Strain identifier

BacDive ID: 7420

Type strain: Yes

Species: Microbacterium oleivorans

Strain history: CIP <- 2005, A. Schippers, Bundesanstalt Geowissenschfaften Roshstoffe, Hannover, Germany: strain BAS69 <- K. Bosecker

NCBI tax ID(s): 1223528 (strain), 273677 (species)

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General

@ref: 6287

BacDive-ID: 7420

DSM-Number: 16091

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped

description: Microbacterium oleivorans DSM 16091 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from oil storage cavern 126.

NCBI tax id

NCBI tax idMatching level
1223528strain
273677species

strain history

@refhistory
6287<- A. Schippers; BAS69 <- K. Bosecker
67770NCIMB 14003 <-- A. Schippers BAS69 <-- K. Bosecker.
121409CIP <- 2005, A. Schippers, Bundesanstalt Geowissenschfaften Roshstoffe, Hannover, Germany: strain BAS69 <- K. Bosecker

doi: 10.13145/bacdive7420.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium oleivorans
  • full scientific name: Microbacterium oleivorans Schippers et al. 2005

@ref: 6287

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium oleivorans

full scientific name: Microbacterium oleivorans Schippers et al. 2005 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31321positiverod-shapedno
121409positiverod-shapedno

colony morphology

  • @ref: 121409

pigmentation

  • @ref: 31321
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6287TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
38295MEDIUM 338 - for Sanguibacter keddieiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (3.000 g);Trypto casein soy agar (30.000 g)
121409CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338

culture temp

@refgrowthtypetemperaturerange
6287positivegrowth28mesophilic
31321positivegrowth30-37mesophilic
31321positiveoptimum33.5mesophilic
38295positivegrowth30mesophilic
67770positivegrowth28mesophilic
121409positivegrowth10-37
121409nogrowth41thermophilic
121409nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31321aerobe
121409obligate aerobe

spore formation

  • @ref: 31321
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31321NaClpositivegrowth02-04 %
31321NaClpositiveoptimum3 %
121409NaClpositivegrowth0-8 %
121409NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31321178794-hydroxybenzoate+carbon source
3132122599arabinose+carbon source
3132135391aspartate+carbon source
3132117057cellobiose+carbon source
3132128757fructose+carbon source
3132128260galactose+carbon source
3132124265gluconate+carbon source
3132117234glucose+carbon source
3132127570histidine+carbon source
3132124996lactate+carbon source
3132125115malate+carbon source
3132117306maltose+carbon source
3132129864mannitol+carbon source
3132137684mannose+carbon source
3132128053melibiose+carbon source
3132117148putrescine+carbon source
3132115361pyruvate+carbon source
3132126546rhamnose+carbon source
3132133942ribose+carbon source
3132117814salicin+carbon source
313219300suberic acid+carbon source
3132117992sucrose+carbon source
3132127082trehalose+carbon source
3132118222xylose+carbon source
313214853esculin+hydrolysis
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose+builds acid from
683716731melezitose+builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside+builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
12140916947citrate-carbon source
1214094853esculin+hydrolysis
12140917632nitrate-reduction
12140916301nitrite-reduction
12140917632nitrate-respiration

metabolite production

  • @ref: 121409
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12140915688acetoin-
12140917234glucose-

enzymes

@refvalueactivityec
31321catalase+1.11.1.6
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
121409oxidase-
121409beta-galactosidase+3.2.1.23
121409alcohol dehydrogenase-1.1.1.1
121409gelatinase+/-
121409amylase+
121409DNase-
121409caseinase-3.4.21.50
121409catalase+1.11.1.6
121409tween esterase-
121409gamma-glutamyltransferase-2.3.2.2
121409lecithinase-
121409lysine decarboxylase-4.1.1.18
121409ornithine decarboxylase-4.1.1.17
121409phenylalanine ammonia-lyase-4.3.1.24
121409protease-
121409tryptophan deaminase-
121409urease-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
121409-++++++-++++++-++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121409+--+-+--+++++-+--+-+/-+-++++++++++-++---++--+/----+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121409+++++--+-+++---++++-++++-+-----+-+++--+----------++--+---+--+------------+-+--+++-----+--+++-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6287oil storage cavern 126EtzelGermanyDEUEurope
67770Oil storage cavern 126 near EtzelGermanyDEUEurope
121409Oil storage cavernGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Container (Reservoir)
#Engineered#Industrial#Oil reservoir

taxonmaps

  • @ref: 69479
  • File name: preview.99_1416.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_137;97_148;98_165;99_1416&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: AJ698725
  • Sequence Identity:
  • Total samples: 3482
  • soil counts: 587
  • aquatic counts: 444
  • animal counts: 2350
  • plant counts: 101

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
62871Risk group (German classification)
1214091Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31321
  • description: Microbacterium oleivorans partial 16S rRNA gene, type strain DSM 16091T
  • accession: AJ698725
  • length: 1490
  • database: nuccore
  • NCBI tax ID: 273677

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium oleivorans NBRC 1030751223528.5wgspatric1223528
66792Microbacterium oleivorans NBRC 1030752731957587draftimg1223528
67770Microbacterium oleivorans NBRC 103075GCA_001552475contigncbi1223528

GC content

  • @ref: 67770
  • GC-content: 69
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.907yes
gram-positiveyes92.458no
anaerobicno99.554yes
aerobicyes92.861no
halophileno93.365no
spore-formingno91.576no
thermophileno99.272no
glucose-utilyes85.719no
flagellatedno97.289yes
glucose-fermentno88.449no

External links

@ref: 6287

culture collection no.: DSM 16091, NCIMB 14003, BAS 69, JCM 14341, CIP 108712, IAM 15236, NBRC 103075

straininfo link

  • @ref: 76869
  • straininfo: 131639

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774639Microbacterium oleivorans sp. nov. and Microbacterium hydrocarbonoxydans sp. nov., novel crude-oil-degrading Gram-positive bacteria.Schippers A, Bosecker K, Sproer C, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.63305-02005Actinomycetales/*classification/genetics/metabolism/ultrastructure, Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Gram-Positive Bacteria/classification/metabolism, Molecular Sequence Data, Petroleum/*metabolism, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityMetabolism
Phylogeny18599704Microbacterium aquimaris sp. nov., isolated from seawater.Kim KK, Lee KC, Oh HM, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.65763-02008Actinomycetales/chemistry/*classification/genetics/metabolism, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Species SpecificityGenetics
Phylogeny33502309Microbacterium caowuchunii sp. nov. and Microbacterium lushaniae sp. nov., isolated from plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau of PR China.Tian Z, Yang J, Lai XH, Pu J, Jin D, Luo X, Huang Y, Li J, Zhang G, Wang S, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0046622021Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Contents/microbiology, Lagomorpha/*microbiology, Microbacterium/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6287Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16091)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16091
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
31321Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2763628776041
38295Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6371
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
76869Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131639.1StrainInfo: A central database for resolving microbial strain identifiers
121409Curators of the CIPCollection of Institut Pasteur (CIP 108712)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108712