Strain identifier

BacDive ID: 11112

Type strain: Yes

Species: Nocardioides oleivorans

Strain history: CIP <- 2005, DSMZ

NCBI tax ID(s): 273676 (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: 6286

BacDive-ID: 11112

DSM-Number: 16090

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

description: Nocardioides oleivorans DSM 16090 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Oil sample.

NCBI tax id

  • NCBI tax id: 273676
  • Matching level: species

strain history

@refhistory
6286<- A. Schippers <- K. Bosecker, BAS3
383622005, DSMZ
67770NCIMB 14004 <-- A. Schippers BAS3 <-- K. Bosecker.
121410CIP <- 2005, DSMZ

doi: 10.13145/bacdive11112.20230509.8.1

Name and taxonomic classification

LPSN

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

@ref: 6286

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides oleivorans

full scientific name: Nocardioides oleivorans Schippers et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31420positive1.1 µm0.3 µmrod-shapedno
121410positiverod-shapedno

pigmentation

  • @ref: 31420
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
38362MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
6286TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yesName: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535
6286GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yesName: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/65
121410CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
31420positivegrowth25-30mesophilic
31420positiveoptimum30mesophilic
38362positivegrowth30mesophilic
67770positivegrowth28mesophilic
6286positivegrowth28mesophilic
121410positivegrowth10-41
121410nogrowth45thermophilic

culture pH

@refabilitytypepH
31420positivegrowth7-7.3
31420positiveoptimum7.15

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31420aerobe
121410obligate aerobe

spore formation

  • @ref: 31420
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31420NaClpositivegrowth2 %
31420NaClpositiveoptimum2 %
121410NaClpositivegrowth0-4 %
121410NaClnogrowth6 %
121410NaClnogrowth8 %
121410NaClnogrowth10 %

murein

  • @ref: 6286
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

observation

@refobservation
31420aggregates in clumps
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3142030089acetate+carbon source
3142016449alanine+carbon source
3142035391aspartate+carbon source
3142017057cellobiose+carbon source
3142028757fructose+carbon source
3142028260galactose+carbon source
3142024265gluconate+carbon source
3142017234glucose+carbon source
3142027570histidine+carbon source
3142024996lactate+carbon source
3142025017leucine+carbon source
3142025115malate+carbon source
3142017306maltose+carbon source
3142029864mannitol+carbon source
3142037684mannose+carbon source
3142028053melibiose+carbon source
3142018401phenylacetate+carbon source
3142026271proline+carbon source
3142017272propionate+carbon source
3142017148putrescine+carbon source
3142015361pyruvate+carbon source
3142026546rhamnose+carbon source
3142017992sucrose+carbon source
3142027082trehalose+carbon source
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
6837128847D-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
6837143943methyl alpha-D-mannoside-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
12141016947citrate-carbon source
1214104853esculin+hydrolysis
121410606565hippurate+hydrolysis
12141017632nitrate-reduction
12141016301nitrite-reduction
12141017632nitrate-respiration

metabolite production

  • @ref: 121410
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12141015688acetoin-
12141017234glucose-

enzymes

@refvalueactivityec
121410oxidase-
121410beta-galactosidase+3.2.1.23
121410alcohol dehydrogenase-1.1.1.1
121410gelatinase+
121410amylase-
121410DNase+
121410caseinase+3.4.21.50
121410catalase+1.11.1.6
121410tween esterase+
121410gamma-glutamyltransferase+2.3.2.2
121410lecithinase-
121410lipase-
121410lysine decarboxylase-4.1.1.18
121410ornithine decarboxylase-4.1.1.17
121410phenylalanine ammonia-lyase+4.3.1.24
121410protease+
121410tryptophan deaminase-
121410urease+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
121410-+++++++--++++-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121410------------------------+------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6286Oil sampleGifhornGermanyDEUEurope
67770Crude oil sample from the oilfield Oerrel of the Gifhorn TroughGermanyDEUEurope
121410Crude oilGermanyDEUEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Industrial
  • Cat3: #Oil reservoir

taxonmaps

  • @ref: 69479
  • File name: preview.99_67788.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_2445;97_2980;98_3734;99_67788&stattab=map
  • Last taxonomy: Nocardioides oleivorans
  • 16S sequence: AJ698724
  • Sequence Identity:
  • Total samples: 702
  • soil counts: 322
  • aquatic counts: 27
  • animal counts: 139
  • plant counts: 214

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
62861Risk group (German classification)
1214101Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6286
  • description: Nocardioides oleivorans partial 16S rRNA gene, type strain DSM 16090T
  • accession: AJ698724
  • length: 1479
  • database: ena
  • NCBI tax ID: 273676

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides oleivorans strain CGMCC 4.6882273676.3wgspatric273676
66792Nocardioides oleivorans CGMCC 4.68822867494351draftimg273676
67770Nocardioides oleivorans CGMCC 4.6882GCA_004137255contigncbi273676

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno75.927no
gram-positiveyes92.12yes
anaerobicno98.865no
halophileno96.607no
spore-formingno81.058yes
glucose-utilyes89.922no
aerobicyes92.256yes
thermophileno99.449yes
flagellatedno94.018yes
glucose-fermentno89.648no

External links

@ref: 6286

culture collection no.: DSM 16090, NCIMB 14004, BAS 3, JCM 14342, CGMCC 4.6882, CIP 108901, IAM 15341

straininfo link

  • @ref: 80361
  • straininfo: 305282

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16014472Nocardioides oleivorans sp. nov., a novel crude-oil-degrading bacterium.Schippers A, Schumann P, Sproer CInt J Syst Evol Microbiol10.1099/ijs.0.63500-02005Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Petroleum/*metabolism, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny17220437Nocardioides furvisabuli sp. nov., isolated from black sand.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.64444-02007Actinomycetales/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny18175721Nocardioides hwasunensis sp. nov.Lee SD, Lee DW, Kim JSInt J Syst Evol Microbiol10.1099/ijs.0.65015-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA Fingerprinting/methods, DNA, Bacterial/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny27654931Nocardioides flavus sp. nov., isolated from marine sediment.Wang S, Zhou Y, Zhang GInt J Syst Evol Microbiol10.1099/ijsem.0.0015072016Actinomycetales/*classification/genetics/isolation & purification, Bacteria, Aerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryEnzymology
Phylogeny27902315Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave.Han MX, Fang BZ, Tian Y, Zhang WQ, Jiao JY, Liu L, Zhang ZT, Xiao M, Wei DQ, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0016762017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny28771135Nocardioides sonneratiae sp. nov., an endophytic actinomycete isolated from a branch of Sonneratia apetala.Li F, Tuo L, Su ZW, Wei XQ, Zhang XY, Gao CH, Huang RMInt J Syst Evol Microbiol10.1099/ijsem.0.0019792017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lythraceae/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31135330Nocardioides zhouii sp. nov., isolated from the Hailuogou Glacier in China.Zhang GQ, Liu Q, Liu HC, Zhou YG, Xin YHInt J Syst Evol Microbiol10.1099/ijsem.0.0034712019Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Ice Cover/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34542392Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula.Chhetri G, Kim I, Kang M, Kim J, So Y, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0050122021*Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nocardioides, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *TagetesTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6286Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16090)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16090
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
31420Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2772728776041
38362Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6582
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
80361Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID305282.1StrainInfo: A central database for resolving microbial strain identifiers
121410Curators of the CIPCollection of Institut Pasteur (CIP 108901)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108901