Strain identifier

BacDive ID: 7424

Type strain: Yes

Species: Microbacterium ulmi

Strain Designation: XIL02

Strain history: CIP <- 2004, CECT <- E. Velaquez, Salamance, Spain: strain XIL02

NCBI tax ID(s): 179095 (species)

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General

@ref: 6651

BacDive-ID: 7424

DSM-Number: 16931

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

description: Microbacterium ulmi XIL02 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from decayed wood .

NCBI tax id

  • NCBI tax id: 179095
  • Matching level: species

strain history

@refhistory
6651<- M. Trujillo <- R. Riva; XIL 02
67770CECT 5976 <-- E. Velázquez XIL02.
123715CIP <- 2004, CECT <- E. Velaquez, Salamance, Spain: strain XIL02

doi: 10.13145/bacdive7424.20230509.8.1

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 ulmi
  • full scientific name: Microbacterium ulmi Rivas et al. 2004

@ref: 6651

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium ulmi

full scientific name: Microbacterium ulmi Rivas et al. 2004

strain designation: XIL02

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29943positiverod-shapedno
69480no91.879
69480positive100
123715positiverod-shapedno

colony morphology

  • @ref: 123715

pigmentation

  • @ref: 29943
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6651XED-AGAR (DSMZ Medium 1026)yeshttps://mediadive.dsmz.de/medium/1026Name: XED-AGAR (DSMZ Medium 1026) Composition: Agar 18.0 g/l Xylan 7.0 g/l Yeast extract 3.0 g/l Distilled water
6651R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
38270MEDIUM 594 - for Microbacterium ulmiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (4.000 g);Xylan (7.000 g)
123715CIP Medium 594yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=594

culture temp

@refgrowthtypetemperaturerange
6651positivegrowth28mesophilic
29943positivegrowth15-37
38270positivegrowth25mesophilic
67770positivegrowth28mesophilic
123715positivegrowth15-37
123715nogrowth10psychrophilic
123715nogrowth41thermophilic
123715nogrowth45thermophilic

culture pH

  • @ref: 29943
  • ability: positive
  • type: growth
  • pH: 05-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29943aerobe
123715obligate aerobe

spore formation

@refspore formationconfidence
29943no
69481no100
69480no99.966

halophily

@refsaltgrowthtested relationconcentration
123715NaClpositivegrowth0-2 %
123715NaClnogrowth4 %
123715NaClnogrowth6 %
123715NaClnogrowth8 %
123715NaClnogrowth10 %

murein

  • @ref: 6651
  • murein short key: B02
  • type: B1ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly2-L-Lys

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-13

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2994322599arabinose+carbon source
2994317057cellobiose+carbon source
2994328757fructose+carbon source
2994317306maltose+carbon source
2994329864mannitol+carbon source
2994337684mannose+carbon source
2994318401phenylacetate+carbon source
299434853esculin+hydrolysis
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
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-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
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-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
6837117754glycerol-builds acid from
12371516947citrate-carbon source
1237154853esculin+hydrolysis
123715606565hippurate-hydrolysis
12371517632nitrate-reduction
12371516301nitrite-reduction
12371517632nitrate-respiration

antibiotic resistance

  • @ref: 123715
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123715
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12371515688acetoin-
12371517234glucose+

enzymes

@refvalueactivityec
29943gelatinase+
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
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
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)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
123715oxidase+
123715beta-galactosidase+3.2.1.23
123715alcohol dehydrogenase-1.1.1.1
123715gelatinase-
123715amylase+
123715DNase+
123715caseinase-3.4.21.50
123715catalase+1.11.1.6
123715tween esterase-
123715gamma-glutamyltransferase-2.3.2.2
123715lecithinase-
123715lipase-
123715lysine decarboxylase-4.1.1.18
123715ornithine decarboxylase-4.1.1.17
123715phenylalanine ammonia-lyase-4.3.1.24
123715tryptophan deaminase-
123715urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123715-++--++-+-++-+-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123715----------+++----+/---------++/----+---+/-----------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123715++-++----++----++----+-+---------+--------------------------+--------------+----------+-++---------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
6651decayed wood (Ulmus nigra)Ulmus nigraSalamancaSpainESPEurope
67770Sawdust from a decade tree Ulmus nigraUlmus nigra
123715Sawdust of Ulmus nigraSalamancaSpainESPEurope2001

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Decomposing plant
#Host#Plants#Tree
#Host Body Product#Plant#Timber

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66511Risk group (German classification)
1237151Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6651
  • description: Microbacterium ulmi strain XIL02 16S ribosomal RNA gene, complete sequence
  • accession: AY062021
  • length: 1517
  • database: ena
  • NCBI tax ID: 179095

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium ulmi strain CECT 5976179095.3wgspatric179095
66792Microbacterium ulmi strain JCM 14282179095.4wgspatric179095
66792Microbacterium ulmi CECT 59762824374264draftimg179095
67770Microbacterium ulmi CECT 5976GCA_011759705scaffoldncbi179095
67770Microbacterium ulmi JCM 14282GCA_013004565contigncbi179095

GC content

@refGC-contentmethod
665169
6777069thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.379yes
gram-positiveyes91.695yes
anaerobicno99.455yes
aerobicyes89.226no
halophileno91.08no
spore-formingno90.513yes
glucose-utilyes86.938no
flagellatedno97.978yes
thermophileno96.149yes
glucose-fermentno89.827no

External links

@ref: 6651

culture collection no.: DSM 16931, CECT 5976, LMG 20991, JCM 14282, CIP 108339, IAM 15295, NCAIM B.02300, NCIMB 14309

straininfo link

  • @ref: 76873
  • straininfo: 85132

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023968Microbacterium ulmi sp. nov., a xylanolytic, phosphate-solubilizing bacterium isolated from sawdust of Ulmus nigra.Rivas R, Trujillo ME, Sanchez M, Mateos PF, Martinez-Molina E, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.02724-02004Actinomycetales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, *Dust, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Ulmus/*microbiologyGenetics
Phylogeny16514023Microbacterium paludicola sp. nov., a novel xylanolytic bacterium isolated from swamp forest.Park HY, Kim KK, Jin L, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63945-02006Actinomycetales/*classification/genetics/isolation & purification/physiology, DNA, Ribosomal/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Trees, Xylans/*metabolismTranscriptome
Phylogeny18984689Microbacterium kribbense sp. nov., isolated from soil.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.2008/001222-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny22058326Microbacterium immunditiarum sp. nov., an actinobacterium isolated from landfill surface soil, and emended description of the genus Microbacterium.Krishnamurthi S, Bhattacharya A, Schumann P, Dastager SG, Tang SK, Li WJ, Chakrabarti TInt J Syst Evol Microbiol10.1099/ijs.0.033373-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Refuse Disposal, Sequence Analysis, DNA, Soil/analysis, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6651Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16931)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16931
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
29943Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2631228776041
38270Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5950
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
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
76873Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID85132.1StrainInfo: A central database for resolving microbial strain identifiers
123715Curators of the CIPCollection of Institut Pasteur (CIP 108339)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108339