Name: Paracoccus versutus A2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13705

Type strain:

Species: Paracoccus versutus

Strain Designation: A2

Culture col. no.: DSM 582, ATCC 25364, CCM 2505, IAM 12814, JCM 20754, CIP 107117, IFO 14567, LMD 80.62, LMD 81.78, NBRC 14567, NCCB 80062, NCCB 81078, VKM B-2163

Strain history: CIP <- 2001, CCM <- B.F Taylor and D.S. Hoare

NCBI tax ID(s): 34007 (species)

SI-ID 38520

ATCC 25364, DSM 582, CCM 2505, IAM 12814, IFO 14567, VKM B-2163, LMD 80.62, LMD 81.78, KCTC 2846, CIP 107117, NCCB 80062, NCCB 81078, NBRC 14567, JCM 20754

Special Collections

Other strains from Paracoccus versutus

Section

When using BacDive for research please cite our paper

Paracoccus versutus A2 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from soil.

Gram-negative
rod-shaped
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Paracoccus*
	Species	**Paracoccus versutus**
	Full Scientific Name (LPSN)	Paracoccus versutus (Harrison 1983) Katayama et al. 1996

	Synonym	Thiobacillus rapidicrescens
	Synonym	Thiobacillus versutus

Information on morphological and physiological properties Morphology

[Ref.: #123826]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %96.5
[Ref.: #125439]	Gram stain	negative Confidence in %99.3

[Ref.: #123826]	Cell shape	rod-shaped

[Ref.: #123826]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #299]

Culture medium

STARKEYA NOVELLA MEDIUM (DSMZ Medium 69)

[Ref.: #299]

Culture medium growth

[Ref.: #299]

Culture medium link

Medium recipe at MediaDive

[Ref.: #299]

Culture medium composition

expand / minimize

[Ref.: #33605]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #33605]

Culture medium growth

[Ref.: #33605]

Culture medium composition

expand / minimize

[Ref.: #123826]

Culture medium

CIP Medium 72

[Ref.: #123826]

Culture medium growth

[Ref.: #123826]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #299]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #299]

Culture medium growth

[Ref.: #299]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #299]		growth	30 °C
[Ref.: #33605]		growth	25 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #123826]		growth	25-41 °C
[Ref.: #123826]	no	growth	5 °C
[Ref.: #123826]	no	growth	10 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %95.7

[Ref.: #125438]	Ability of spore formation	no Confidence in %91.123
[Ref.: #125439]	Ability of spore formation	no Confidence in %97.4

	Salt	Tested relation		Salt conc.
[Ref.: #123826]	NaCl		growth	0-6	%
[Ref.: #123826]	NaCl	no	growth	8	%
[Ref.: #123826]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #123826]	esculin ChEBI	-	hydrolysis
[Ref.: #123826]	nitrate ChEBI	+	reduction
[Ref.: #123826]	nitrate ChEBI	+	respiration
[Ref.: #123826]	nitrite ChEBI	+	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #123826]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #123826]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #123826]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #123826]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #123826]	amylase	-
[Ref.: #123826]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #123826]	caseinase	-	3.4.21.50
[Ref.: #123826]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #123826]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #123826]	gelatinase	-
[Ref.: #123826]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #123826]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #123826]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #123826]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #123826]	oxidase	+
[Ref.: #123826]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #123826]	tryptophan deaminase	-
[Ref.: #123826]	tween esterase	+
[Ref.: #123826]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	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
[Ref.: #123826]	2011	not determinedn.d.	+	+	+	+	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-	-	+	-	+	-	-	+	+	+	+	+	+	-	+	+	+	+	+	+	-	-	-	+	-	-	-	-	-	-	+	+	-	-	-	-	-	-	+	+	-	+	+	+	+	+	-	+	+	-	-	-	+	+	-	+	-	+	-	-	-	+	+	-	-	+	-	-	+	-	+	+	+	+	-	+	-	-	+	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #123826]	10079	-	+	+	+	-	+	-	-	-	-	-	+	-	-	-	+	-	-	-	-

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

[Ref.: #299]	Sample type/isolated from	soil

[Ref.: #67770]	Sample type/isolated from	Soil

[Ref.: #123826]	Sample type/isolated from	Enrichment medium for Thiobacillus denitrificans
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence Y16932 (>99% sequence identity) for Paracoccus from Microbeatlas

Aquatic Samples	2441
Soil Samples	932
Animal Samples	1611
Plant Samples	205
Total Samples	5189

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

[Ref.: #299]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123826]	Biosafety level	1	Risk group (French classification)

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

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #299]	Paracoccus versutus 16S ribosomal RNA gene, partial sequence	AY014174	1457	GenBank ENA	34007 tax ID
[Ref.: #67770]	Paracoccus versutus gene for 16S rRNA, partial sequence, strain: NBRC 14567	AB680633	1386	GenBank ENA	34007 tax ID
[Ref.: #124043]	Paracoccus versutus strain NBRC 14567 16S ribosomal RNA gene, partial sequence.	ON406415	1386	GenBank ENA	34007 tax ID	*
[Ref.: #20218]	Paracoccus versutus 16S rRNA gene, strain DSM 582	Y16931	1393	GenBank ENA	34007 tax ID	*
[Ref.: #20218]	Paracoccus versutus 16S rRNA gene, strain ATCC 25364	Y16932	1393	GenBank ENA	34007 tax ID	*
[Ref.: #20218]	Paracoccus versutus gene for 16S rRNA, strain: IAM 12814	D32243	1383	GenBank ENA	34007 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Paracoccus versutus DSM 582	GCA_000763885	contig	GenBank ENA	34007 tax ID
[Ref.: #67770]	Paracoccus versutus DSM 582	GCA_003387045	scaffold	GenBank ENA	34007 tax ID
[Ref.: #66792]	Paracoccus versutus DSM 582	34007.4	wgs	PATRIC	34007 tax ID	*
[Ref.: #66792]	Paracoccus versutus strain DSM 582	34007.16	wgs	PATRIC	34007 tax ID	*
[Ref.: #66792]	Paracoccus versutus DSM 582	2713897089	draft	JGI IMG/M	34007 tax ID	*
[Ref.: #66792]	Paracoccus versutus DSM 582	2615840723	draft	JGI IMG/M	34007 tax ID	*

[Ref.: #299]	GC-content	65.0 mol%
[Ref.: #67770]	GC-content	67.6 mol%	genome sequence analysis

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paracoccus versutus DSM 582 PATRIC: 34007.4
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.5	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.298	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	91.123	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	85.08	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96.435	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	52.642	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paracoccus versutus DSM 582 NCBI: GCA_003387045
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	97.4
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	67.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.3
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	95.7

Availability in culture collections External links

[Ref.: #299]

Culture collection no.

DSM 582, ATCC 25364, CCM 2505, IAM 12814, JCM 20754, CIP 107117, IFO 14567, LMD 80.62, LMD 81.78, NBRC 14567, NCCB 80062, NCCB 81078, VKM B-2163

[Ref.: #82890]

SI-ID 38520

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Involvement of membrane vesicles in long-chain-AHL delivery in Paracoccus species.	Morinaga K, Nagakubo T, Nomura N, Toyofuku M	Environ Microbiol Rep	10.1111/1758-2229.12843	2020	*
Enzymology	Distribution of amine oxidases and amine dehydrogenases in bacteria grown on primary amines and characterization of the amine oxidase from Klebsiella oxytoca.	Hacisalihoglu A, Jongejan JA, Duine JA	Microbiology (Reading)	10.1099/00221287-143-2-505	1997	*
Enzymology	Porin from Thiobacillus versutus.	Woitzik D, Benz R, Lustig A, Weckesser J	FEMS Microbiol Lett	10.1016/0378-1097(89)90238-3	1989	*

References

#299	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 582

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#33605 ; 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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#82890

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-ID38520.1 )

#123826 Collection of Institut Pasteur ; Curators of the CIP; CIP 107117

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#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 .

* These data were automatically processed and therefore are not curated

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Paracoccus versutus DSM 582

Paracoccus versutus DSM 582

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