Strain identifier

BacDive ID: 7373

Type strain: Yes

Species: Microbacterium lacticum

Strain Designation: 5

Strain history: CIP <- 1969, F. Gasser, Inst. Pasteur, Paris, France <- ATCC <- C.S. Pederson: strain 5 <- S. Orla-Jensen

NCBI tax ID(s): 33885 (species)

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General

@ref: 8806

BacDive-ID: 7373

DSM-Number: 20427

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

description: Microbacterium lacticum 5 is an obligate aerobe, Gram-positive, rod-shaped bacterium of the family Microbacteriaceae.

NCBI tax id

  • NCBI tax id: 33885
  • Matching level: species

strain history

@refhistory
8806<- H. Seiler <- ATCC <- C.S. Pederson <- J. Orla-Jensen
67770IAM 1640 <-- Shionogi & Co., Ltd. <-- ATCC 8180 <-- C. S. Pederson 5 <-- S. Orla-Jensen.
120523CIP <- 1969, F. Gasser, Inst. Pasteur, Paris, France <- ATCC <- C.S. Pederson: strain 5 <- S. Orla-Jensen

doi: 10.13145/bacdive7373.20240916.9.1

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 lacticum
  • full scientific name: Microbacterium lacticum Orla-Jensen 1919 (Approved Lists 1980)

@ref: 8806

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium lacticum

full scientific name: Microbacterium lacticum Orla-Jensen 1919

strain designation: 5

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
120523positiverod-shapedno
69480no91.875
69480positive93.477

colony morphology

@refcolony colorincubation periodmedium used
18441Ivory (1014)10-14 daysISP 2
18441Sulfur white10-14 daysISP 3
18441Sulfur white10-14 daysISP 4
18441Lemon yellow (1012)10-14 daysISP 5
18441Lemon yellow (1012)10-14 daysISP 6
18441Beige (1001)10-14 daysISP 7
120523

multicellular morphology

@refforms multicellular complexmedium name
18441noISP 2
18441noISP 3
18441noISP 4
18441noISP 5
18441noISP 6
18441noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8806CORYNEBACTERIUM 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
18441ISP 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
18441ISP 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
18441ISP 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
18441ISP 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
18441ISP 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
18441ISP 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:
37339MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120523CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
18441positiveoptimum28
8806positivegrowth30
37339positivegrowth30
67770positivegrowth28
120523positivegrowth25-37
120523nogrowth10

Physiology and metabolism

oxygen tolerance

  • @ref: 120523
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
18441NaClpositivemaximum7.5 %
120523NaClpositivegrowth0-2 %
120523NaClnogrowth4 %
120523NaClnogrowth6 %
120523NaClnogrowth8 %
120523NaClnogrowth10 %

murein

  • @ref: 8806
  • murein short key: B01
  • type: B1alpha {Gly} [L-Lys] D-Glu(Hyg)-Gly-L-Lys

observation

  • @ref: 67770
  • observation: quinones: MK-11 (MK-10, MK-12)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1844117234glucose+
1844122599arabinose+
1844117992sucrose+
1844118222xylose+
1844117268myo-inositol+
1844129864mannitol-
1844128757fructose-
1844126546rhamnose+
1844116634raffinose+
1844162968cellulose-
68371Potassium 5-ketogluconate-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
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-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
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
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12052316947citrate-carbon source
120523606565hippurate+hydrolysis
12052317632nitrate+reduction
12052316301nitrite-reduction
12052317632nitrate-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: 120523
  • 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
12052335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12052315688acetoin-
12052317234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
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
120523oxidase-
120523beta-galactosidase+3.2.1.23
120523alcohol dehydrogenase-1.1.1.1
120523gelatinase+/-
120523amylase+
120523DNase+
120523caseinase+3.4.21.50
120523catalase+1.11.1.6
120523tween esterase-
120523gamma-glutamyltransferase-2.3.2.2
120523lecithinase-
120523lipase-
120523lysine decarboxylase-4.1.1.18
120523ornithine decarboxylase-4.1.1.17
120523phenylalanine ammonia-lyase+4.3.1.24
120523protease-
120523tryptophan deaminase-
120523urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18441-++-++++-++++------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18441-++-++++-++++------
120523-++-+++--+++++++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18441+----------

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8806----------++++----+---+-++++++------++------------
120523+/---------++++----++--++/-+/-+/-++++------++--+------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120523+++-+----+++++-+-++------------+--+--------------+---+----+++-----------+--+---++-----+-+-------+--

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88061Risk group (German classification)
184411German classification
1205231Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8806M.lacticum (DSM20427) 16S rRNA geneX774411474nuccore33885
67770Microbacterium lacticum gene for 16S rRNA, partial sequenceAB0074151456nuccore33885

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium lacticum JCM 1379GCA_014646835scaffoldncbi33885
66792Microbacterium lacticum strain DSM 2042733885.18wgspatric33885
66792Microbacterium lacticum strain JCM 137933885.20wgspatric33885
66792Microbacterium lacticum strain NBRC 1413533885.17wgspatric33885
66792Microbacterium lacticum DSM 204272818991429draftimg33885
67770Microbacterium lacticum NBRC 14135GCA_006539445contigncbi33885
67770Microbacterium lacticum DSM 20427GCA_006716815contigncbi33885

GC content

@refGC-contentmethod
880669.3
6777069.3thermal denaturation, midpoint method (Tm)
6777074.9thermal denaturation, midpoint method (Tm)
6777070thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes93.477no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.385no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes80.212no
69480spore-formingspore-formingAbility to form endo- or exosporesno80.092no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.895yes
69480flagellatedmotile2+Ability to perform flagellated movementno91.875no

External links

@ref: 8806

culture collection no.: DSM 20427, ATCC 8180, NCDO 747, NCIB 8540, NRRL B-24233, JCM 1379, BCRC 11036, CCM 1584, CCUG 28998, CCUG 50753, CGMCC 1.1911, CIP 69.3, HAMBI 2287, IAM 1640, IFO 14135, IMET 10712, IMSNU 21284, KCTC 1305, KCTC 1625, KCTC 9230, LMG 21671, LMG 4047, NBRC 14135, NCIMB 8540, VKM Ac-1145, VTT E-072707

straininfo link

  • @ref: 76822
  • straininfo: 89333

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16449451Microbacterium koreense sp. nov., from sea water in the South Sea of Korea.Lee JS, Lee KC, Park YHInt J Syst Evol Microbiol10.1099/ijs.0.63854-02006Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny34807813Microbacterium paulum sp. nov., isolated from microfiltered milk.Bellassi P, Fontana A, Callegari ML, Cappa F, Morelli LInt J Syst Evol Microbiol10.1099/ijsem.0.0051192021Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Microbacterium/classification/isolation & purification, Milk/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8806Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20427)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20427
18441Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20427.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
37339Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10410
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/
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
76822Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID89333.1StrainInfo: A central database for resolving microbial strain identifiers
120523Curators of the CIPCollection of Institut Pasteur (CIP 69.3)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2069.3