Strain identifier

BacDive ID: 7395

Type strain: Yes

Species: Microbacterium aurum

Strain Designation: H-5

Strain history: CIP <- 1994, IFO <- K. Kishimoto, Takeda Chem. Ind. Ldt, Hikari Plant, Japan

NCBI tax ID(s): 36805 (species)

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General

@ref: 3326

BacDive-ID: 7395

DSM-Number: 8600

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

description: Microbacterium aurum H-5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from corn steep liquor.

NCBI tax id

  • NCBI tax id: 36805
  • Matching level: species

strain history

@refhistory
3326<- IFO <- K. Kishimoto, Takeda Chemical Ind., Ltd., H-5
67770IFO 15204 <-- K. Kishimoto H-5.
116640CIP <- 1994, IFO <- K. Kishimoto, Takeda Chem. Ind. Ldt, Hikari Plant, Japan

doi: 10.13145/bacdive7395.20250331.9.3

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 aurum
  • full scientific name: Microbacterium aurum Yokota et al. 1993

@ref: 3326

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium aurum

full scientific name: Microbacterium aurum Yokota et al. 1993

strain designation: H-5

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
116640positiverod-shapedno
125439positive97.5
125438no92.875
125438positive90.495

colony morphology

@refincubation periodmedium usedcolony color
1973110-14 daysISP 2
1973110-14 daysISP 3Zinc yellow
1973110-14 daysISP 4Zinc yellow
1973110-14 daysISP 5Zinc yellow
1973110-14 daysISP 6Zinc yellow
1973110-14 daysISP 7Zinc yellow
116640

multicellular morphology

@refforms multicellular complexmedium name
19731noISP 2
19731noISP 3
19731noISP 4
19731noISP 5
19731noISP 6
19731noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3326TRYPTICASE 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
19731ISP 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
19731ISP 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:
19731ISP 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
19731ISP 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
19731ISP 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
19731ISP 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
40912MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116640CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
116640CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
19731positiveoptimum28
3326positivegrowth30
40912positivegrowth30
55760positivegrowth22-42
67770positivegrowth30
116640positivegrowth25-41
116640nogrowth10
116640nogrowth15
116640nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
55760aerobe
116640obligate aerobe
125439obligate aerobe98.3

halophily

@refsaltgrowthtested relationconcentration
116640NaClpositivegrowth0-4 %
116640NaClnogrowth6 %
116640NaClnogrowth8 %
116640NaClnogrowth10 %

murein

  • @ref: 3326
  • murein short key: B02
  • type: B1ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly2-L-Lys

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11664016947citrate-carbon source
1166404853esculin-hydrolysis
116640606565hippurate+hydrolysis
11664017632nitrate-reduction
11664016301nitrite-reduction
116640132112sodium thiosulfate+builds gas from
11664017632nitrate-respiration
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-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
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
68371Potassium 2-ketogluconate-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
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
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-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

antibiotic resistance

  • @ref: 116640
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116640
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11664015688acetoin-
11664017234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
116640oxidase-
116640beta-galactosidase+3.2.1.23
116640alcohol dehydrogenase-1.1.1.1
116640gelatinase-
116640amylase+
116640DNase-
116640caseinase-3.4.21.50
116640catalase+1.11.1.6
116640gamma-glutamyltransferase-2.3.2.2
116640lecithinase-
116640lipase-
116640lysine decarboxylase-4.1.1.18
116640ornithine decarboxylase-4.1.1.17
116640phenylalanine ammonia-lyase-4.3.1.24
116640protease-
116640tryptophan deaminase-
116640urease-3.5.1.5
68382esterase lipase (C 8)+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19731+-+-++++-+-+++++-+-
116640-+++++-+-+-++-+--+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116640---------++++-+/---+---+--+/------++--++---+/-------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116640+++++--++++----+------++-------+-+-------------------------++-+---------+--+--+-------+----------+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3326corn steep liquorYamaguchiJapanJPNAsia
55760Corn steep liquorHiroshima Prefecture,HikariJapanJPNAsia
67770Corn steep liquor
116640Corn steep liquorYamaguchiJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Beverage
#Engineered#Food production#Fermented
#Host#Plants#Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33261Risk group (German classification)
197311Risk group (German classification)
1166401Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbacterium aurum 16S rRNA geneY172291472nuccore36805
20218Microbacterium aurum gene for 16S rRNA, partial sequenceAB0074181440nuccore36805
20218Microbacterium aurum 16S rRNA geneD213401341nuccore36805

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium aurum KACC 15219GCA_001974985completencbi36805
66792Microbacterium aurum DSM 8600GCA_016907815contigncbi36805
66792Microbacterium aurum strain DSM 860036805.16wgspatric36805
66792Microbacterium aurum strain KACC 1521936805.5completepatric36805
66792Microbacterium aurum KACC 152192773857884completeimg36805
66792Microbacterium aurum DSM 86002893677331draftimg36805

GC content

@refGC-contentmethod
332669high performance liquid chromatography (HPLC)
6777069.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.495no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.035yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.965yes
125438spore-formingspore-formingAbility to form endo- or exosporesno78.79no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.895yes
125438motile2+flagellatedAbility to perform flagellated movementno92.875no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno79.7
125439BacteriaNetmotilityAbility to perform movementno66.4
125439BacteriaNetgram_stainReaction to gram-stainingpositive97.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.3

External links

@ref: 3326

culture collection no.: DSM 8600, ATCC 51345, IFO 15204, NBRC 15204, NRRL B-24210, CCUG 43279, CCM 4522, CIP 103994, JCM 9179, IAM 15207, KACC 15219, VKM Ac-1950, VKM Ac-2076

straininfo link

  • @ref: 76844
  • straininfo: 42938

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3326Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8600)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8600
19731Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8600.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
40912Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15852
55760Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43279)https://www.ccug.se/strain?id=43279
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
68382Automatically annotated from API zym
76844Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42938.1StrainInfo: A central database for resolving microbial strain identifiers
116640Curators of the CIPCollection of Institut Pasteur (CIP 103994)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103994
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1