Strain identifier

BacDive ID: 6164

Type strain: Yes

Species: Devosia riboflavina

Strain Designation: 4R3337, Merck & Co. 4R3337, 4 R 3337

Strain history: CIP <- 1959, J.W. Foster, Merck and Co, "Pseudomonas riboflavina": strain 4 R 3337

NCBI tax ID(s): 46914 (species)

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General

@ref: 3065

BacDive-ID: 6164

DSM-Number: 7230

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Devosia riboflavina 4R3337 is a mesophilic, motile bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 46914
  • Matching level: species

strain history

@refhistory
3065<- LMG <- ATCC <- Merck & Co. <- W. Foster, 4R3337, USA ("Pseudomonas riboflavina")
373301959, J.W. Foster, Merck and Co, "Pseudomonas riboflavina": strain 4 R 3337
67770K. Komagata <-- R. Hugh 1114 <-- ATCC 9526 <-- Merck & Co., Inc..
122233CIP <- 1959, J.W. Foster, Merck and Co, "Pseudomonas riboflavina": strain 4 R 3337

doi: 10.13145/bacdive6164.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Devosiaceae
  • genus: Devosia
  • species: Devosia riboflavina
  • full scientific name: Devosia riboflavina (ex Foster 1944) Nakagawa et al. 1996

@ref: 3065

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Devosiaceae

genus: Devosia

species: Devosia riboflavina

full scientific name: Devosia riboflavina (ex Foster 1944) Nakagawa et al. 1996

strain designation: 4R3337, Merck & Co. 4R3337, 4 R 3337

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes92.611
6948099.932negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3065NUTRIENT AGAR (OXOID CM3) WITH PHOSPHATE (DSMZ Medium 605a)yeshttps://mediadive.dsmz.de/medium/605aName: NUTRIENT AGAR (OXOID CM3) WITH PHOSPHATE (DSMZ Medium 605a) Composition: Agar 15.0 g/l Peptone 5.0 g/l NaCl 5.0 g/l Na2HPO4 x 12 H2O 2.39 g/l Yeast extract 2.0 g/l Lab-Lemco beef extract 1.0 g/l KH2PO4 0.45 g/l Distilled water
37330MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122233CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3065positivegrowth28mesophilic
37330positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.989

compound production

  • @ref: 3065
  • compound: lumichrome

observation

  • @ref: 67770
  • observation: quinones: Q-10

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3065soilUSAUSANorth America
67770Riboflavin-rich soilUSAUSANorth America

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
30651Risk group (German classification)
1222331Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas riboflavina gene for 16S ribosomal RNA, partial sequenceD494231433ena46914
20218Brevundimonas diminuta DNA for 16S rRNA, partial sequenceD494221415ena293
20218Devosia riboflavina gene for 16S rRNA, partial sequence, strain: NBRC 13584AB6804511407ena46914
20218Brevundimonas diminuta gene for 16S rRNA, partial sequence, strain: NBRC 3140AB6800171388ena293
3065Devosia riboflavina partial 16S rRNA gene, type strain DSM 7230AJ5490861422ena46914

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Devosia riboflavina strain IFO1358446914.3wgspatric46914
66792Devosia riboflavina IFO135842597490201draftimg46914
67770Devosia riboflavina IFO13584GCA_000743575contigncbi46914

GC content

  • @ref: 67770
  • GC-content: 61.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.301no
anaerobicno98.442no
halophileno90.447no
spore-formingno96.04no
glucose-utilyes92.723no
aerobicyes93.518no
flagellatedno72.645no
thermophileno99.569yes
motileyes80.307no
glucose-fermentno89.7no

External links

@ref: 3065

culture collection no.: DSM 7230, ATCC 9526, CCEB 535, CCM 1979, CIP 59.10, IAM 14524, IFO 3140, LMG 2277, NBRC 3140, NCIB 8177, JCM 13427, BCRC 11904, CCUG 1825, IFO 13584, JCM 21244, NBRC 13584, NCIMB 8177, NRIC 0826, NRRL B-2463, NRRL B-784

straininfo link

  • @ref: 75649
  • straininfo: 92397

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8573489Transfer of "Pseudomonas riboflavina" (Foster 1944), a gram-negative, motile rod with long-chain 3-hydroxy fatty acids, to Devosia riboflavina gen. nov., sp. nov., nom. rev.Nakagawa Y, Sakane T, Yokota AInt J Syst Bacteriol10.1099/00207713-46-1-161996Base Sequence, Fatty Acids/*analysis, Molecular Sequence Data, Phylogeny, Pseudomonas/chemistry/*classification/genetics/ultrastructure, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny17082412Devosia soli sp. nov., isolated from greenhouse soil in Korea.Yoo SH, Weon HY, Kim BY, Hong SB, Kwon SW, Cho YH, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64214-02006Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Caseins/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enzymes/metabolism, Fatty Acids/analysis, Genes, rRNA, Hyphomicrobiaceae/*classification/*isolation & purification, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Starch/metabolism, Tyrosine/metabolismMetabolism
Phylogeny18398183Devosia chinhatensis sp. nov., isolated from a hexachlorocyclohexane (HCH) dump site in India.Kumar M, Verma M, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.65574-02008Base Sequence, DNA Primers/genetics, DNA, Bacterial/genetics, Fatty Acids/metabolism, Genes, Bacterial, Hexachlorocyclohexane/metabolism, Hyphomicrobiaceae/*classification/genetics/*isolation & purification/metabolism, India, Microscopy, Electron, Transmission, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Soil Pollutants/metabolism, Terminology as TopicMetabolism
Genetics25278537Draft Genome Sequences of Devosia sp. Strain 17-2-E-8 and Devosia riboflavina Strain IFO13584.Hassan YI, Lepp D, He J, Zhou TGenome Announc10.1128/genomeA.00994-142014
Phylogeny32375940Devosia marina sp. nov., isolated from deep seawater of the South China Sea, and reclassification of Devosia subaequoris as a later heterotypic synonym of Devosia soli.Liu Y, Du J, Zhang J, Lai Q, Shao Z, Zhu HInt J Syst Evol Microbiol10.1099/ijsem.0.0041302020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Hyphomicrobiaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNATranscriptome
Phylogeny35212618Devosia salina sp. nov., isolated from South China Sea sediment.Pang Y, Lu W, Chen M, Yan Y, Lin M, Zhang W, Zhou ZInt J Syst Evol Microbiol10.1099/ijsem.0.0052582022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, *Hyphomicrobiaceae/classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3065Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7230)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7230
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37330Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/9748
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/
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
75649Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92397.1StrainInfo: A central database for resolving microbial strain identifiers
122233Curators of the CIPCollection of Institut Pasteur (CIP 59.10)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2059.10