Strain identifier

BacDive ID: 290

Type strain: Yes

Species: Oceanimonas baumannii

Strain Designation: GB6

Strain history: CIP <- 2002, NCIMB <- G.R. Brown: strain GB6

NCBI tax ID(s): 129578 (species)

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General

@ref: 5909

BacDive-ID: 290

DSM-Number: 15594

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

description: Oceanimonas baumannii GB6 is an obligate aerobe, mesophilic, motile bacterium that was isolated from estuarine mud.

NCBI tax id

  • NCBI tax id: 129578
  • Matching level: species

strain history

@refhistory
5909<- G. R. Brown, School of Sci., Univ. Sunderland, UK; GB6
116764CIP <- 2002, NCIMB <- G.R. Brown: strain GB6

doi: 10.13145/bacdive290.20230509.8.1

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 baumannii
  • full scientific name: Oceanimonas baumannii corrig. Brown et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Oceanomonas baumannii

@ref: 5909

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Aeromonadales

family: Aeromonadaceae

genus: Oceanimonas

species: Oceanimonas baumannii

full scientific name: Oceanimonas baumannii Brown et al. 2001

strain designation: GB6

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes99.011
6948099.998negative
116764yesnegativerod-shaped

pigmentation

  • @ref: 116764
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5909TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
5909BACTO 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
37122MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116764CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5909positivegrowth28mesophilic
37122positivegrowth25mesophilic
116764positivegrowth10-41
116764nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116764
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.987

halophily

  • @ref: 116764
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

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
116764citrate+carbon source16947
116764esculin-hydrolysis4853
116764nitrate+reduction17632
116764nitrite+reduction16301
116764nitrate-respiration17632

antibiotic resistance

  • @ref: 116764
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116764
  • 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
116764oxidase+
116764beta-galactosidase-3.2.1.23
116764alcohol dehydrogenase-1.1.1.1
116764gelatinase-
116764amylase-
116764DNase-
116764caseinase-3.4.21.50
116764catalase+1.11.1.6
116764tween esterase-
116764lecithinase-
116764lipase-
116764lysine decarboxylase-4.1.1.18
116764ornithine decarboxylase-4.1.1.17
116764protease-
116764tryptophan deaminase-
116764urease-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
116764-+++-+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116764-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116764-------------------+-----------------------------++--+--------++---+---+++-+---+++++----+++++++-+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5909estuarine mudSunderland, mouth of the river WearUnited KingdomGBREurope
116764Environment, Mud, estuary of the river WearSunderlandUnited KingdomGBREurope1998

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Brackish
#Environmental#Terrestrial#Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_81567.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_11;96_2774;97_3412;98_56706;99_81567&stattab=map
  • Last taxonomy: Oceanimonas baumannii subclade
  • 16S sequence: AF168367
  • Sequence Identity:
  • Total samples: 60
  • soil counts: 8
  • aquatic counts: 37
  • animal counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59091Risk group (German classification)
1167641Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5909
  • description: Oceanimonas baumannii strain GB6 16S ribosomal RNA gene, partial sequence
  • accession: AF168367
  • length: 1296
  • database: ena
  • NCBI tax ID: 129578

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Oceanimonas baumannii DSM 15594GCA_004365405scaffoldncbi129578
66792Oceanimonas baumannii ATCC 700832GCA_002245495contigncbi129578
66792Oceanimonas baumannii strain ATCC 700832129578.3wgspatric129578
66792Oceanimonas baumannii strain DSM 15594129578.4wgspatric129578
66792Oceanimonas baumannii DSM 155942593339295draftimg129578

GC content

  • @ref: 5909
  • GC-content: 54.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes95.932no
flagellatedyes88.717no
gram-positiveno98.767no
anaerobicno98.795no
aerobicyes88.726no
halophileyes76.383no
spore-formingno95.733no
thermophileno98.594yes
glucose-utilyes82.781no
glucose-fermentyes64.774no

External links

@ref: 5909

culture collection no.: DSM 15594, ATCC 700832, KCTC 12927, NCIMB 13685, CIP 107717

straininfo link

  • @ref: 69972
  • straininfo: 362262

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
Cultivation11728713Potassium uptake and retention by Oceanomonas baumannii at low water activity in the presence of phenol.Brown GR, Cummings SPFEMS Microbiol Lett10.1111/j.1574-6968.2001.tb10922.x2001Cell Membrane/chemistry, Cell Membrane Permeability, Culture Media, Gammaproteobacteria/*drug effects/growth & development/*metabolism, Lipids/analysis, Osmolar Concentration, Phenol/*pharmacology, Potassium Chloride/*metabolism, WaterMetabolism
Metabolism12776923Combined solvent and water activity stresses on turgor regulation and membrane adaptation in Oceanimonas baumannii ATCC 700832.Brown GR, Sutcliffe IC, Cummings SPAntonie Van Leeuwenhoek10.1023/a:10233489283762003Adaptation, Physiological, Aeromonadaceae/chemistry/growth & development/*metabolism, Cell Membrane/chemistry/*metabolism, Fatty Acids/metabolism, Membrane Lipids/metabolism, Membrane Proteins/metabolism, Phenols/metabolism, Phospholipids/metabolism, Seawater, Sodium Chloride/pharmacology, Solvents/*chemistry, Succinic Acid/metabolism, Water/*chemistryStress
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
Genetics28883154Draft Genome Sequence of the Marine Bacterium Oceanimonas baumannii ATCC 700832(T).McClelland WD, Trachtenberg AM, Brennan MA, MacLea KSGenome Announc10.1128/genomeA.01007-172017

Reference

@idauthorscataloguedoi/urltitle
5909Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15594)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15594
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
37122Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5184
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)
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
69972Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362262.1StrainInfo: A central database for resolving microbial strain identifiers
116764Curators of the CIPCollection of Institut Pasteur (CIP 107717)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107717