Hydrogenophaga atypica (CCUG 53902, CIP 108118, DSM 15342)

Name: Hydrogenophaga atypica (CCUG 53902, CIP 108118, DSM 15342)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2971

Type strain

Culture col. no. CCUG 53902 CIP 108118 DSM 15342 BSB 31-8

NCBI tax ID(s) 249409

Special Collections DSMZ CCUG CIP

History <- P. Kämpfer; BSB 31-8 <- R. Schulze CIP <- 2003, DSMZ <- P. Kämpfer, Giessen Univ., Giessen, Germany <- R. Schulze, Germany

Links

Hydrogenophaga atypica CCUG 53902 is an obligate aerobe, mesophilic, Gram-negative prokaryote that was isolated from activated sludge.

Gram-negative motile rod-shaped obligate aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 135114

CIP 108118,DSM 15342,CCUG 53902

@ref 20215

Last LPSN update 2026-02-09 11:18:24

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Hydrogenophaga

Species Hydrogenophaga atypica

Full scientific name Hydrogenophaga atypica Kämpfer et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
116546	negative	rod-shaped

Pigmentation

@ref	Production	Name
116546		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5857	HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428)	Medium recipe at MediaDive	Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water
5857	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
33201	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116546	CIP Medium 328	Medium recipe at CIP
116546	CIP Medium 72	Medium recipe at CIP
5857	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5857	positive	growth	28	mesophilic
33201	positive	growth	30	mesophilic
116546	positive	growth	25-37	mesophilic
116546	negative	growth	5
116546	negative	growth	10
116546	negative	growth	41

Physiology and metabolism

Oxygen tolerance

116546

Oxygen toleranceobligate aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
116546	NaCl	positive	growth	0 %
116546	NaCl		growth	2 %
116546	NaCl		growth	4 %
116546	NaCl		growth	6 %
116546	NaCl		growth	8 %
116546	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
116546	16947 ChEBI	citrate	-	carbon source
116546	4853 ChEBI	esculin	-	hydrolysis
116546	17632 ChEBI	nitrate	+	reduction
116546	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
116546	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116546	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116546	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
116546	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
116546	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116546	caseinase	-	3.4.21.50
116546	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
116546	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
116546	gelatinase	-
116546	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
116546	lipase	-
68382	lipase (C 14)	-		from API zym
116546	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116546	ornithine decarboxylase	-	4.1.1.17
116546	oxidase	+
116546	protease	-
68382	trypsin	-	3.4.21.4	from API zym
116546	tryptophan deaminase	-
116546	tween esterase	-
116546	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
116546	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
116546	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-	+	-	-	-	-	+	-	+	+	-	-	-	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Activated sludge

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
5857	activated sludge		Munich	Germany	DEU	Europe
60070	Activated sludge	1995	München	Germany	DEU	Europe
116546	Environment, Activated sludge		München	Germany	DEU	Europe	1995

Taxonmaps

69479

Global distribution of 16S sequence AJ585992 (>99% sequence identity) for Hydrogenophaga from Microbeatlas

Aquatic Samples	41
Soil Samples	2
Animal Samples	1
Plant Samples	2
Total Samples	46

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5857	1	Risk group (German classification) According to TRBA 466
116546	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM4266521v1 assembly for Hydrogenophaga atypica CCUG 53902	scaffold	GCA_042665215	249409	60.6

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5857	Hydrogenophaga atypica partial 16S rRNA gene, type strain BSB 41.8T	AJ585992	1527		249409

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hydrogenophaga borbori sp. nov., isolated from activated sludge.	Choi GM, Lee SY, Kim SY, Wee JH, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.003787	2020
Phylogeny	Hydrogenophaga soli sp. nov., isolated from rice field soil.	Yang D, Cha S, Choi J, Seo T	Int J Syst Evol Microbiol	10.1099/ijsem.0.002277	2017
Phylogeny	Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge.	Kampfer P, Schulze R, Jackel U, Malik KA, Amann R, Spring S	Int J Syst Evol Microbiol	10.1099/ijs.0.03041-0	2005

References

#5857	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15342
#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 )
#33201	; Curators of the CIP;
#60070	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53902
#68382	Automatically annotated from API zym .
#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 .
#116546	Collection of Institut Pasteur ; Curators of the CIP; CIP 108118
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 atypica (CCUG 53902, CIP 108118, DSM 15342)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042665215

16S sequences

Genome-based predictions

Literature

Literature

References

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