Strain identifier

BacDive ID: 7380

Type strain: Yes

Species: Microbacterium liquefaciens

Strain Designation: Mbm 15

Strain history: CIP <- 1986, DSM <- NCIB <- K. Robinson: strain Mbm15, Microbacterium liquefaciens

NCBI tax ID(s): 33918 (species)

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

@ref: 8984

BacDive-ID: 7380

DSM-Number: 20638

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

description: Microbacterium liquefaciens Mbm 15 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from milk.

NCBI tax id

  • NCBI tax id: 33918
  • Matching level: species

strain history

@refhistory
8984<- NCIB <- K. Robinson, Mbm 15 (Microbacterium liquefaciens)
67770DSM 20638 <-- NCIB 11509 <-- K. Robinson Mbm 15.
120624CIP <- 1986, DSM <- NCIB <- K. Robinson: strain Mbm15, Microbacterium liquefaciens

doi: 10.13145/bacdive7380.20230509.8.1

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 liquefaciens
  • full scientific name: Microbacterium liquefaciens (Collins et al. 1983 ex Orla-Jensen 1919) Takeuchi and Hatano 1998
  • synonyms

    • @ref: 20215
    • synonym: Aureobacterium liquefaciens

@ref: 8984

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium liquefaciens

full scientific name: Microbacterium liquefaciens (Collins et al. 1983) Takeuchi and Hatano 1998

strain designation: Mbm 15

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120624positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18766Golden yellow10-14 daysISP 2
18766Sulfur white10-14 daysISP 3
18766Light ivory10-14 daysISP 4
1876610-14 daysISP 5
18766Zinc yellow10-14 daysISP 6
1876610-14 daysISP 7
120624

multicellular morphology

@refforms multicellular complexmedium name
18766noISP 2
18766noISP 3
18766noISP 4
18766noISP 5
18766noISP 6
18766noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8984CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
18766ISP 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
18766ISP 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:
18766ISP 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
18766ISP 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
18766ISP 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
18766ISP 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
40416MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120624CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120624CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18766positiveoptimum28mesophilic
8984positivegrowth30mesophilic
40416positivegrowth30mesophilic
51372positivegrowth37mesophilic
67770positivegrowth30mesophilic
120624positivegrowth10-37
120624nogrowth41thermophilic
120624nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
51372aerobe
120624obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.983

halophily

@refsaltgrowthtested relationconcentration
18766NaClpositivemaximum5 %
120624NaClpositivegrowth0-4 %
120624NaClnogrowth6 %
120624NaClnogrowth8 %
120624NaClnogrowth10 %

murein

  • @ref: 8984
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1876662968cellulose-
1876616634raffinose-
1876626546rhamnose-
1876628757fructose+
1876629864mannitol-
1876617268myo-inositol-
1876618222xylose-
1876617992sucrose-
1876622599arabinose-
1876617234glucose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12062416947citrate-carbon source
1206244853esculin+hydrolysis
120624606565hippurate+hydrolysis
12062417632nitrate-reduction
12062416301nitrite-reduction
12062417632nitrate-respiration
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 120624
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12062435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12062415688acetoin-
12062417234glucose-

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
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
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
120624oxidase-
120624beta-galactosidase+3.2.1.23
120624alcohol dehydrogenase-1.1.1.1
120624gelatinase+
120624amylase-
120624DNase+
120624caseinase+3.4.21.50
120624catalase+1.11.1.6
120624tween esterase-
120624gamma-glutamyltransferase-2.3.2.2
120624lecithinase-
120624lipase-
120624lysine decarboxylase-4.1.1.18
120624ornithine decarboxylase-4.1.1.17
120624phenylalanine ammonia-lyase-4.3.1.24
120624protease+
120624tryptophan deaminase-
120624urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18766+++-+++--+-++-++-+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18766+++-+++----++-++-+-
120624+---+++--++++-++-+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18766+----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120624+++-+----+++-------------------+-------+-------------------+---------+-----+-------------++--------

Isolation, sampling and environmental information

isolation

@refsample type
8984milk
51372Milk
67770Milk
120624Food, Milk

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Milk
#Engineered#Food production#Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_191.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_137;97_148;98_165;99_191&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: X77444
  • Sequence Identity:
  • Total samples: 42253
  • soil counts: 10113
  • aquatic counts: 9581
  • animal counts: 16954
  • plant counts: 5605

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
89841Risk group (German classification)
187661Risk group (German classification)
1206241Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8984
  • description: A.liquefaciens (DSM 20638) 16S rRNA gene
  • accession: X77444
  • length: 1474
  • database: ena
  • NCBI tax ID: 33918

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium liquefaciens JCM 3879GCA_014648755scaffoldncbi33918
66792Microbacterium liquefaciens strain JCM 387933918.5wgspatric33918
66792Microbacterium liquefaciens strain NBRC 1503733918.3wgspatric33918
67770Microbacterium liquefaciens NBRC 15037GCA_006539765contigncbi33918

GC content

@refGC-contentmethod
898468.6
6777072.5thermal denaturation, midpoint method (Tm)
6777068.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.369no
gram-positiveyes92.434no
anaerobicno99.396yes
aerobicyes94.734yes
halophileno83.442no
spore-formingno91.648no
thermophileno99.581yes
glucose-utilyes79.766yes
motileno82.957no
glucose-fermentno92.198no

External links

@ref: 8984

culture collection no.: DSM 20638, ATCC 43647, NCIB 11509, NRRL B-24237, CCUG 33091, JCM 3879, BCRC 14859, CGMCC 1.1934, CIP 102402, HAMBI 1895, IAM 15185, IFO 15037, IMSNU 21275, KCTC 9227, LMG 16342, NBRC 15037, NCIMB 11509, VKM Ac-1018

straininfo link

  • @ref: 76829
  • straininfo: 45479

Reference

@idauthorscataloguedoi/urltitle
8984Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20638)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20638
18766Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20638.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
40416Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14084
51372Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33091)https://www.ccug.se/strain?id=33091
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
68379Automatically annotated from API Coryne
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
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
76829Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45479.1StrainInfo: A central database for resolving microbial strain identifiers
120624Curators of the CIPCollection of Institut Pasteur (CIP 102402)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102402