Strain identifier

BacDive ID: 289

Type strain: Yes

Species: Oceanimonas doudoroffii

Strain Designation: 70

Strain history: CIP <- 1974, M. Véron, Necker Hosp., France <- P. Baumann: strain 70

NCBI tax ID(s): 84158 (species)

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General

@ref: 2953

BacDive-ID: 289

DSM-Number: 7028

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

description: Oceanimonas doudoroffii 70 is an obligate aerobe, mesophilic, motile bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 84158
  • Matching level: species

strain history

@refhistory
2953<- ATCC <- P. Baumann; 70
67770IAM 14168 <-- ATCC 27123 <-- P. Baumann 70.
118969CIP <- 1974, M. Véron, Necker Hosp., France <- P. Baumann: strain 70

doi: 10.13145/bacdive289.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Aeromonadales
  • family: Aeromonadaceae
  • genus: Oceanimonas
  • species: Oceanimonas doudoroffii
  • full scientific name: Oceanimonas doudoroffii corrig. (Baumann et al. 1972) Brown et al. 2001

  • synonyms

    @refsynonym
    20215Pseudomonas doudoroffii
    20215Oceanomonas doudoroffii

@ref: 2953

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Aeromonadales

family: Aeromonadaceae

genus: Oceanimonas

species: Oceanimonas doudoroffii

full scientific name: Oceanimonas doudoroffii (Baumann et al. 1972) Brown et al. 2001

strain designation: 70

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.158
6948099.997negative
118969yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2953TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
2953BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
2953SEA WATER AGAR (DSMZ Medium 246)yeshttps://mediadive.dsmz.de/medium/246Name: SEA WATER AGAR (DSMZ Medium 246) Composition: Agar 20.0 g/l Peptone 10.0 g/l Beef extract 10.0 g/l Tap water Sea water
34144Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118969CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
118969CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
2953positivegrowth25mesophilic
2953positivegrowth28mesophilic
34144positivegrowth30mesophilic
67770positivegrowth25mesophilic
118969positivegrowth25-41
118969nogrowth5psychrophilic
118969nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118969
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
118969NaClpositivegrowth0-8 %
118969NaClnogrowth10 %

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
118969citrate+carbon source16947
118969esculin-hydrolysis4853
118969nitrate+reduction17632
118969nitrite-reduction16301
118969nitrate-respiration17632

antibiotic resistance

  • @ref: 118969
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 118969
  • 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
118969oxidase+
118969beta-galactosidase+3.2.1.23
118969alcohol dehydrogenase+1.1.1.1
118969gelatinase-
118969amylase-
118969DNase-
118969caseinase-3.4.21.50
118969catalase+1.11.1.6
118969tween esterase-
118969lecithinase-
118969lipase-
118969lysine decarboxylase-4.1.1.18
118969ornithine decarboxylase-4.1.1.17
118969protease-
118969tryptophan deaminase-
118969urease+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
118969-+++-+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118969-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118969-+-------------------------------------------+-++++--+-------+++---+---+++++---+++++----+++++++---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2953seawater
67770Seawater off coast, by enrichment with allantoinOahu, HIUSAUSANorth America
118969Environment, Seawater by enrichment with allantoin

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_31264.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_11;96_2774;97_3412;98_23250;99_31264&stattab=map
  • Last taxonomy: Oceanimonas doudoroffii subclade
  • 16S sequence: AB681912
  • Sequence Identity:
  • Total samples: 77
  • soil counts: 7
  • aquatic counts: 31
  • animal counts: 39

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
29531Risk group (German classification)
1189691Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Oceanimonas doudoroffii gene for 16S rRNA, partial sequence, strain: NBRC 103032AB6819121469ena84158
2953Oceanimonas doudoroffii strain ATCC 27123 16S ribosomal RNA gene, partial sequenceAF0947241466ena84158
2953Oceanimonas doudoroffii gene for 16S rRNA, partial sequenceAB0193901484ena84158
2953Oceanimonas doudoroffii gene for 16S rRNA, strain: ATCC 27123AB0213711506ena84158

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Oceanimonas doudoroffii strain ATCC 2712384158.3wgspatric84158
66792Oceanimonas doudoroffii DSM 70282506520053draftimg84158
67770Oceanimonas doudoroffii ATCC 27123GCA_002242685contigncbi84158

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes93.736no
flagellatedyes84.659no
gram-positiveno98.566no
anaerobicno99.158no
halophileyes82.966no
spore-formingno94.673no
glucose-utilyes85.444no
aerobicyes90.934no
thermophileno97.445no
glucose-fermentyes55.861no

External links

@ref: 2953

culture collection no.: DSM 7028, ATCC 27123, IAM 14168, JCM 21046, CCUG 12373, CCUG 16001, CIP 74.09, DSM 50408, ICPB 3526, LMG 2180, NBRC 103032, NCIMB 1965, CIP 74.9

straininfo link

  • @ref: 69971
  • straininfo: 359487

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11211275Reclassification of [Pseudomonas] doudoroffii (Baumann et al. 1983) into the genus Oceanomonas gen. nov. as Oceanomonas doudoroffii comb. nov., and description of a phenol-degrading bacterium from estuarine water as Oceanomonas baumannii sp. nov.Brown GR, Sutcliffe IC, Cummings SPInt J Syst Evol Microbiol10.1099/00207713-51-1-672001Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fresh Water/*microbiology, Gammaproteobacteria/*classification/genetics/isolation & purification/metabolism, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenols/*metabolism, Phenotype, Phylogeny, Polymerase Chain Reaction, Pseudomonas/*classification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny14657118Oceanisphaera litoralis gen. nov., sp. nov., a novel halophilic bacterium from marine bottom sediments.Romanenko LA, Schumann P, Zhukova NV, Rohde M, Mikhailov VV, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.02774-02003Aeromonadaceae/*classification/isolation & purification/physiology/ultrastructure, Geologic Sediments/*microbiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Seawater/*microbiologyGenetics
Phylogeny15830805Oceanimonas smirnovii sp. nov., a novel organism isolated from the Black Sea.Ivanova EP, Onyshchenko OM, Christen R, Zhukova NV, Lysenko AM, Shevchenko LS, Buljan V, Hambly B, Kiprianova EASyst Appl Microbiol10.1016/j.syapm.2004.11.0022005Aeromonadaceae/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, UkraineGenetics
Genetics28883151Genome Sequence of Oceanimonas doudoroffii ATCC 27123(T).Brennan MA, Trachtenberg AM, McClelland WD, MacLea KSGenome Announc10.1128/genomeA.00996-172017

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2953Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7028)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7028
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
34144Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10699
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
69971Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID359487.1StrainInfo: A central database for resolving microbial strain identifiers
118969Curators of the CIPCollection of Institut Pasteur (CIP 74.9)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2074.9