Strain identifier

BacDive ID: 11299

Type strain: Yes

Species: Oleiphilus messinensis

Strain Designation: ME102

Strain history: CIP <- 2002, P. Golyshin, GBF, Braunschweig, Germany: strain ME102

NCBI tax ID(s): 141451 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 5064

BacDive-ID: 11299

DSM-Number: 13489

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

description: Oleiphilus messinensis ME102 is an obligate aerobe, mesophilic, motile bacterium that was isolated from sea water, sediments from the depth of 8 m.

NCBI tax id

  • NCBI tax id: 141451
  • Matching level: species

strain history

@refhistory
5064<- P. N. Golyshin; ME102
399062002, Dr. P. Golyshin, GBF, Braunschweig, Germany: strain ME102
120916CIP <- 2002, P. Golyshin, GBF, Braunschweig, Germany: strain ME102

doi: 10.13145/bacdive11299.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Oleiphilaceae
  • genus: Oleiphilus
  • species: Oleiphilus messinensis
  • full scientific name: Oleiphilus messinensis Golyshin et al. 2002

@ref: 5064

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Oleiphilaceae

genus: Oleiphilus

species: Oleiphilus messinensis

full scientific name: Oleiphilus messinensis Golyshin et al. 2002

strain designation: ME102

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.818
6948099.992negative
120916yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5064ONR7a MEDIUM (DSMZ Medium 950)yeshttps://mediadive.dsmz.de/medium/950Name: ONR7a MEDIUM (DSMZ Medium 950; with strain-specific modifications) Composition: NaCl 22.79 g/l Agar 15.0 g/l Agarose 12.0 g/l MgCl2 x 6 H2O 11.18 g/l Sodium acetate 5.0 g/l Na2SO4 3.98 g/l CaCl2 x 2 H2O 1.46 g/l TAPSO 1.3 g/l KCl 0.72 g/l NH4Cl 0.27 g/l Na2HPO4 x 7 H2O 0.089 g/l NaBr 0.083 g/l NaHCO3 0.031 g/l H3BO3 0.027 g/l SrCl2 x 6 H2O 0.024 g/l NaF 0.0026 g/l FeCl2 x 4 H2O 0.002 g/l Distilled water
39906Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120916CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5064positivegrowth28mesophilic
39906positivegrowth25mesophilic
120916positivegrowth15-41
120916nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120916
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
120916NaClpositivegrowth4-6 %
120916NaClnogrowth0 %
120916NaClnogrowth2 %
120916NaClnogrowth8 %
120916NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1209164853esculin-hydrolysis
12091617632nitrate-builds gas from
12091617632nitrate+reduction
12091616301nitrite-builds gas from
12091616301nitrite-reduction

metabolite production

  • @ref: 120916
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
120916oxidase-
120916beta-galactosidase+3.2.1.23
120916alcohol dehydrogenase-1.1.1.1
120916gelatinase+
120916amylase+
120916caseinase+3.4.21.50
120916catalase+1.11.1.6
120916tween esterase+
120916gamma-glutamyltransferase-2.3.2.2
120916lecithinase+
120916lipase+
120916lysine decarboxylase-4.1.1.18
120916ornithine decarboxylase-4.1.1.17
120916phenylalanine ammonia-lyase-4.3.1.24
120916protease+
120916tryptophan deaminase-
120916urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120916--++-+--++-+-+-+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5064sea water, sediments from the depth of 8 mSicily, MessinaItalyITAEurope
120916Environment, Seawater, sediment samplesMessina harborItalyITAEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
50641Risk group (German classification)
1209161Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Oleiphilus messinensis 16S rRNA gene, isolate ME102
  • accession: AJ295154
  • length: 1437
  • database: ena
  • NCBI tax ID: 141451

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Oleiphilus messinensis ME102GCA_002162375completencbi141451
66792Oleiphilus messinensis DSM 13489GCA_900108075scaffoldncbi141451
66792Oleiphilus messinensis strain DSM 13489141451.6wgspatric141451
66792Oleiphilus messinensis ME1022773857794completeimg141451
66792Oleiphilus messinensis DSM 134892634166903draftimg141451

GC content

  • @ref: 5064
  • GC-content: 49

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes92.737no
gram-positiveno98.828no
anaerobicno97.751no
aerobicyes88.203no
halophileyes59.99no
spore-formingno93.674no
thermophileno99.684no
glucose-utilyes70.597no
motileyes91.116no
glucose-fermentno89.387no

External links

@ref: 5064

culture collection no.: DSM 13489, LMG 20357, CIP 107588

straininfo link

  • @ref: 80532
  • straininfo: 84720

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12054256Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons.Golyshin PN, Chernikova TN, Abraham WR, Lunsdorf H, Timmis KN, Yakimov MMInt J Syst Evol Microbiol10.1099/00207713-52-3-9012002Alkanes/metabolism, Biodegradation, Environmental, Culture Media, Cytochrome P-450 CYP4A, Cytochrome P-450 Enzyme System/genetics, DNA, Ribosomal/analysis, Gammaproteobacteria/*classification/genetics/growth & development/ultrastructure, Geologic Sediments/*microbiology, Hydrocarbons/*metabolism, Lipids/analysis, Mixed Function Oxygenases/genetics, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAMetabolism
Genetics28802691The genome analysis of Oleiphilus messinensis ME102 (DSM 13489(T)) reveals backgrounds of its obligate alkane-devouring marine lifestyle.Toshchakov SV, Korzhenkov AA, Chernikova TN, Ferrer M, Golyshina OV, Yakimov MM, Golyshin PNMar Genomics10.1016/j.margen.2017.07.0052017Alkanes/*metabolism, Biodegradation, Environmental, Gammaproteobacteria/*genetics/physiology, *Genome, Bacterial, Geologic Sediments/microbiology, Italy, PhylogenyPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5064Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13489)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13489
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
39906Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5040
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
68382Automatically annotated from API zym
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
80532Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID84720.1StrainInfo: A central database for resolving microbial strain identifiers
120916Curators of the CIPCollection of Institut Pasteur (CIP 107588)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107588