Strain identifier

BacDive ID: 7397

Type strain: Yes

Species: Microbacterium keratanolyticum

Strain history: CIP <- 1993, IFO <- 1972, S. Suzuki, Fac. Sci., Nagoya Univ., Japan, Pseudomonas sp.

NCBI tax ID(s): 67574 (species)

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General

@ref: 3328

BacDive-ID: 7397

DSM-Number: 8606

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

description: Microbacterium keratanolyticum DSM 8606 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 67574
  • Matching level: species

strain history

@refhistory
3328<- IFO <- S. Suzuki (Pseudomonas sp.)
67770IFO 13309 <-- S. Suzuki (Pseudomonas sp.).
120403CIP <- 1993, IFO <- 1972, S. Suzuki, Fac. Sci., Nagoya Univ., Japan, Pseudomonas sp.

doi: 10.13145/bacdive7397.20230509.8.1

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 keratanolyticum
  • full scientific name: Microbacterium keratanolyticum (Yokota et al. 1993) Takeuchi and Hatano 1998

  • synonyms

    • @ref: 20215
    • synonym: Aureobacterium keratanolyticum

@ref: 3328

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium keratanolyticum

full scientific name: Microbacterium keratanolyticum (Yokota et al. 1993) Takeuchi and Hatano 1998

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120403positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
20206Lemon yellow (1012)10-14 daysISP 2
20206Lemon yellow (1012)10-14 daysISP 3
20206Lemon yellow (1012)10-14 daysISP 4
20206Lemon yellow (1012)10-14 daysISP 5
20206Lemon yellow (1012)10-14 daysISP 6
20206Lemon yellow (1012)10-14 daysISP 7
1204031

multicellular morphology

@refforms multicellular complexmedium name
20206noISP 2
20206noISP 3
20206noISP 4
20206noISP 5
20206noISP 6
20206noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3328TRYPTICASE 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
20206ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20206ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20206ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20206ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20206ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20206ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
40801MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120403CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120403CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20206positiveoptimum28mesophilic
3328positivegrowth30mesophilic
40801positivegrowth30mesophilic
67770positivegrowth30mesophilic
120403positivegrowth15-37
120403nogrowth10psychrophilic
120403nogrowth41thermophilic
120403nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120403
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.989

compound production

  • @ref: 3328
  • compound: keratan sulfate-endogalactosidase

halophily

@refsaltgrowthtested relationconcentration
120403NaClpositivegrowth0-4 %
120403NaClnogrowth6 %
120403NaClnogrowth8 %
120403NaClnogrowth10 %

murein

  • @ref: 3328
  • murein short key: B09
  • type: B2alpha {Gly} [L-Orn] D-Glu-D-Orn

observation

@refobservation
67770Production of Keratan sulfate-degrading enzymes
67770quinones: MK-12, MK-13

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
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
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
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-fructose-builds acid from15824
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
68368nitrate-reduction17632
68368melibiose-fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-glucose-fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
120403citrate-carbon source16947
120403esculin+hydrolysis4853
120403hippurate-hydrolysis606565
120403nitrate-reduction17632
120403nitrite-reduction16301
120403tributyrin-hydrolysis35020
120403sodium thiosulfate+builds gas from132112
120403nitrate-respiration17632
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379urea+hydrolysis16199
68379gelatin+hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

antibiotic resistance

  • @ref: 120403
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12040335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12040315688acetoin-
12040317234glucose-

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
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
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
120403oxidase-
120403beta-galactosidase+3.2.1.23
120403alcohol dehydrogenase-1.1.1.1
120403gelatinase+/-
120403amylase-
120403DNase+
120403caseinase+3.4.21.50
120403catalase+1.11.1.6
120403gamma-glutamyltransferase-2.3.2.2
120403lecithinase-
120403lipase-
120403lysine decarboxylase-4.1.1.18
120403ornithine decarboxylase-4.1.1.17
120403phenylalanine ammonia-lyase-4.3.1.24
120403protease-
120403tryptophan deaminase-
120403urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20206---+--+--++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseControlNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20206+++-++-+++
120403+++-++-+-+-+-+-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUINOSorRHASACMELNO2N2
120403-------------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120403+/---------+/-+/--+/---------+/---+/--+/-+/---+/-+/--------+/----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120403+-+++--+-++----+--+------------+---+--------------------+--++-----------------+-------+----------+-

Isolation, sampling and environmental information

isolation

@refsample type
3328soil
67770Soil
120403Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33281Risk group (German classification)
202061German classification
1204031Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Aureobacterium keratanolyticum 16S rRNA geneY147861408ena67574
20218Microbacterium keratanolyticum 16S rRNA geneY172331461ena67574
20218Microbacterium keratanolyticum gene for 16S rRNA, partial sequenceAB0047171520ena67574

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium keratanolyticum DSM 8606GCA_016907255contigncbi67574
66792Microbacterium keratanolyticum strain DSM 860667574.6wgspatric67574
66792Microbacterium keratanolyticum DSM 86062893531040draftimg67574

GC content

  • @ref: 3328
  • GC-content: 66.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes90.588no
anaerobicno99.281no
halophileno88.045no
spore-formingno84.821no
glucose-utilyes80.307no
thermophileno99.624yes
flagellatedno88.951no
motileyes70.106no
aerobicyes94.833no
glucose-fermentno90.793yes

External links

@ref: 3328

culture collection no.: DSM 8606, ATCC 35057, CCM 4375, CIP 103815, IFO 13309, NBRC 13309, NRRL B-24211, CCUG 43280, JCM 9173, BCRC 11905, IAM 13165, KCTC 9918, LMG 16470, NCIMB 12401, VKM Ac-1958

straininfo link

  • @ref: 76846
  • straininfo: 8201

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8347513Proposal of six new species in the genus Aureobacterium and transfer of Flavobacterium esteraromaticum Omelianski to the genus Aureobacterium as Aureobacterium esteraromaticum comb. nov.Yokota A, Takeuchi M, Sakane T, Weiss NInt J Syst Bacteriol10.1099/00207713-43-3-5551993Bacterial Typing Techniques, Base Composition, Carbohydrate Sequence, DNA, Bacterial/chemistry, Fatty Acids/analysis, Flavobacterium/chemistry/*classification/cytology, Gram-Positive Asporogenous Rods/chemistry/*classification/cytology, Molecular Sequence Data, Mycolic Acids/analysis, Peptidoglycan/chemistry, Vitamin K/analysisGenetics
Phylogeny19060085Microbacterium profundi sp. nov., isolated from deep-sea sediment of polymetallic nodule environments.Wu YH, Wu M, Wang CS, Wang XG, Yang JY, Oren A, Xu XWInt J Syst Evol Microbiol10.1099/ijs.0.2008/000455-02008Actinomycetales/*classification/genetics/*physiology/ultrastructure, *Environment, Geologic Sediments/*microbiology, *Metals, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3328Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8606)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8606
20206Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8606.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
40801Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15654
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
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
76846Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8201.1StrainInfo: A central database for resolving microbial strain identifiers
120403Curators of the CIPCollection of Institut Pasteur (CIP 103815)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103815