Acidovorax caeni (DSM 19327, LMG 24103, R-24608)

Name: Acidovorax caeni (DSM 19327, LMG 24103, R-24608)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2903

Type strain

Strain Designation R-24608

Culture col. no. DSM 19327 LMG 24103 R-24608

NCBI tax ID(s) 343013

Special Collections DSMZ Literature strains

History <- K. Heylen, Ghent University, Belgium

Links

Acidovorax caeni R-24608 is a facultative aerobe, mesophilic, Gram-negative prokaryote that was isolated from activated sludge.

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

Name and taxonomic classification

SI-ID 132460

DSM 19327,LMG 24103

@ref 20215

Last LPSN update 2025-12-16 09:47:25

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Acidovorax

Species Acidovorax caeni

Full scientific name Acidovorax caeni Heylen et al. 2008

Synonyms (1)

Paenacidovorax caeni

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32368	negative	1.8 µm	0.9 µm	rod-shaped
125438	negative				98.485
125439	negative				99.6

Pigmentation

32368

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8047	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8047	positive	growth	28	mesophilic
32368	positive	growth	15-37

Culture pH

@ref	Ability	Type	PH	PH range
32368	positive	growth	5.5-10.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

32368

Oxygen tolerancefacultative aerobe

Spore formation

@ref	Spore formation	Confidence
32368
125439		99.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32368	NaCl	positive	growth	0.5-2 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32368	28644 ChEBI	2-oxopentanoate	+	carbon source
32368	16449 ChEBI	alanine	+	carbon source
32368	35391 ChEBI	aspartate	+	carbon source
32368	15740 ChEBI	formate	+	carbon source
32368	29987 ChEBI	glutamate	+	carbon source
32368	17754 ChEBI	glycerol	+	carbon source
32368	28087 ChEBI	glycogen	+	carbon source
32368	24996 ChEBI	lactate	+	carbon source
32368	25017 ChEBI	leucine	+	carbon source
32368	25115 ChEBI	malate	+	carbon source
32368	51850 ChEBI	methyl pyruvate	+	carbon source
32368	26271 ChEBI	proline	+	carbon source
32368	17272 ChEBI	propionate	+	carbon source
32368	17822 ChEBI	serine	+	carbon source
32368	30031 ChEBI	succinate	+	carbon source
32368	26986 ChEBI	threonine	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32368	catalase	+	1.11.1.6
32368	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	suberin monomers biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	coenzyme A metabolism	100	4 of 4
66794	denitrification	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	valine metabolism	100	9 of 9
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	propanol degradation	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	vitamin K metabolism	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	tryptophan metabolism	68.42	26 of 38
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	lipid metabolism	64.52	20 of 31
66794	pyrimidine metabolism	64.44	29 of 45
66794	proline metabolism	63.64	7 of 11
66794	oxidative phosphorylation	62.64	57 of 91
66794	urea cycle	61.54	8 of 13
66794	gallate degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	non-pathway related	57.89	22 of 38
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	degradation of sugar alcohols	56.25	9 of 16
66794	cysteine metabolism	55.56	10 of 18
66794	nitrate assimilation	55.56	5 of 9
66794	allantoin degradation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	pentose phosphate pathway	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	lysine metabolism	50	21 of 42
66794	pantothenate biosynthesis	50	3 of 6
66794	biotin biosynthesis	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	Entner Doudoroff pathway	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	sulfate reduction	46.15	6 of 13
66794	phenol degradation	45	9 of 20
66794	vitamin B12 metabolism	44.12	15 of 34
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	arachidonate biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	cholesterol biosynthesis	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	sphingosine metabolism	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	methane metabolism	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	carotenoid biosynthesis	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of pentoses	28.57	8 of 28
66794	metabolism of disaccharids	27.27	3 of 11
66794	vitamin E metabolism	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	ascorbate metabolism	22.73	5 of 22
66794	chlorophyll metabolism	22.22	4 of 18
66794	arachidonic acid metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Activated sludge

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8047	activated sludge	Ghent	Belgium	BEL	Europe

Taxonmaps

69479

Global distribution of 16S sequence AM084006 (>99% sequence identity) for Acidovorax caeni subclade from Microbeatlas

Aquatic Samples	18053
Soil Samples	3656
Animal Samples	10287
Plant Samples	4307
Total Samples	36303

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8047	1	Risk group (German 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	IMG-taxon 2634166357 annotated assembly for Paenacidovorax caeni R-24608	contig	GCA_900116825	343013.6	2634166357	343013	56.06
66792	Draft Genome assembly for Paenacidovorax caeni R-24608	contig	GCA_001298675		2740892283	343013	48.63

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8047	Acidovorax caeni 16S rRNA gene, type strain R-24608T	AM084006	1518		343013

GC content

32368

GC-content (mol%)65.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenacidovorax caeni R-24608
NCBI: GCA_900116825

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.60	no
125439	motility	BacteriaNetⓘ	yes	88.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	85.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acidovorax caeni strain R-24608
PATRIC: 343013.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	yes
125438	anaerobic	anaerobicⓘ	no	95.72	yes
125438	spore-forming	spore-formingⓘ	no	89.77	yes
125438	aerobic	aerobicⓘ	yes	70.86	yes
125438	thermophilic	thermophileⓘ	no	97.97	yes
125438	flagellated	motile2+ⓘ	yes	84.53	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Acidovorax monticola sp. nov., isolated from soil.	Chaudhary DK, Kim J	Antonie Van Leeuwenhoek	10.1007/s10482-018-1083-z	2018
Phylogeny	Acidovorax kalamii sp. nov., isolated from a water sample of the river Ganges.	Pal D, Kaur N, Sudan SK, Bisht B, Krishnamurthi S, Mayilraj S	Int J Syst Evol Microbiol	10.1099/ijsem.0.002736	2018
Phylogeny	Tibeticola sediminis gen. nov., sp. nov., a thermophilic bacterium isolated from a hot spring.	Khan IU, Hussain F, Tian Y, Habib N, Xian WD, Jiang Z, Amin A, Yuan CG, Zhou EM, Zhi XY, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001777	2017
Genetics	First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608 (DSM 19327).	Ehsani E, Jauregui R, Geffers R, Jarek M, Boon N, Pieper DH, Vilchez-Vargas R	Genome Announc	10.1128/genomeA.01378-15	2015
Phylogeny	Comamonas humi sp. nov., isolated from soil.	Hatayama K	Int J Syst Evol Microbiol	10.1099/ijs.0.067439-0	2014
Phylogeny	Acidovorax caeni sp. nov., a denitrifying species with genetically diverse isolates from activated sludge.	Heylen K, Lebbe L, De Vos P	Int J Syst Evol Microbiol	10.1099/ijs.0.65387-0	2008

References

#8047	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19327
#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 )
#28596	IJSEM 73 2008 ( DOI 10.1099/ijs.0.65387-0 , PubMed 18175686 )
#32368	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 #28596
#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 )
#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 .
#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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Acidovorax caeni (DSM 19327, LMG 24103, R-24608)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900116825

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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