Name: Acidovorax caeni R-24608
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2903

Type strain:

Species: Acidovorax caeni

Strain Designation: R-24608

Culture col. no.: DSM 19327, LMG 24103

Strain history: <- K. Heylen, Ghent University, Belgium

NCBI tax ID(s): 343013 (species)

SI-ID 132460

DSM 19327, LMG 24103

Special Collections

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Acidovorax*
	Species	**Acidovorax caeni**
	Full Scientific Name (LPSN)	Acidovorax caeni Heylen et al. 2008

Synonym

Paenacidovorax caeni

Information on morphological and physiological properties Morphology

[Ref.: #32368]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.485

[Ref.: #32368]	Cell length	1.8 µm

[Ref.: #32368]	Cell width	0.9 µm

[Ref.: #32368]	Cell shape	rod-shaped

[Ref.: #32368]	Motility	yes

[Ref.: #32368]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8047]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #8047]

Culture medium growth

[Ref.: #8047]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8047]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #8047]			growth	28 °C
[Ref.: #32368]			growth	15-37 °C

	pH	Kind of pH		pH
[Ref.: #32368]			growth	5.5-10.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32368]

Oxygen tolerance

facultative aerobe

[Ref.: #32368]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32368]		NaCl		growth	0.5-2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32368]	2-oxopentanoate ChEBI	+	carbon source
[Ref.: #32368]	alanine ChEBI	+	carbon source
[Ref.: #32368]	aspartate ChEBI	+	carbon source
[Ref.: #32368]	formate ChEBI	+	carbon source
[Ref.: #32368]	glutamate ChEBI	+	carbon source
[Ref.: #32368]	glycerol ChEBI	+	carbon source
[Ref.: #32368]	glycogen ChEBI	+	carbon source
[Ref.: #32368]	lactate ChEBI	+	carbon source
[Ref.: #32368]	leucine ChEBI	+	carbon source
[Ref.: #32368]	malate ChEBI	+	carbon source
[Ref.: #32368]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #32368]	proline ChEBI	+	carbon source
[Ref.: #32368]	propionate ChEBI	+	carbon source
[Ref.: #32368]	serine ChEBI	+	carbon source
[Ref.: #32368]	succinate ChEBI	+	carbon source
[Ref.: #32368]	threonine ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32368]		catalase	+	1.11.1.6
[Ref.: #32368]		cytochrome oxidase	+	1.9.3.1

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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #8047]	Sample type/isolated from	activated sludge
[Ref.: #8047]	Geographic location (country and/or sea, region)	Ghent
[Ref.: #8047]	Country	Belgium
[Ref.: #8047]	Country ISO 3 Code	BEL
[Ref.: #8047]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Activated sludge

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #8047]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #8047]	Acidovorax caeni 16S rRNA gene, type strain R-24608T	AM084006	1518	GenBank ENA	343013 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paenacidovorax caeni R-24608	GCA_900116825	contig	GenBank ENA	343013 tax ID	*
[Ref.: #66792]	Paenacidovorax caeni R-24608	GCA_001298675	contig	GenBank ENA	343013 tax ID	*
[Ref.: #66792]	Acidovorax caeni strain R-24608	343013.6	wgs	PATRIC	343013 tax ID	*
[Ref.: #66792]	Acidovorax caeni R-24608	2740892283	draft	JGI IMG/M	343013 tax ID	*
[Ref.: #66792]	Acidovorax caeni DSM 19327	2634166357	draft	JGI IMG/M	343013 tax ID	*

[Ref.: #32368]

GC-content

65.7 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Acidovorax caeni strain R-24608 PATRIC: 343013.6
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Acidovorax caeni strain R-24608 PATRIC: 343013.6
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.485	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.717	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.768	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	70.86	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.973	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	84.53	no

Availability in culture collections External links

[Ref.: #8047]

Culture collection no.

DSM 19327, LMG 24103

[Ref.: #72426]

SI-ID 132460

Literature:

Only first 10 entries are displayed. Click here to see all.

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 )

#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 (see below)

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#72426

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID132460.1 )

#28596

IJSEM 73 2008 ( DOI 10.1099/ijs.0.65387-0 , PubMed 18175686 )

* These data were automatically processed and therefore are not curated

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Acidovorax caeni strain R-24608

Acidovorax caeni strain R-24608

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