Strain identifier

BacDive ID: 7419

Type strain: Yes

Species: Microbacterium hydrocarbonoxydans

Strain Designation: BNP48

Strain history: CIP <- 2005, A. Schippers, Bundesanstalt Geowissenschaften Rohstoffe, Hannover, Germany: strain BNP48 <- K. Bosecker

NCBI tax ID(s): 1223527 (strain), 273678 (species)

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General

@ref: 6285

BacDive-ID: 7419

DSM-Number: 16089

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

description: Microbacterium hydrocarbonoxydans BNP48 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from oil contaminated soil.

NCBI tax id

NCBI tax idMatching level
273678species
1223527strain

strain history

@refhistory
6285<- A. Schippers; BNP48 <- K. Bosecker
67770NCIMB 14002 <-- A. Schippers BNP48 <-- K. Bosecker.
120000CIP <- 2005, A. Schippers, Bundesanstalt Geowissenschaften Rohstoffe, Hannover, Germany: strain BNP48 <- K. Bosecker

doi: 10.13145/bacdive7419.20230509.8.1

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 hydrocarbonoxydans
  • full scientific name: Microbacterium hydrocarbonoxydans Schippers et al. 2005

@ref: 6285

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium hydrocarbonoxydans

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

strain designation: BNP48

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31321positiverod-shapedyes
120000positiverod-shapedyes

colony morphology

  • @ref: 120000

pigmentation

  • @ref: 31321
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6285TRYPTICASE 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
37448MEDIUM 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)
120000CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338

culture temp

@refgrowthtypetemperaturerange
6285positivegrowth28mesophilic
31321positivegrowth30-37mesophilic
31321positiveoptimum33.5mesophilic
37448positivegrowth30mesophilic
67770positivegrowth28mesophilic
120000positivegrowth25-37mesophilic
120000nogrowth5psychrophilic
120000nogrowth15psychrophilic
120000nogrowth41thermophilic
120000nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31321aerobe
120000obligate aerobe

spore formation

  • @ref: 31321
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31321NaClpositivegrowth02-04 %
31321NaClpositiveoptimum3 %
120000NaClpositivegrowth0-4 %
120000NaClnogrowth6 %
120000NaClnogrowth8 %
120000NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3132130089acetate+carbon source
3132116449alanine+carbon source
3132122599arabinose+carbon source
3132135391aspartate+carbon source
3132117057cellobiose+carbon source
3132116947citrate+carbon source
3132128757fructose+carbon source
3132128260galactose+carbon source
3132124265gluconate+carbon source
3132117234glucose+carbon source
3132128087glycogen+carbon source
3132127570histidine+carbon source
31321182404-hydroxy-L-proline+carbon source
3132124996lactate+carbon source
3132125115malate+carbon source
3132117306maltose+carbon source
3132129864mannitol+carbon source
3132137684mannose+carbon source
31321506227N-acetylglucosamine+carbon source
3132118401phenylacetate+carbon source
3132126271proline+carbon source
3132117272propionate+carbon source
3132117148putrescine+carbon source
3132115361pyruvate+carbon source
3132126546rhamnose+carbon source
3132133942ribose+carbon source
3132117822serine+carbon source
3132117992sucrose+carbon source
3132127082trehalose+carbon source
3132118222xylose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837117151xylitol-builds acid from
6837116634raffinose-builds acid from
6837115443inulin-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
683714853esculin-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-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
6837117113erythritol-builds acid from
12000016947citrate-carbon source
1200004853esculin+hydrolysis
120000606565hippurate+hydrolysis
12000017632nitrate-reduction
12000016301nitrite-reduction
12000017632nitrate-respiration

metabolite production

  • @ref: 120000
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12000015688acetoin-
12000017234glucose-

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
120000oxidase-
120000beta-galactosidase+3.2.1.23
120000alcohol dehydrogenase-1.1.1.1
120000gelatinase+
120000amylase-
120000DNase-
120000caseinase-3.4.21.50
120000catalase+1.11.1.6
120000tween esterase-
120000gamma-glutamyltransferase-2.3.2.2
120000lecithinase-
120000lipase-
120000lysine decarboxylase-4.1.1.18
120000ornithine decarboxylase-4.1.1.17
120000phenylalanine ammonia-lyase-4.3.1.24
120000tryptophan deaminase-
120000urease-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
120000-++++++-+-++-+-+++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120000+/--+/-+/-+/-+/----++++/--+/---+-+/-+/--+/-+/--+/-+/-+--+/-+/--+/--+/-+/--+/-+/-+/---+/---+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120000+++++--+-++----++---++++++-----+-+-+---+---+++--+----+--+---+--------------+--+----------+++++++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6285oil contaminated soilGermanyDEUEurope
67770Oil-contaminated soilGermanyDEUEurope
120000Environment, Oil contaminated soilGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4048.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_137;97_148;98_165;99_4048&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: AJ698726
  • Sequence Identity:
  • Total samples: 995
  • soil counts: 365
  • aquatic counts: 111
  • animal counts: 470
  • plant counts: 49

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
62851Risk group (German classification)
1200001Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31321
  • description: Microbacterium hydrocarbonoxydans partial 16S rRNA gene, type strain DSM 16089T
  • accession: AJ698726
  • length: 1495
  • database: nuccore
  • NCBI tax ID: 273678

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium hydrocarbonoxydans NBRC 1030741223527.3wgspatric1223527
66792Microbacterium hydrocarbonoxydans strain DSM 16089273678.5wgspatric273678
66792Microbacterium hydrocarbonoxydans NBRC 1030742731957586draftimg1223527
66792Microbacterium hydrocarbonoxydans DSM 160892634166363draftimg273678
67770Microbacterium hydrocarbonoxydans NBRC 103074GCA_001552455contigncbi1223527
67770Microbacterium hydrocarbonoxydans DSM 16089GCA_900105205contigncbi273678

GC content

  • @ref: 67770
  • GC-content: 68.6
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes69.101yes
gram-positiveyes92.41yes
anaerobicno99.6yes
aerobicyes94.26yes
halophileno88.817no
spore-formingno87.843yes
thermophileno99.556yes
glucose-utilyes85.419no
flagellatedno90.499no
glucose-fermentno91.403no

External links

@ref: 6285

culture collection no.: DSM 16089, NCIMB 14002, JCM 14340, CIP 108713, IAM 15235, NBRC 103074

straininfo link

  • @ref: 76868
  • straininfo: 131640

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
Phylogeny20081025Microbacterium ginsengiterrae sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.Kim YJ, Kim MK, Bui TPN, Kim HB, Srinivasan S, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.015784-02010Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry, beta-Glucosidase/metabolismGenetics
Phylogeny22199224Microbacterium murale sp. nov., isolated from an indoor wall.Kampfer P, Schafer J, Lodders N, Martin KInt J Syst Evol Microbiol10.1099/ijs.0.037705-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Environmental Microbiology, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6285Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16089)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16089
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
37448Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6372
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
76868Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131640.1StrainInfo: A central database for resolving microbial strain identifiers
120000Curators of the CIPCollection of Institut Pasteur (CIP 108713)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108713