Hydrogenophaga flava (DSM 619, ATCC 33667, NBRC 102514)

Name: Hydrogenophaga flava (DSM 619, ATCC 33667, NBRC 102514)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2963

Type strain

Culture col. no. DSM 619 ATCC 33667 NBRC 102514 LMG 2185 KCTC 1648 9 more

NCBI tax ID(s) 1349752 65657

Special Collections DSMZ CCUG JCM KCTC CIP

Links

Hydrogenophaga flava DSM 619 is a mesophilic prokaryote that was isolated from ditch mud.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 3010

LMG 2185,ATCC 33667,CCUG 1658,DSM 619,CIP 103271,CCM 4453,CECT 4106,CCRC 13889,CFBP 2438,KCTC 1648,BCRC 13889,CCUG 22894,IAM 14931,NBRC 102514,JCM 21413

@ref 20215

Last LPSN update 2025-12-16 09:47:26

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Hydrogenophaga

Species Hydrogenophaga flava

Full scientific name Hydrogenophaga flava (Niklewski 1910) Willems et al. 1989

Synonyms (2)

Pseudomonas flava
"Hydrogenomonas flava"

BacDive ID	Other strains from **Hydrogenophaga flava** (1)	Type strain
138508	H. flava CIP 75.29

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	100
125439	negative	98.6

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
324	MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)	Medium recipe at MediaDive	Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
324	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
34235	MEDIUM 18 - for Hydrogenophaga, Vogesella and Pseudomonas genera		Distilled water make up to (1000.000 ml);Sodium chloride (3.000 g);Agar(12.000 g);Yeast extract (3.000 g);Peptone (0.600 g)
119363	CIP Medium 18	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
324	positive	growth	30	mesophilic
34235	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98

Spore formation

@ref	Spore formation	Confidence
125439		98.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Mud (Sludge)

Isolation

@ref	Sample type
324	ditch mud
67770	Ditch mud
119363	Environment, Ditch mud

Taxonmaps

69479

Global distribution of 16S sequence AF078771 (>99% sequence identity) for Hydrogenophaga from Microbeatlas

Aquatic Samples	295
Soil Samples	9
Animal Samples	23
Plant Samples	410
Total Samples	737

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
324	1	Risk group (German classification) According to TRBA 466
119363	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	ASM157114v1 assembly for Hydrogenophaga flava NBRC 102514	contig	GCA_001571145	1349752.3	2731957619	1349752	62.97

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Hydrogenophaga flava gene for 16S rRNA, strain: DSM 619	AB021420	1519	65657
20218	Hydrogenophaga flava 16S rRNA gene, strain DSM 619	AJ420328	1494	65657
20218	Hydrogenophaga flava gene for 16S rRNA, partial sequence, strain: NBRC 102514	AB681848	1454	65657
324	Hydrogenophaga flava 16S ribosomal RNA gene, partial sequence	AF078771	1513	65657

GC content

324

GC-content (mol%)67.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Hydrogenophaga flava NBRC 102514
NCBI: GCA_001571145

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	yes	89.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hydrogenophaga flava NBRC 102514
PATRIC: 1349752.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	92.55	no
125438	spore-forming	spore-formingⓘ	no	89.56	no
125438	aerobic	aerobicⓘ	yes	83.59	no
125438	thermophilic	thermophileⓘ	no	99.45	yes
125438	flagellated	motile2+ⓘ	yes	87.07	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Diversity of Betaproteobacteria revealed by novel primers suggests their role in arsenic cycling.	Chakraborty A, DasGupta CK, Bhadury P.	Heliyon	10.1016/j.heliyon.2019.e03089	2020
Metabolism	Biodegradation of methyl tert-butyl ether by a pure bacterial culture.	Hatzinger PB, McClay K, Vainberg S, Tugusheva M, Condee CW, Steffan RJ.	Appl Environ Microbiol	10.1128/aem.67.12.5601-5607.2001	2001
	A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples.	Widmer F, Seidler RJ, Gillevet PM, Watrud LS, Di Giovanni GD.	Appl Environ Microbiol	10.1128/aem.64.7.2545-2553.1998	1998
Phylogeny	Microbial community structures and bacteria-Cylindrospermopsis raciborskii interactions in Yilong Lake.	Jin Y, Ren S, Wu Y, Zhang X, Chen Z, Xie B.	FEMS Microbiol Ecol	10.1093/femsec/fiae048	2024
Phylogeny	PCR Primer Design for 16S rRNAs for Experimental Horizontal Gene Transfer Test in Escherichia coli.	Miyazaki K, Sato M, Tsukuda M.	Front Bioeng Biotechnol	10.3389/fbioe.2017.00014	2017
Phylogeny	Saccharopolyspora rhizosphaerae sp. nov., an actinomycete isolated from rhizosphere soil in Thailand.	Intra B, Euanorasetr J, Take A, Inahashi Y, Mori M, Panbangred W, Matsumoto A.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003307	2019
Phylogeny	Hydrogenophaga luteola sp. nov. isolated from reed pond water.	Du J, Yang JE, Singh H, Akter S, Won K, Yin CS, Jin FX, Yi TH	Antonie Van Leeuwenhoek	10.1007/s10482-015-0525-0	2015
Phylogeny	Hydrogenophaga temperata sp. nov., a betaproteobacterium isolated from compost in Korea.	Kim YJ, Kim MK, Weon HY, Kim HB, Yang DC	J Gen Appl Microbiol	10.2323/jgam.56.419	2010

References

#324	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 619
#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 )
#34235	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#69479	João 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.: MicrobeAtlas 1.0 beta .
#119363	Collection of Institut Pasteur ; Curators of the CIP; CIP 103271
#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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Hydrogenophaga flava (DSM 619, ATCC 33667, NBRC 102514)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001571145

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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