Paracoccus contaminans (WPAn02, RKI 16-01929, LMG 29738)

Name: Paracoccus contaminans (WPAn02, RKI 16-01929, LMG 29738)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133282

Type strain

Strain Designation WPAn02, RKI16-01929

Culture col. no. WPAn02 RKI 16-01929 LMG 29738 CCM 8701 CIP 111112 1 more

NCBI tax ID(s) 1945662

Special Collections CIP Literature strains

History 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain WPAn02 CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain WPAn02

Links

Paracoccus contaminans WPAn02 is an aerobe, Gram-negative, coccus-shaped bacterium that was isolated from contaminated axenic water microcosm.

Gram-negative coccus-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 412579

LMG 29738,CIP 111112

@ref 20215

Last LPSN update 2026-02-09 11:31:55

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Paracoccus

Species Paracoccus contaminans

Full scientific name Paracoccus contaminans Kämpfer et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
25118	negative	1 µm	1 µm	coccus-shaped
125438	negative				97.982
118738				coccus-shaped

Colony morphology

@ref	Colony size	Colony color	Incubation period	Medium used
25118	2 mm	beige	2 days	NA (Nutrient Agar)

Culture and growth conditions

Culture medium

@ref	Name	Composition	Medium link
25118	NA (Nutrient Agar)
25118	brain–heart infusion agar
25118	TSA (Trypticase soy agar)
25118	Reasoner's 2A agar (R2A)
25118	MacConkey agar
42176	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati	Distilled water make up to (1000.000 ml);R2A agar (18.200 g)
118738	CIP Medium 566		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
25118	positive	growth	10.0-45.0
25118	negative	growth	4
25118	negative	growth	45
42176	positive	growth	25

Culture pH

@ref	Ability	Type	PH
25118	positive	growth	5.0-7.5

Physiology and metabolism

Oxygen tolerance

25118

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
25118
125438		93.271

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25118	NaCl	positive	growth	0.0-1.0 %(w/v)
25118	NaCl		growth	2 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25118	30916 ChEBI	2-oxoglutarate	-	carbon source
25118	16193 ChEBI	3-hydroxybenzoate	-	carbon source
25118	37054 ChEBI	3-hydroxybutyrate	-	carbon source
25118	17879 ChEBI	4-hydroxybenzoate	-	carbon source
25118	30089 ChEBI	acetate	+	carbon source
25118	17128 ChEBI	adipate	-	carbon source
25118	18305 ChEBI	arbutin	-	carbon source
25118	35391 ChEBI	aspartate	-	carbon source
25118	78208 ChEBI	azelaate	-	carbon source
25118	17057 ChEBI	cellobiose	-	carbon source
25118	16383 ChEBI	cis-aconitate	-	carbon source
25118	16947 ChEBI	citrate	-	carbon source
25118	15824 ChEBI	D-fructose	+	carbon source
25118	12936 ChEBI	D-galactose	+	carbon source
25118	17634 ChEBI	D-glucose	+	carbon source
25118	16899 ChEBI	D-mannitol	-	carbon source
25118	16024 ChEBI	D-mannose	+	carbon source
25118	16988 ChEBI	D-ribose	+	carbon source
25118	17924 ChEBI	D-sorbitol	+	carbon source
25118	16551 ChEBI	D-trehalose	-	carbon source
25118	65327 ChEBI	D-xylose	-	carbon source
25118	29806 ChEBI	fumarate	+	carbon source
25118	16865 ChEBI	gamma-aminobutyric acid	-	carbon source
25118	24265 ChEBI	gluconate	-	carbon source
25118	17859 ChEBI	glutaric acid	-	carbon source
25118	17240 ChEBI	itaconate	-	carbon source
25118	16977 ChEBI	L-alanine	+	carbon source
25118	30849 ChEBI	L-arabinose	+	carbon source
25118	15971 ChEBI	L-histidine	+	carbon source
25118	15603 ChEBI	L-leucine	-	carbon source
25118	15729 ChEBI	L-ornithine	-	carbon source
25118	17295 ChEBI	L-phenylalanine	-	carbon source
25118	62345 ChEBI	L-rhamnose	-	carbon source
25118	17115 ChEBI	L-serine	+	carbon source
25118	16828 ChEBI	L-tryptophan	-	carbon source
25118	24996 ChEBI	lactate	+	carbon source
25118	68428 ChEBI	maltitol	-	carbon source
25118	17306 ChEBI	maltose	+	carbon source
25118	28053 ChEBI	melibiose	-	carbon source
25118	36986 ChEBI	mesaconate	-	carbon source
25118	17268 ChEBI	myo-inositol	-	carbon source
25118	28037 ChEBI	N-acetylgalactosamine	-	carbon source
25118	506227 ChEBI	N-acetylglucosamine	-	carbon source
25118	18401 ChEBI	phenylacetate	-	carbon source
25118	17272 ChEBI	propionate	-	carbon source
25118	17148 ChEBI	putrescine	-	carbon source
25118	15361 ChEBI	pyruvate	+	carbon source
25118	15963 ChEBI	ribitol	-	carbon source
25118	17814 ChEBI	salicin	-	carbon source
25118	9300 ChEBI	suberic acid	-	carbon source
25118	17992 ChEBI	sucrose	-	carbon source
25118	15708 ChEBI	trans-aconitate	-	carbon source

Enzymes

@ref	Value	Activity	Ec
25118	catalase	+	1.11.1.6
25118	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	denitrification	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	octane oxidation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	folate polyglutamylation	100	1 of 1
66794	valine metabolism	100	9 of 9
66794	palmitate biosynthesis	100	22 of 22
66794	gluconeogenesis	100	8 of 8
66794	allantoin degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	methylglyoxal degradation	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	photosynthesis	78.57	11 of 14
66794	pyrimidine metabolism	77.78	35 of 45
66794	NAD metabolism	77.78	14 of 18
66794	serine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	purine metabolism	76.6	72 of 94
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	glutamate and glutamine metabolism	75	21 of 28
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	lysine metabolism	71.43	30 of 42
66794	citric acid cycle	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	tyrosine metabolism	71.43	10 of 14
66794	threonine metabolism	70	7 of 10
66794	myo-inositol biosynthesis	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	oxidative phosphorylation	67.03	61 of 91
66794	cyanate degradation	66.67	2 of 3
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	glutathione metabolism	64.29	9 of 14
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	degradation of pentoses	64.29	18 of 28
66794	pentose phosphate pathway	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	sulfate reduction	61.54	8 of 13
66794	tryptophan metabolism	60.53	23 of 38
66794	propionate fermentation	60	6 of 10
66794	vitamin K metabolism	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	3-chlorocatechol degradation	60	3 of 5
66794	degradation of sugar acids	60	15 of 25
66794	alanine metabolism	58.62	17 of 29
66794	arginine metabolism	58.33	14 of 24
66794	lipid metabolism	58.06	18 of 31
66794	d-mannose degradation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	urea cycle	53.85	7 of 13
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	cyclohexanol degradation	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	resorcinol degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	nitrate assimilation	44.44	4 of 9
66794	propanol degradation	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	ascorbate metabolism	40.91	9 of 22
66794	coenzyme M biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	carnitine metabolism	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	polyamine pathway	34.78	8 of 23
66794	arachidonic acid metabolism	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	metabolism of disaccharids	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	alginate biosynthesis	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Contamination
#Environmental	#Aquatic
#Host	#Microbial

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture
25118	contaminated axenic water microcosm					R2A agar (Reasoner's 2A agar)
118738	Other, Contaminant of an axenic E. coli culture in 7% NaCl	Weningerode	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KX427102 (>99% sequence identity) for Paracoccus contaminans subclade from Microbeatlas

Aquatic Samples	127
Soil Samples	31
Animal Samples	590
Plant Samples	7
Total Samples	755

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
118738	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM210555v1 assembly for Paracoccus contaminans RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T	complete	GCA_002105555	1945662.3	2751185828	1945662	96.07

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
25118	Paracoccus contaminans strain WPAn02 16S ribosomal RNA gene, partial sequence	KX427102	1397		1945662

GC content

@ref	GC-content (mol%)	Method
25118	66.1	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paracoccus contaminans strain RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T
PATRIC: 1945662.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.98	yes
125438	anaerobic	anaerobicⓘ	no	94.87	yes
125438	spore-forming	spore-formingⓘ	no	93.27	yes
125438	aerobic	aerobicⓘ	yes	80.39	no
125438	thermophilic	thermophileⓘ	no	92.59	yes
125438	flagellated	motile2+ⓘ	no	57.20	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome Sequence of Paracoccus contaminans LMG 29738(T), Isolated from a Water Microcosm.	Aurass P, Karste S, Trost E, Glaeser SP, Kampfer P, Flieger A	Genome Announc	10.1128/genomeA.00487-17	2017
Phylogeny	Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa.	Rai A, N S, G S, A S, G D, Ch S, Ch V R	Int J Syst Evol Microbiol	10.1099/ijsem.0.003962	2020
Phylogeny	Paracoccus contaminans sp. nov., isolated from a contaminated water microcosm.	Kampfer P, Aurass P, Karste S, Flieger A, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijsem.0.001478	2016

References

#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 )
#25118	P. A. Kämpfer, P.,Karste, S.,Flieger, A.,Glaeser, S. P.: Paracoccus contaminans sp. nov., isolated from a contaminated water microcosm. IJSEM 66: 5101 - 5105 2016 ( DOI 10.1099/ijsem.0.001478 , PubMed 27599853 )
#42176	; Curators of the CIP;
#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 .
#118738	Collection of Institut Pasteur ; Curators of the CIP; CIP 111112
#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 )
#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 )

Rate our new design

Content

About us

Paracoccus contaminans (WPAn02, RKI 16-01929, LMG 29738)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

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_002105555

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media