Strain identifier

BacDive ID: 13777

Type strain: Yes

Species: Rubellimicrobium mesophilum

Strain history: <- CJ Kim, KRIBB

NCBI tax ID(s): 442562 (strain), 1123067 (species)

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General

@ref: 8030

BacDive-ID: 13777

DSM-Number: 19309

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

description: Rubellimicrobium mesophilum DSM 19309 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment soil sample.

NCBI tax id

NCBI tax idMatching level
442562strain
1123067species

strain history

@refhistory
8030<- C.-J. Kim, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; MSL 20 <- Y. J. Ju
67771<- CJ Kim, KRIBB

doi: 10.13145/bacdive13777.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Rubellimicrobium
  • species: Rubellimicrobium mesophilum
  • full scientific name: Rubellimicrobium mesophilum Dastager et al. 2008

@ref: 8030

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Rubellimicrobium

species: Rubellimicrobium mesophilum

full scientific name: Rubellimicrobium mesophilum Dastager et al. 2008 emend. Riedel et al. 2014

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32502negative1.6-3.4 µm0.4-0.7 µmrod-shapedyes
67771negative
69480negative99.993

colony morphology

  • @ref: 8030
  • incubation period: 3-7 days

pigmentation

  • @ref: 32502
  • production: yes

multimedia

  • @ref: 8030
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_19309.jpg
  • caption: Medium 830 (1:5) 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 8030
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
8030positivegrowth28mesophilic
32502positivegrowth20-37
32502positiveoptimum28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32502positivegrowth07-11alkaliphile
32502positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32502aerobe
67771aerobe

spore formation

@refspore formationconfidence
32502no
69481no99
69480no99.937

observation

  • @ref: 32502
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3250228757fructose+carbon source
3250227570histidine+carbon source
3250225017leucine+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
8030catalase+1.11.1.6
8030cytochrome-c oxidase+1.9.3.1
32502catalase+1.11.1.6
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
8030+------+------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8030sediment soil sampleBigeum islandRepublic of KoreaKORAsia
67771From farming fieldBikeum islandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Sediment
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 8030
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8030
  • description: Rubellimicrobium sp. MSL 20 16S ribosomal RNA gene, partial sequence
  • accession: EF547368
  • length: 1429
  • database: ena
  • NCBI tax ID: 442562

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rubellimicrobium mesophilum DSM 19309GCA_000600335scaffoldncbi442562
66792Rubellimicrobium mesophilum DSM 19309442562.3wgspatric442562
66792Rubellimicrobium mesophilum DSM 193092523533591draftimg442562

GC content

@refGC-contentmethod
803072.3
803069.65sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno87.285no
motileno87.285no
flagellatedno97.641no
flagellatedno97.641no
gram-positiveno97.301yes
gram-positiveno97.301yes
anaerobicno98.214yes
anaerobicno98.214yes
halophileno76.839no
halophileno76.839no
spore-formingno94.655yes
spore-formingno94.655yes
thermophileno94.099no
glucose-utilyes86.626yes
glucose-utilyes86.626yes
aerobicyes85.348yes
aerobicyes85.348yes
thermophileno94.099no
glucose-fermentno86.18yes
glucose-fermentno86.18yes

External links

@ref: 8030

culture collection no.: DSM 19309, KCTC 22012, MSL 20

straininfo link

  • @ref: 82956
  • straininfo: 402500

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18676459Rubellimicrobium mesophilum sp. nov., a mesophilic, pigmented bacterium isolated from soil.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.65590-02008Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification/physiology, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Genetics25197472Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309(T)), a representative of the Roseobacter group isolated from soil, and emended description of the species.Riedel T, Spring S, Fiebig A, Petersen J, Goker M, Klenk HPStand Genomic Sci10.4056/sigs.56210122014

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8030Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19309)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19309
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
32502Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2872228776041
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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
82956Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402500.1StrainInfo: A central database for resolving microbial strain identifiers