Strain identifier

BacDive ID: 2969

Type strain: Yes

Species: Hydrogenophaga intermedia

Strain Designation: S1

Strain history: CIP <- 2001, A. Stolz, Stuttgart Univ., Stuttgart, Germany: strain S1

NCBI tax ID(s): 65786 (species)

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General

@ref: 2277

BacDive-ID: 2969

DSM-Number: 5680

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile

description: Hydrogenophaga intermedia S1 is an obligate aerobe, mesophilic, motile bacterium that was isolated from air.

NCBI tax id

  • NCBI tax id: 65786
  • Matching level: species

strain history

@refhistory
2277<- B.J. Feigel, S1 (Hydrogenophaga sp.)
337302001, A. Stolz, Univ., Stuttgart, Germany: strain S1
67770IAM 14919 <-- DSM 5680 <-- B. J. Feigel S1.
120144CIP <- 2001, A. Stolz, Stuttgart Univ., Stuttgart, Germany: strain S1

doi: 10.13145/bacdive2969.20230509.8.1

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 intermedia
  • full scientific name: Hydrogenophaga intermedia Contzen et al. 2001

@ref: 2277

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Hydrogenophaga

species: Hydrogenophaga intermedia

full scientific name: Hydrogenophaga intermedia Contzen et al. 2001

strain designation: S1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.539
6948099.999negative
120144yesnegativerod-shaped

pigmentation

  • @ref: 120144
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2277NUTRIENT 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
33730MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
120144CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
2277positivegrowth28mesophilic
33730positivegrowth25mesophilic
67770positivegrowth27mesophilic
120144positivegrowth25-41
120144nogrowth5psychrophilic
120144nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120144
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.978

halophily

@refsaltgrowthtested relationconcentration
120144NaClnogrowth0 %
120144NaClnogrowth2 %
120144NaClnogrowth4 %
120144NaClnogrowth6 %
120144NaClnogrowth8 %
120144NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120144citrate-carbon source16947
120144esculin-hydrolysis4853
120144nitrate+reduction17632
120144nitrite-reduction16301
120144nitrate-respiration17632

antibiotic resistance

  • @ref: 120144
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120144
  • 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
120144oxidase+
120144beta-galactosidase-3.2.1.23
120144alcohol dehydrogenase-1.1.1.1
120144gelatinase-
120144amylase-
120144DNase-
120144caseinase-3.4.21.50
120144catalase+1.11.1.6
120144tween esterase-
120144lecithinase-
120144lipase-
120144lysine decarboxylase-4.1.1.18
120144ornithine decarboxylase-4.1.1.17
120144tryptophan deaminase-
120144urease+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
120144--++-+--------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120144-------------------------------+-----------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120144-------------------+---+--------------------------------------------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
2277airBonnGermanyDEUEurope
67770AirGermanyDEUEurope
120144Environment, Waste waterGermanyDEUEurope1988

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Air

taxonmaps

  • @ref: 69479
  • File name: preview.99_2323.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_872;97_1487;98_1812;99_2323&stattab=map
  • Last taxonomy: Hydrogenophaga
  • 16S sequence: AF019037
  • Sequence Identity:
  • Total samples: 9570
  • soil counts: 3472
  • aquatic counts: 3956
  • animal counts: 1012
  • plant counts: 1130

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
22771Risk group (German classification)
1201441Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Hydrogenophaga intermedia gene for 16S rRNA, partial sequence, strain: NBRC 102510AB6818441454ena65786
20218Hydrogenophaga intermedia 16S ribosomal RNA gene, complete sequenceAF0190371481ena65786

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hydrogenophaga intermedia strain DSM 568065786.5wgspatric65786
66792Hydrogenophaga intermedia S12619619207draftimg65786
67770Hydrogenophaga intermedia NBRC 102510GCA_001571205contigncbi1349790
67770Hydrogenophaga intermedia S1GCA_000723405contigncbi65786
67770Hydrogenophaga intermedia DSM 5680GCA_005938115contigncbi65786

GC content

  • @ref: 67770
  • GC-content: 68.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.053no
anaerobicno98.865no
halophileno92.343no
spore-formingno94.632no
glucose-utilno56.333no
thermophileno99.053yes
flagellatedyes63.163no
motileyes79.686no
aerobicyes96.433no
glucose-fermentno92.214no

External links

@ref: 2277

culture collection no.: DSM 5680, JCM 21401, IAM 14919, CIP 107269

straininfo link

  • @ref: 72491
  • straininfo: 47978

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11249018Hydrogenophaga intermedia sp. nov., a 4-aminobenzenesulfonate degrading organism.Contzen M, Moore ER, Blumel S, Stolz A, Kampfer PSyst Appl Microbiol10.1016/S0723-2020(00)80022-32000Bacterial Typing Techniques, Betaproteobacteria/*classification/genetics/metabolism/ultrastructure, Biodegradation, Environmental, Culture Media, DNA, Ribosomal/analysis/genetics, Evolution, Molecular, Gram-Negative Aerobic Bacteria/classification/enzymology, Molecular Sequence DataCultivation
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/urltitlejournalpubmed
2277Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5680)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5680
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
33730Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4686
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
72491Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID47978.1StrainInfo: A central database for resolving microbial strain identifiers
120144Curators of the CIPCollection of Institut Pasteur (CIP 107269)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107269