Strain identifier

BacDive ID: 13774

Type strain: Yes

Species: Rubellimicrobium thermophilum

Strain Designation: C-lvkR2A-2, C-lvk-R2A-2

Strain history: CIP <- 2006, CCUG <- 2005, M. Salkinoja-Salonen, Helsinki, Finland <- M.Kolari, Helsinki, Finland:strain C-lvk-R2A-2

NCBI tax ID(s): 1123069 (strain), 295419 (species)

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General

@ref: 6564

BacDive-ID: 13774

DSM-Number: 16684

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

description: Rubellimicrobium thermophilum C-lvkR2A-2 is an aerobe, thermophilic, Gram-negative bacterium that was isolated from coloured deposits in a pulp dryer.

NCBI tax id

NCBI tax idMatching level
295419species
1123069strain

strain history

@refhistory
6564<- M. Salkinoja-Salonen, Helsinki Univ., Dept. Appl. Chem. and Microbiol.; C-lvkR2A-2 <- M. Kolari
123508CIP <- 2006, CCUG <- 2005, M. Salkinoja-Salonen, Helsinki, Finland <- M.Kolari, Helsinki, Finland:strain C-lvk-R2A-2

doi: 10.13145/bacdive13774.20230509.8.1

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 thermophilum
  • full scientific name: Rubellimicrobium thermophilum Denner et al. 2006

@ref: 6564

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Rubellimicrobium

species: Rubellimicrobium thermophilum

full scientific name: Rubellimicrobium thermophilum Denner et al. 2006

strain designation: C-lvkR2A-2, C-lvk-R2A-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31531negative02-04 µm0.6-0.8 µmrod-shapedyes
69480negative99.981
123508negativerod-shapedyes

colony morphology

  • @ref: 59328
  • incubation period: 2 days

pigmentation

  • @ref: 31531
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6564R2A 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
37498MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
123508CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
6564positivegrowth45-52thermophilic
31531positivegrowth28-37mesophilic
31531positiveoptimum28-37mesophilic
37498positivegrowth45thermophilic
59328positivegrowth42-45thermophilic

culture pH

@refabilitytypepH
31531positivegrowth7
31531positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31531aerobe
59328aerobe
123508facultative anaerobe

spore formation

@refspore formationconfidence
31531no
69481no94
69480no99.997

observation

  • @ref: 31531
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3153130089acetate+carbon source
3153115963ribitol+carbon source
3153122599arabinose+carbon source
3153117057cellobiose+carbon source
3153128757fructose+carbon source
3153128260galactose+carbon source
3153124265gluconate+carbon source
3153117234glucose+carbon source
3153124996lactate+carbon source
3153125115malate+carbon source
3153117306maltose+carbon source
3153129864mannitol+carbon source
3153137684mannose+carbon source
3153128053melibiose+carbon source
3153118257ornithine+carbon source
3153126271proline+carbon source
3153115361pyruvate+carbon source
3153126546rhamnose+carbon source
3153133942ribose+carbon source
3153117814salicin+carbon source
3153130911sorbitol+carbon source
3153117992sucrose+carbon source
3153127082trehalose+carbon source
3153118222xylose+carbon source
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
12350817632nitrate-reduction
12350816301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12350835581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31531catalase+1.11.1.6
31531cytochrome oxidase+1.9.3.1
31531urease+3.5.1.5
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123508oxidase+
123508catalase+1.11.1.6
123508urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
6564--++-++/-+/------+-+----
123508--++-++----+-+-++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
6564-----+++++++-++-+/-+/---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dateisolation date
6564coloured deposits in a pulp dryerFinlandFINEurope
59328Water,paper machineFinlandFINEurope2001
123508Environment, Water, paper machineFinlandFINEurope2001

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Industrial
  • Cat3: #Engineered product

taxonmaps

  • @ref: 69479
  • File name: preview.99_55370.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_532;96_24693;97_30919;98_39559;99_55370&stattab=map
  • Last taxonomy: Rubellimicrobium thermophilum subclade
  • 16S sequence: AJ844281
  • Sequence Identity:
  • Total samples: 1427
  • soil counts: 458
  • aquatic counts: 473
  • animal counts: 451
  • plant counts: 45

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65641Risk group (German classification)
1235081Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6564
  • description: Rubellimicrobium thermophilum 16S rRNA gene, type strain C-lvk-R2A-2
  • accession: AJ844281
  • length: 1449
  • database: ena
  • NCBI tax ID: 295419

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rubellimicrobium thermophilum DSM 16684GCA_000442315scaffoldncbi1123069
66792Rubellimicrobium thermophilum DSM 166841123069.3wgspatric1123069
66792Rubellimicrobium thermophilum DSM 166842521172529draftimg1123069

GC content

@refGC-content
656470.0
3153170

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileno54.411yes
flagellatedno93.915no
gram-positiveno97.936yes
anaerobicno97.607yes
aerobicyes86.485yes
halophileno72.276no
spore-formingno97.668yes
thermophileno73.992no
glucose-utilyes88.674yes
glucose-fermentno89.82yes

External links

@ref: 6564

culture collection no.: DSM 16684, CCUG 51817, HAMBI 2421, CIP 109278

straininfo link

  • @ref: 82953
  • straininfo: 297313

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738114Rubellimicrobium thermophilum gen. nov., sp. nov., a red-pigmented, moderately thermophilic bacterium isolated from coloured slime deposits in paper machines.Denner EBM, Kolari M, Hoornstra D, Tsitko I, Kampfer P, Busse HJ, Salkinoja-Salonen MInt J Syst Evol Microbiol10.1099/ijs.0.63751-02006DNA, Bacterial/genetics/isolation & purification, Fatty Acids/analysis, Industry, Microscopy, Electron, Molecular Sequence Data, Myxococcales/*classification/genetics/growth & development/isolation & purification, Paper, Phylogeny, Rhodobacteraceae/*classification/genetics/isolation & purification/ultrastructureEnzymology
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
Phylogeny19196786Rubellimicrobium aerolatum sp. nov., isolated from an air sample in Korea.Weon HY, Son JA, Yoo SH, Hong SB, Jeon YA, Kwon SW, Koo BSInt J Syst Evol Microbiol10.1099/ijs.0.65856-02009*Air Microbiology, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/chemistry/*classification/genetics/isolation & purification, Species SpecificityGenetics
Phylogeny20567903Rubellimicrobium roseum sp. nov., a Gram-negative bacterium isolated from the forest soil sample.Cao YR, Jiang Y, Wang Q, Tang SK, He WX, Xue QH, Xu LH, Jiang CLAntonie Van Leeuwenhoek10.1007/s10482-010-9452-22010Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/*analysis, DNA, Ribosomal/analysis, Genes, rRNA, Hot Temperature, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Soil, *Soil MicrobiologyStress
Genetics24501632Genome sequence of the reddish-pigmented Rubellimicrobium thermophilum type strain (DSM 16684(T)), a member of the Roseobacter clade.Fiebig A, Riedel T, Gronow S, Petersen J, Klenk HP, Goker MStand Genomic Sci10.4056/sigs.42479112013
Phylogeny31346832Rubellimicrobium rubrum sp. nov., a novel bright reddish bacterium isolated from a lichen sample.Jiang LQ, Zhang K, Li GD, Wang XY, Shi SB, Li QY, An DF, Lang L, Wang LS, Jiang CL, Jiang YAntonie Van Leeuwenhoek10.1007/s10482-019-01304-52019Aerobiosis, *Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Lichens/*microbiology, Locomotion, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6564Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16684)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16684
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
31531Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2782528776041
37498Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7001
59328Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51817)https://www.ccug.se/strain?id=51817
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
68369Automatically annotated from API 20NE
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
82953Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297313.1StrainInfo: A central database for resolving microbial strain identifiers
123508Curators of the CIPCollection of Institut Pasteur (CIP 109278)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109278