Devosia riboflavina (DSM 7230, ATCC 9526, CCEB 535)

Name: Devosia riboflavina (DSM 7230, ATCC 9526, CCEB 535)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6164

Type strain

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

Culture col. no. DSM 7230 ATCC 9526 CCEB 535 CCM 1979 CIP 59.10 18 more

NCBI tax ID(s) 46914

Special Collections DSMZ CCUG JCM CIP

Links

Devosia riboflavina 4R3337 is a mesophilic prokaryote that was isolated from soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 92397

LMG 2277,ATCC 9526,CCM 1979,IFO 13584,IFO 3140,NCIB 8177,CCUG 1825,DSM 7230,NCIMB 8177,CIP 59.10,IFO 13284,IAM 14524,NBRC 3140,NBRC 13584,NRRL B-2463,NRRL B-784,BCRC 11904,CCRC 11904,JCM 21244

@ref 20215

Last LPSN update 2025-12-16 09:48:15

Domain Pseudomonadati

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

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	95.769
125439	negative	94.3

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3065	NUTRIENT AGAR (OXOID CM3) WITH PHOSPHATE (DSMZ Medium 605a)	Medium recipe at MediaDive	Name: 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
37330	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
122233	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
3065	positive	growth	28	mesophilic
37330	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	92.6

Spore formation

@ref	Spore formation	Confidence
125438		92.022

Compound production

3065

Compoundlumichrome

Observation

67770

Observationquinones: Q-10

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
3065	soil	USA	USA	North America
67770	Riboflavin-rich soil	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3065	1	Risk group (German classification) According to TRBA 466
122233	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM74357v1 assembly for Devosia riboflavina IFO13584	contig	GCA_000743575	46914.3	2597490201	46914	55.21

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Pseudomonas riboflavina gene for 16S ribosomal RNA, partial sequence	D49423	1433	46914
20218	Devosia riboflavina gene for 16S rRNA, partial sequence, strain: NBRC 13584	AB680451	1407	46914
3065	Devosia riboflavina partial 16S rRNA gene, type strain DSM 7230	AJ549086	1422	46914

GC content

@ref	GC-content (mol%)	Method
67770	61.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Devosia riboflavina IFO13584
NCBI: GCA_000743575

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	87.90	no
125439	motility	BacteriaNetⓘ	no	56.00	no
125439	gram_stain	BacteriaNetⓘ	negative	94.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Devosia riboflavina strain IFO13584
PATRIC: 46914.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.77	no
125438	anaerobic	anaerobicⓘ	no	96.09	no
125438	spore-forming	spore-formingⓘ	no	92.02	no
125438	aerobic	aerobicⓘ	yes	85.69	no
125438	thermophilic	thermophileⓘ	no	97.58	no
125438	flagellated	motile2+ⓘ	yes	64.63	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Two-Component Flavin-Dependent Riboflavin Monooxygenase Degrades Riboflavin in Devosia riboflavina.	Kanazawa H, Shigemoto R, Kawasaki Y, Oinuma KI, Nakamura A, Masuo S, Takaya N.	J Bacteriol	10.1128/jb.00022-18	2018
Metabolism	Efficient production of lumichrome by Microbacterium sp. strain TPU 3598.	Yamamoto K, Asano Y.	Appl Environ Microbiol	10.1128/aem.02166-15	2015
	Bacterial Epimerization as a Route for Deoxynivalenol Detoxification: the Influence of Growth and Environmental Conditions.	He JW, Hassan YI, Perilla N, Li XZ, Boland GJ, Zhou T.	Front Microbiol	10.3389/fmicb.2016.00572	2016
Phylogeny	A 16S rRNA Gene and Draft Genome Database for the Murine Oral Bacterial Community.	Joseph S, Aduse-Opoku J, Hashim A, Hanski E, Streich R, Knowles SCL, Pedersen AB, Wade WG, Curtis MA.	mSystems	10.1128/msystems.01222-20	2021
Metabolism	Microbial Biotransformation to Obtain New Antifungals.	Bianchini LF, Arruda MF, Vieira SR, Campelo PM, Gregio AM, Rosa EA.	Front Microbiol	10.3389/fmicb.2015.01433	2015
Genetics	The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.	Lluch J, Servant F, Paisse S, Valle C, Valiere S, Kuchly C, Vilchez G, Donnadieu C, Courtney M, Burcelin R, Amar J, Bouchez O, Lelouvier B.	PLoS One	10.1371/journal.pone.0142334	2015
Genetics	Draft Genome Sequences of Devosia sp. Strain 17-2-E-8 and Devosia riboflavina Strain IFO13584.	Hassan YI, Lepp D, He J, Zhou T	Genome Announc	10.1128/genomeA.00994-14	2014
Phylogeny	Devosia salina sp. nov., isolated from South China Sea sediment.	Pang Y, Lu W, Chen M, Yan Y, Lin M, Zhang W, Zhou Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.005258	2022
Phylogeny	Devosia 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 H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004130	2020
Phylogeny	Devosia chinhatensis sp. nov., isolated from a hexachlorocyclohexane (HCH) dump site in India.	Kumar M, Verma M, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.65574-0	2008
Phylogeny	Devosia soli sp. nov., isolated from greenhouse soil in Korea.	Yoo SH, Weon HY, Kim BY, Hong SB, Kwon SW, Cho YH, Go SJ, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.64214-0	2006
Phylogeny	Transfer 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 A	Int J Syst Bacteriol	10.1099/00207713-46-1-16	1996

References

#3065	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7230
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#37330	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#122233	Collection of Institut Pasteur ; Curators of the CIP; CIP 59.10
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Devosia riboflavina (DSM 7230, ATCC 9526, CCEB 535)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000743575

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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