Pseudacidovorax intermedius (DSM 21352, CCUG 54492, CIP 109510)

Name: Pseudacidovorax intermedius (DSM 21352, CCUG 54492, CIP 109510)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3026

Type strain

Strain Designation CC-21

Culture col. no. DSM 21352 CCUG 54492 CIP 109510 CC-21

NCBI tax ID(s) 433924

Special Collections DSMZ CCUG CIP Literature strains

History DSMZ <- P. Kämpfer, University Giessen <- A. B. Arun CIP <- 2007, P. Kämpfer, Giessen Univ., Germany: strain CC-21

Links

Pseudacidovorax intermedius CC-21 is a facultative aerobe, Gram-negative, motile bacterium that was isolated from soil of soy bean field.

Gram-negative motile rod-shaped facultative aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 323991

CCUG 54492,CIP 109510,DSM 21352

@ref 20215

Last LPSN update 2026-05-29 08:25:36

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Pseudacidovorax

Species Pseudacidovorax intermedius

Full scientific name Pseudacidovorax intermedius Kämpfer et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32237	negative	1.75 µm	0.5 µm	rod-shaped
120153	negative			rod-shaped
125438	negative				97.5
125439	negative				91.696

Pigmentation

32237

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15634	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
37747	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120153	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
15634	positive	growth	28
32237	positive	growth	30
37747	positive	growth	30
60200	positive	growth	28-42

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
32237	facultative aerobe
60200	aerobe
120153	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.066

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32237	37054 ChEBI	3-hydroxybutyrate	+	carbon source
32237	30089 ChEBI	acetate	+	carbon source
32237	16449 ChEBI	alanine	+	carbon source
32237	22599 ChEBI	arabinose	+	carbon source
32237	35391 ChEBI	aspartate	+	carbon source
32237	16947 ChEBI	citrate	+	carbon source
32237	28757 ChEBI	fructose	+	carbon source
32237	17234 ChEBI	glucose	+	carbon source
32237	24996 ChEBI	lactate	+	carbon source
120153	17632 ChEBI	nitrate	-	reduction
120153	16301 ChEBI	nitrite	-	reduction
32237	26271 ChEBI	proline	+	carbon source
32237	17272 ChEBI	propionate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120153	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
32237	catalase	+	1.11.1.6
120153	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
32237	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
120153	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
120153	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	gallate degradation	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	cyanate degradation	100	3 of 3
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	lactate fermentation	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	sulfopterin metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	ceramide biosynthesis	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	acetate fermentation	100	4 of 4
66794	aerobactin biosynthesis	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	valine metabolism	100	9 of 9
66794	quinate degradation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	leucine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	citric acid cycle	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	purine metabolism	81.91	77 of 94
66794	threonine metabolism	80	8 of 10
66794	starch degradation	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	3-phenylpropionate degradation	80	12 of 15
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	vitamin B1 metabolism	76.92	10 of 13
66794	methionine metabolism	76.92	20 of 26
66794	non-pathway related	76.32	29 of 38
66794	degradation of sugar acids	76	19 of 25
66794	degradation of sugar alcohols	75	12 of 16
66794	glycogen biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	degradation of aromatic, nitrogen containing compounds	75	9 of 12
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	phenol degradation	75	15 of 20
66794	tryptophan metabolism	73.68	28 of 38
66794	oxidative phosphorylation	73.63	67 of 91
66794	metabolism of disaccharids	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	tyrosine metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	histidine metabolism	68.97	20 of 29
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	degradation of pentoses	67.86	19 of 28
66794	lipid metabolism	67.74	21 of 31
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	pyrimidine metabolism	64.44	29 of 45
66794	vitamin B6 metabolism	63.64	7 of 11
66794	pentose phosphate pathway	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	vitamin K metabolism	60	3 of 5
66794	lysine metabolism	57.14	24 of 42
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	allantoin degradation	55.56	5 of 9
66794	degradation of hexoses	55.56	10 of 18
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	carnitine metabolism	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	resorcinol degradation	50	1 of 2
66794	isoprenoid biosynthesis	50	13 of 26
66794	glycine metabolism	50	5 of 10
66794	biotin biosynthesis	50	2 of 4
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	carotenoid biosynthesis	45.45	10 of 22
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	propanol degradation	42.86	3 of 7
66794	bile acid biosynthesis, neutral pathway	41.18	7 of 17
66794	3-chlorocatechol degradation	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	vitamin B12 metabolism	38.24	13 of 34
66794	ascorbate metabolism	36.36	8 of 22
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	coenzyme M biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9

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
120153	-	+	+	+	-	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15634	soil of soy bean field	Kaohsiung County	Taiwan, Province of China	TWN	Asia
60200	Soil	Kaohsiung County	Taiwan, Province of China	TWN	Asia
120153	Environment, Soil samples	Kaohsiung county	Taiwan, Province of China	TWN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF469609 (>99% sequence identity) for Pseudacidovorax intermedius subclade from Microbeatlas

Aquatic Samples	573
Soil Samples	40
Animal Samples	165
Plant Samples	124
Total Samples	902

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15634	1	Risk group (German classification) According to TRBA 466
120153	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
66792	ASM335047v1 assembly for Pseudacidovorax intermedius DSM 21352	scaffold	GCA_003350475	433924.4	2770939510	433924	72.12

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15634	Pseudacidovorax intermedius strain CC-21 16S ribosomal RNA gene, partial sequence	EF469609	1491		433924

GC content

32237

GC-content (mol%)70.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM335047v1 assembly for Pseudacidovorax intermedius DSM 21352
NCBI: GCA_003350475

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	83.28	no
125439	gram_stain	BacteriaNetⓘ	negative	91.70	no
125439	motility	BacteriaNetⓘ	yes	81.94	no
125439	spore_formation	BacteriaNetⓘ	no	99.07	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudacidovorax intermedius DSM 21352
NCBI: GCA_003350475.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	yes
125438	anaerobic	anaerobicⓘ	no	94.14	no
125438	aerobic	aerobicⓘ	yes	86.76	no
125438	spore-forming	spore-formingⓘ	no	85.00	no
125438	thermophilic	thermophileⓘ	no	98.83	yes
125438	flagellated	motile2+ⓘ	yes	77.91	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudacidovorax intermedius gen. nov., sp. nov., a novel nitrogen-fixing betaproteobacterium isolated from soil.	Kampfer P, Thummes K, Chu HI, Tan CC, Arun AB, Chen WM, Lai WA, Shen FT, Rekha PD, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.65175-0	2008

References

#15634	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21352
#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 )
#28478	IJSEM 491 2008 ( DOI 10.1099/ijs.0.65175-0 , PubMed 18218955 )
#32237	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28478
#37747	; Curators of the CIP;
#60200	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54492
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#120153	Collection of Institut Pasteur ; Curators of the CIP; CIP 109510
#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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Pseudacidovorax intermedius (DSM 21352, CCUG 54492, CIP 109510)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003350475

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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