Strain identifier

BacDive ID: 7396

Type strain: Yes

Species: Microbacterium dextranolyticum

Strain Designation: M-73

Strain history: CIP <- 1994, IFO <- M. Kobayashi, Dept. Agr. Chem., Tohoku Univ., Japan

NCBI tax ID(s): 36806 (species)

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General

@ref: 3329

BacDive-ID: 7396

DSM-Number: 8607

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

description: Microbacterium dextranolyticum M-73 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 36806
  • Matching level: species

strain history

@refhistory
3329<- IFO <- M. Kobayashi, M-73 (Flavobacterium sp.)
67770IFO 14592 <-- M. Kobayashi M-73.
118924CIP <- 1994, IFO <- M. Kobayashi, Dept. Agr. Chem., Tohoku Univ., Japan

doi: 10.13145/bacdive7396.20230509.8.1

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

@ref: 3329

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium dextranolyticum

full scientific name: Microbacterium dextranolyticum Yokota et al. 1993

strain designation: M-73

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
118924positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19732Beige10-14 daysISP 2
19732Beige10-14 daysISP 3
19732Beige10-14 daysISP 4
1973210-14 daysISP 5
19732Beige10-14 daysISP 6
1973210-14 daysISP 7
118924

multicellular morphology

@refforms multicellular complexmedium name
19732noISP 2
19732noISP 3
19732noISP 4
19732noISP 5
19732noISP 6
19732noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3329TRYPTICASE 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
19732ISP 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
19732ISP 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:
19732ISP 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
19732ISP 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
19732ISP 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
19732ISP 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
40911MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118924CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
19732positiveoptimum28mesophilic
3329positivegrowth30mesophilic
40911positivegrowth30mesophilic
54305positivegrowth30-37mesophilic
67770positivegrowth30mesophilic
118924positivegrowth10-37
118924nogrowth41thermophilic
118924nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
54305aerobe
118924obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.945

compound production

@refcompound
3329alpha-1,2 dextranase debranching
20216Dextran alpha-1,2 debranching enzyme

halophily

@refsaltgrowthtested relationconcentration
118924NaClpositivegrowth0-4 %
118924NaClnogrowth6 %
118924NaClnogrowth8 %
118924NaClnogrowth10 %

murein

  • @ref: 3329
  • murein short key: B01
  • type: B1alpha {Gly} [L-Lys] D-Glu(Hyg)-Gly-L-Lys

observation

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

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
68371turanose-builds acid from32528
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
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
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-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
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
68371glycerol-builds acid from17754
118924citrate-carbon source16947
118924esculin+hydrolysis4853
118924hippurate+hydrolysis606565
118924nitrate-reduction17632
118924nitrite-reduction16301
118924nitrate-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: 118924
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118924
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11892415688acetoin+
11892417234glucose+

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
68382alpha-chymotrypsin-3.4.21.1
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
118924oxidase-
118924beta-galactosidase+3.2.1.23
118924alcohol dehydrogenase-1.1.1.1
118924gelatinase-
118924amylase+
118924DNase+
118924caseinase-3.4.21.50
118924catalase+1.11.1.6
118924gamma-glutamyltransferase-2.3.2.2
118924lecithinase-
118924lipase-
118924lysine decarboxylase-4.1.1.18
118924ornithine decarboxylase-4.1.1.17
118924phenylalanine ammonia-lyase-4.3.1.24
118924protease-
118924tryptophan deaminase-
118924urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    54305C16:04.516
    54305C18:00.818
    54305C14:0 ISO113.618
    54305C15:0 ANTEISO4014.711
    54305C15:0 ISO214.621
    54305C16:0 iso2815.626
    54305C17:0 anteiso20.316.722
    54305C17:0 iso116.629
    54305C18:0 ISO0.717.632
    54305C18:1 ω9c0.717.769
    54305C18:2 ω6,9c/C18:0 ANTE0.917.724
    54305Unidentified0.313.737
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19732+-----+++--+-+++---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19732-++-++++---+--+++--
118924-++-++---+++--+++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118924---+-+----+++----+---------+--+-+++--------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118924+++++--+-+++---+--+-+++--+-+---+-+-+-------------+---------++--++---------------+------------------

Isolation, sampling and environmental information

isolation

@refsample type
3329soil
67770Soil
118924Environment, Soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33291Risk group (German classification)
197321Risk group (German classification)
1189241Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbacterium dextranolyticum 16S rRNA geneY172301477ena36806
20218Microbacterium dextranolytaicum 16S rRNA geneD213411344ena36806
67770Microbacterium dextranolyticum gene for 16S rRNA, partial sequenceAB0074171437ena36806

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium dextranolyticum DSM 8607GCA_016907295contigncbi36806
66792Microbacterium dextranolyticum strain DSM 860736806.4wgspatric36806
66792Microbacterium dextranolyticum DSM 86072893534022draftimg36806

GC content

@refGC-contentmethod
332968high performance liquid chromatography (HPLC)
6777068.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes95.626no
anaerobicno99.56yes
halophileno88.716no
spore-formingno92.966no
glucose-utilyes87.031no
aerobicyes92.273yes
motileno90.241no
flagellatedno97.967no
thermophileno99.452no
glucose-fermentno90.352no

External links

@ref: 3329

culture collection no.: CCUG 38517, DSM 8607, ATCC 51344, IFO 14592, NBRC 14592, JCM 9180, CCM 4523, CIP 103993, IAM 15202, NCIMB 13387, NRRL B-23242, VKM Ac-1940, VKM Ac-2077

straininfo link

  • @ref: 76845
  • straininfo: 42937

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3329Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8607)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8607
19732Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8607.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
40911Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15851
54305Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38517)https://www.ccug.se/strain?id=38517
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
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
76845Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42937.1StrainInfo: A central database for resolving microbial strain identifiers
118924Curators of the CIPCollection of Institut Pasteur (CIP 103993)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103993