
23087 | 16523 | D-serine | - | oxidation |
23087 | 23652 | dextrin | - | oxidation |
23087 | 17126 | DL-carnitine | - | oxidation |
23087 | 17113 | erythritol | - | oxidation |
23087 | 16000 | ethanolamine | - | oxidation |
23087 | 28066 | gentiobiose | - | oxidation |
23087 | 29042 | glucose 1-phosphate | - | oxidation |
23087 | 32323 | glucuronamide | - | oxidation |
23087 | 17754 | glycerol | - | oxidation |
23087 | 14336 | glycerol 1-phosphate | - | oxidation |
23087 | 28087 | glycogen | - | oxidation |
23087 | 73804 | glycyl L-aspartic acid | - | oxidation |
23087 | 17596 | inosine | - | oxidation |
23087 | 17240 | itaconate | - | oxidation |
23087 | 16977 | L-alanine | - | oxidation |
23087 | 30849 | L-arabinose | - | oxidation |
23087 | 18287 | L-fucose | - | oxidation |
23087 | 29985 | L-glutamate | - | oxidation |
23087 | 15603 | L-leucine | - | oxidation |
23087 | 15729 | L-ornithine | - | oxidation |
23087 | 17295 | L-phenylalanine | - | oxidation |
23087 | 18183 | L-pyroglutamic acid | - | oxidation |
23087 | 17115 | L-serine | - | oxidation |
23087 | 6359 | lactulose | - | oxidation |
23087 | 15792 | malonate | - | oxidation |
23087 | 28053 | melibiose | - | oxidation |
23087 | 320055 | methyl beta-D-glucopyranoside | - | oxidation |
23087 | 51850 | methyl pyruvate | - | oxidation |
23087 | 73784 | glycyl-l-glutamate | - | oxidation |
23087 | 17272 | propionate | - | oxidation |
23087 | 16634 | raffinose | - | oxidation |
23087 | 41865 | sebacic acid | - | oxidation |
23087 | 143136 | succinamate | - | oxidation |
23087 | 17992 | sucrose | - | oxidation |
23087 | 17748 | thymidine | - | oxidation |
23087 | 27082 | trehalose | - | oxidation |
23087 | 32528 | turanose | - | oxidation |
23087 | 16704 | uridine | - | oxidation |
23087 | 27248 | urocanic acid | - | oxidation |
23087 | 17151 | xylitol | - | oxidation |
23087 | 16634 | raffinose | + | builds acid from |
23087 | 17268 | myo-inositol | + | builds acid from |
23087 | 15971 | L-histidine | + | growth |
23087 | 17306 | maltose | + | growth |
23087 | 30911 | sorbitol | + | growth |
23087 | 53426 | tween 80 | + | hydrolysis |
23087 | 64552 | 2-hydroxybutyrate | + | oxidation |
23087 | 30916 | 2-oxoglutarate | + | oxidation |
23087 | 62064 | 2,3-butanediol | + | oxidation |
23087 | 37054 | 3-hydroxybutyrate | + | oxidation |
23087 | 18240 | 4-hydroxy-L-proline | + | oxidation |
23087 | 15963 | ribitol | + | oxidation |
23087 | 17925 | alpha-D-glucose | + | oxidation |
23087 | 36219 | alpha-lactose | + | oxidation |
23087 | 16383 | cis-aconitate | + | oxidation |
23087 | 15570 | D-alanine | + | oxidation |
23087 | 15895 | D-galactonic acid lactone | + | oxidation |
23087 | 17924 | D-sorbitol | + | oxidation |
23087 | 24996 | lactate | + | oxidation |
23087 | 15740 | formate | + | oxidation |
23087 | 16865 | gamma-aminobutyric acid | + | oxidation |
23087 | 21217 | L-alaninamide | + | oxidation |
23087 | 73786 | L-alanylglycine | + | oxidation |
23087 | 17196 | L-asparagine | + | oxidation |
23087 | 15971 | L-histidine | + | oxidation |
23087 | 17203 | L-proline | + | oxidation |
23087 | 62345 | L-rhamnose | + | oxidation |
23087 | 16857 | L-threonine | + | oxidation |
23087 | 17306 | maltose | + | oxidation |
23087 | 75146 | monomethyl succinate | + | oxidation |
23087 | 17268 | myo-inositol | + | oxidation |
23087 | 28037 | N-acetylgalactosamine | + | oxidation |
23087 | 506227 | N-acetylglucosamine | + | oxidation |
23087 | 50048 | phenylethylamine | + | oxidation |
23087 | 17148 | putrescine | + | oxidation |
23087 | 30031 | succinate | + | oxidation |
23087 | 16094 | thiosulfate | + | oxidation |
23087 | 53423 | tween 40 | + | oxidation |
23087 | 53426 | tween 80 | + | oxidation |
23087 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
23087 | acid phosphatase | - | 3.1.3.2 |
23087 | alkaline phosphatase | + | 3.1.3.1 |
23087 | alpha-chymotrypsin | - | 3.4.21.1 |
23087 | alpha-fucosidase | - | 3.2.1.51 |
23087 | alpha-galactosidase | - | 3.2.1.22 |
23087 | alpha-glucosidase | - | 3.2.1.20 |
23087 | alpha-mannosidase | - | 3.2.1.24 |
23087 | beta-galactosidase | - | 3.2.1.23 |
23087 | beta-glucosidase | - | 3.2.1.21 |
23087 | beta-glucuronidase | - | 3.2.1.31 |
23087 | catalase | + | 1.11.1.6 |
23087 | cystine arylamidase | - | 3.4.11.3 |
23087 | cytochrome oxidase | + | 1.9.3.1 |
23087 | esterase (C 4) | - | |
23087 | esterase lipase (C 8) | + | |
23087 | leucine arylamidase | + | 3.4.11.1 |
23087 | lipase (C 14) | - | |
23087 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
23087 | naphthol-AS-BI-phosphohydrolase | - | |
23087 | trypsin | - | 3.4.21.4 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|
7294 | activated sludge | Pohang | Republic of Korea | KOR | Asia | |||
23087 | R2A agar | 7 days | 20.0 |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17473270 | Hydrogenophaga caeni sp. nov., isolated from activated sludge. | Chung BS, Ryu SH, Park M, Jeon Y, Chung YR, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.64629-0 | 2007 | Bacterial 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 Microbiology | Metabolism |
Phylogeny | 21282897 | Hydrogenophaga temperata sp. nov., a betaproteobacterium isolated from compost in Korea. | Kim YJ, Kim MK, Weon HY, Kim HB, Yang DC | J Gen Appl Microbiol | 10.2323/jgam.56.419 | 2010 | *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 Microbiology | Genetics |
Phylogeny | 28920826 | Hydrogenophaga soli sp. nov., isolated from rice field soil. | Yang D, Cha S, Choi J, Seo T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002277 | 2017 | Bacterial 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/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
7294 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17962) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17962 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
23087 | Bok Sil Chung,Seung Hyun Ryu,Minjeong Park,Yeji Jeon,Young Ryun Chung,Che Ok Jeon | 10.1099/ijs.0.64629-0 | Hydrogenophaga caeni sp. nov., isolated from activated sludge | IJSEM 57: 1126-1130 2007 | 17473270 | |
69479 | João 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 | |||
72494 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID408351.1 | StrainInfo: A central database for resolving microbial strain identifiers |