Strain identifier

BacDive ID: 23104

Type strain: Yes

Species: Microbacterium lemovicicum

Strain Designation: ViU22

Strain history: CIP <- 2014, DSMZ <- V. Chapon, CEA, Cadarache, France: strain ViU22 <- V. Chapon and L. Mondani

NCBI tax ID(s): 1072463 (species)

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General

@ref: 19377

BacDive-ID: 23104

DSM-Number: 25044

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

description: Microbacterium lemovicicum ViU22 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from natural uranium-rich soil.

NCBI tax id

  • NCBI tax id: 1072463
  • Matching level: species

strain history

@refhistory
19377<- V. Chapon, CEA/Cadarache, France; ViU22 <- V. Chapon and L. Mondani
120579CIP <- 2014, DSMZ <- V. Chapon, CEA, Cadarache, France: strain ViU22 <- V. Chapon and L. Mondani

doi: 10.13145/bacdive23104.20230509.8.1

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 lemovicicum
  • full scientific name: Microbacterium lemovicicum Mondani et al. 2013

@ref: 19377

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium lemovicicum

full scientific name: Microbacterium lemovicicum Mondani et al. 2013

strain designation: ViU22

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30956positiverod-shapedno
69480no90.838
69480positive100
120579positiverod-shapedno

pigmentation

  • @ref: 30956
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33652MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
19377TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yesName: 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 waterhttps://mediadive.dsmz.de/medium/92
120579CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
19377positivegrowth28mesophilic
30956positivegrowth15-37
30956positiveoptimum30mesophilic
33652positivegrowth30mesophilic
62796positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 62796
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30956no
69481no100
69480no99.962

halophily

@refsaltgrowthtested relationconcentration
30956NaClpositivegrowth0-4.5 %
30956NaClpositiveoptimum0.5 %

murein

  • @ref: 19377
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 30956
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3095622599arabinose+carbon source
3095628757fructose+carbon source
3095628260galactose+carbon source
3095617234glucose+carbon source
3095617754glycerol+carbon source
3095617306maltose+carbon source
3095629864mannitol+carbon source
3095637684mannose+carbon source
3095616634raffinose+carbon source
3095626546rhamnose+carbon source
3095633942ribose+carbon source
3095617992sucrose+carbon source
3095627082trehalose+carbon source
3095618222xylose+carbon source

enzymes

@refvalueactivityec
30956alkaline phosphatase+3.1.3.1
30956catalase+1.11.1.6
30956gelatinase+
30956pyrazinamidase+3.5.1.B15
30956urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
19377natural uranium-rich soilnear LimogesFranceFRAEurope
62796Soil,natural uranium-richLimogesFranceFRAEurope2007-11-26
120579Environment, Natural uranium-rich soilLimogesFranceFRAEurope

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
193771Risk group (German classification)
1205791Risk group (French classification)

Sequence information

16S sequences

  • @ref: 19377
  • description: Microbacterium lemovicicum strain ViU22 16S ribosomal RNA gene, partial sequence
  • accession: JN243353
  • length: 1400
  • database: ena
  • NCBI tax ID: 1072463

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium lemovicicum Viu22GCA_003991875completencbi1072463
66792Microbacterium lemovicicum Viu222847289766completeimg1072463

GC content

@refGC-contentmethod
1937771.0high performance liquid chromatography (HPLC)
3095671

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.711yes
flagellatedno98.001yes
gram-positiveyes94.621yes
anaerobicno99.631yes
aerobicyes93.807yes
halophileno91.816no
spore-formingno94.984yes
thermophileno99.174no
glucose-utilyes86.343no
glucose-fermentno93.281no

External links

@ref: 19377

culture collection no.: DSM 25044, ATCC BAA 2396, CCUG 62198, CIP 110791, NBRC 110788

straininfo link

  • @ref: 87341
  • straininfo: 398141

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23264499Microbacterium lemovicicum sp. nov., a bacterium isolated from a natural uranium-rich soil.Mondani L, Piette L, Christen R, Bachar D, Berthomieu C, Chapon VInt J Syst Evol Microbiol10.1099/ijs.0.048454-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, France, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, *Uranium, Vitamin K 2/analysisGenetics
Phylogeny27260265Microbacterium gilvum sp. nov., isolated from civet faeces.Chen X, Li QY, Li GD, Xu FJ, Jiang Y, Han L, Jiang CL, Huang XSAntonie Van Leeuwenhoek10.1007/s10482-016-0718-12016Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Animals, Cell Wall/chemistry, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Feces/*microbiology, Malaysia, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Vitamin K 2/metabolism, Viverridae/*microbiologyMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19377Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25044)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25044
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
30956Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2728628776041
33652Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30603
62796Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 62198)https://www.ccug.se/strain?id=62198
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
87341Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398141.1StrainInfo: A central database for resolving microbial strain identifiers
120579Curators of the CIPCollection of Institut Pasteur (CIP 110791)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110791