Strain identifier

BacDive ID: 7407

Type strain: Yes

Species: Microbacterium ketosireducens

Strain Designation: KN-2479

Strain history: CIP <- 1998, IFO <- K. Imai: strain KN-2479

NCBI tax ID(s): 92835 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4755

BacDive-ID: 7407

DSM-Number: 12510

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

description: Microbacterium ketosireducens KN-2479 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 92835
  • Matching level: species

strain history

@refhistory
4755<- IFO <- K. Imai, KN-2479 (Aureobacterium ketoreductum)
67770NBRC 14548 <-- IFO 14548 <-- K. Imai KN-2479.
120409CIP <- 1998, IFO <- K. Imai: strain KN-2479

doi: 10.13145/bacdive7407.20230509.8.1

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 ketosireducens
  • full scientific name: Microbacterium ketosireducens Takeuchi and Hatano 1998

@ref: 4755

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium ketosireducens

full scientific name: Microbacterium ketosireducens Takeuchi and Hatano 1998

strain designation: KN-2479

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120409positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18367Zinc yellow (1018)10-14 daysISP 2
18367Zinc yellow (1018)10-14 daysISP 3
18367Zinc yellow (1018)10-14 daysISP 4
18367Zinc yellow (1018)10-14 daysISP 5
18367Zinc yellow (1018)10-14 daysISP 6
18367Zinc yellow (1018)10-14 daysISP 7
120409

multicellular morphology

@refforms multicellular complexmedium name
18367noISP 2
18367noISP 3
18367noISP 4
18367noISP 5
18367noISP 6
18367noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4755TRYPTICASE 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
18367ISP 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
18367ISP 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:
18367ISP 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
18367ISP 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
18367ISP 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
18367ISP 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
38577MEDIUM 119 - for Azotobacter vinelandiiyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (15.000 g);Yeast extract (2.000 g);Peptone (5.000 g);Tryptone (5.000 g)
120409CIP Medium 1yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=1

culture temp

@refgrowthtypetemperaturerange
18367positiveoptimum28mesophilic
4755positivegrowth30mesophilic
38577positivegrowth30mesophilic
67770positivegrowth30mesophilic
120409positivegrowth15-30
120409nogrowth10psychrophilic
120409nogrowth37mesophilic
120409nogrowth41thermophilic
120409nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120409
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.935

halophily

@refsaltgrowthtested relationconcentration
120409NaClpositivegrowth0-4 %
120409NaClnogrowth8 %
120409NaClnogrowth10 %

murein

  • @ref: 4755
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: 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
68371xylitol-builds acid from17151
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371lactose-builds acid from17716
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose-builds acid from16988
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
120409citrate-carbon source16947
120409esculin+hydrolysis4853
120409hippurate-hydrolysis606565
120409nitrate+reduction17632
120409nitrite-reduction16301
120409sodium thiosulfate-builds gas from132112
120409nitrate-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: 120409
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120409
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12040915688acetoin-
12040917234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
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
68382alpha-chymotrypsin+3.4.21.1
68382leucine arylamidase+3.4.11.1
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
120409oxidase+
120409beta-galactosidase+3.2.1.23
120409alcohol dehydrogenase-1.1.1.1
120409gelatinase+/-
120409amylase+
120409DNase+
120409caseinase+3.4.21.50
120409catalase+1.11.1.6
120409tween esterase-
120409gamma-glutamyltransferase-2.3.2.2
120409lecithinase-
120409lipase-
120409lysine decarboxylase-4.1.1.18
120409ornithine decarboxylase-4.1.1.17
120409phenylalanine ammonia-lyase-4.3.1.24
120409protease+
120409tryptophan deaminase-
120409urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18367--+--++-+++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18367-++-+--++--++-++---
120409-++++++-+++++-+++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120409+/---+/--+/---+/-+/-+/-+/-+/--+/---+/-----+/-+/-+/-+/-+/-+/--+/-+/-+/---+/-+/-+/--+/-+/----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120409+++++-+++++++++++++-++-+-------+-+++-----------------+--++--+--------------+----------+-+++++++-++-

Isolation, sampling and environmental information

isolation

@refsample type
4755soil
67770Soil
120409Environment, Soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
47551Risk group (German classification)
1204091Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4755
  • description: Microbacterium ketosireducens gene for 16S rRNA, partial sequence
  • accession: AB004724
  • length: 1410
  • database: ena
  • NCBI tax ID: 92835

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium ketosireducens strain DSM 1251092835.4wgspatric92835
66792Microbacterium ketosireducens DSM 125102711768172draftimg92835
67770Microbacterium ketosireducens DSM 12510GCA_000956575contigncbi92835

GC content

  • @ref: 4755
  • GC-content: 69.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno91.015no
flagellatedno97.353no
gram-positiveyes92.424no
anaerobicno99.721no
halophileno88.111no
spore-formingno91.326no
glucose-utilyes88.542no
aerobicyes96.014no
thermophileno99.453yes
glucose-fermentno88.198yes

External links

@ref: 4755

culture collection no.: DSM 12510, IFO 14548, NBRC 14548, NRRL B-24221, JCM 12078, CIP 105732, IAM 15201, VKM Ac-2082

straininfo link

  • @ref: 76856
  • straininfo: 49311

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9734054Proposal of six new species in the genus Microbacterium and transfer of Flavobacterium marinotypicum ZoBell and Upham to the genus Microbacterium as Microbacterium maritypicum comb. nov.Takeuchi M, Hatano KInt J Syst Bacteriol10.1099/00207713-48-3-9731998Actinomycetales/chemistry/*classification/genetics, DNA, Bacterial/analysis, Flavobacterium/*classification, Nucleic Acid Hybridization
Phylogeny36509934Description of Microbacterium neungamense sp. nov. isolated from a hot spring.Ganbat D, Jeong GE, Oh D, Lee DW, Lee YJ, Kim SB, Cha IT, Chi WJ, Park SK, Lee JS, Lee SJArch Microbiol10.1007/s00203-022-03343-52022RNA, Ribosomal, 16S/genetics, *Microbacterium/genetics, Phylogeny, Bacterial Typing Techniques, DNA, Bacterial/genetics, Sequence Analysis, DNA, *Fatty Acids/analysis, Nucleic Acid Hybridization, Phospholipids/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4755Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12510)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12510
18367Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12510.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
38577Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17784
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
76856Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49311.1StrainInfo: A central database for resolving microbial strain identifiers
120409Curators of the CIPCollection of Institut Pasteur (CIP 105732)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105732