Paracoccus aminophilus (DSM 8538, ATCC 49673, IAM 14245)

Name: Paracoccus aminophilus (DSM 8538, ATCC 49673, IAM 14245)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13714

Type strain

Strain Designation DM-15

Culture col. no. DSM 8538 ATCC 49673 IAM 14245 JCM 7686 DM-15 5 more

NCBI tax ID(s) 1367847 34003

Special Collections DSMZ JCM CIP

History DSMZ <- JCM <- T. Urakami, DM-15 JCM <-- T. Urakami DM-15. CIP <- 1999, JCM <- T. Urakami: strain DM-15

Links

Paracoccus aminophilus DM-15 is an obligate aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil Niigata Factory of Mitsubishi Gas Chemical Company.

Gram-negative rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 42612

ATCC 49673,JCM 7686,CIP 106077,DSM 8538,IAM 14245,VKM B-2141,IFO 16710,NBRC 16710,KCTC 5068,LMG 23830

@ref 20215

Last LPSN update 2026-05-29 08:28:06

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Paracoccus

Species Paracoccus aminophilus

Full scientific name Paracoccus aminophilus Urakami et al. 1990

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		97.982
125439	negative		95.687
116332	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3239	MEDIUM FOR PARACOCCUS AMINOPHILUS AND P. AMINOVORANS (DSMZ Medium 774)	Medium recipe at MediaDive	Name: MEDIUM FOR PARACOCCUS AMINOPHILUS AND P. AMINOVORANS (DSMZ Medium 774) Composition: Agar 20.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l Distilled water
34679	MEDIUM 199 - for Clavibacter michiganense subsp. insidiosum		Distilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (5.000g);Yeast extract (5.000 g);Peptone (5.000 g)
116332	CIP Medium 364	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
3239	positive	growth	30
34679	positive	growth	30
67770	positive	growth	30
116332	positive	growth	25-41
116332	negative	growth	5
116332	negative	growth	10

Physiology and metabolism

Oxygen tolerance

116332

Oxygen toleranceobligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.112

Halophily

@ref	Salt	Growth	Tested relation	Concentration
116332	NaCl	positive	growth	0-8 %
116332	NaCl		growth	10 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
116332	16947 ChEBI	citrate	-	carbon source
116332	4853 ChEBI	esculin	-	hydrolysis
116332	17632 ChEBI	nitrate	-	reduction
116332	17632 ChEBI	nitrate	-	respiration
116332	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
116332	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116332	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116332	alcohol dehydrogenase	-	1.1.1.1
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
116332	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
116332	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116332	caseinase	-	3.4.21.50
116332	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
116332	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
116332	gelatinase	-
116332	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
116332	lipase	-
68382	lipase (C 14)	-		from API zym
116332	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116332	ornithine decarboxylase	-	4.1.1.17
116332	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
116332	tryptophan deaminase	+
116332	tween esterase	-
116332	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	methane metabolism	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
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	cis-vaccenate biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	octane oxidation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	creatinine degradation	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	photosynthesis	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	proline metabolism	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	allantoin degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	propanol degradation	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	methionine metabolism	84.62	22 of 26
66794	vitamin B1 metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	alanine metabolism	82.76	24 of 29
66794	pyrimidine metabolism	82.22	37 of 45
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	purine metabolism	80.85	76 of 94
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	arginine metabolism	79.17	19 of 24
66794	glutathione metabolism	78.57	11 of 14
66794	tryptophan metabolism	76.32	29 of 38
66794	histidine metabolism	75.86	22 of 29
66794	oxidative phosphorylation	75.82	69 of 91
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	lactate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	vitamin B6 metabolism	72.73	8 of 11
66794	cysteine metabolism	72.22	13 of 18
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	degradation of pentoses	71.43	20 of 28
66794	heme metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	urea cycle	69.23	9 of 13
66794	sulfate reduction	69.23	9 of 13
66794	lysine metabolism	69.05	29 of 42
66794	non-pathway related	68.42	26 of 38
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	IAA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	phenol degradation	65	13 of 20
66794	lipid metabolism	64.52	20 of 31
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	gallate degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	polyamine pathway	56.52	13 of 23
66794	d-mannose degradation	55.56	5 of 9
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	degradation of sugar alcohols	50	8 of 16
66794	carnitine metabolism	50	4 of 8
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	glycogen biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	tyrosine metabolism	50	7 of 14
66794	quinate degradation	50	1 of 2
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	vitamin K metabolism	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	bacilysin biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	d-xylose degradation	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	nitrate assimilation	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	metabolism of disaccharids	27.27	3 of 11
66794	alginate biosynthesis	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22

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
116332	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

API biotype100

@ref	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
116332	not determinedn.d.	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	+	-	-	+	-	+	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
3239	soil Niigata Factory of Mitsubishi Gas Chemical Company	Japan	JPN	Asia
67770	Soil
116332	Environment, Soil	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB681111 (>99% sequence identity) for Paracoccus aminophilus subclade from Microbeatlas

Aquatic Samples	910
Soil Samples	221
Animal Samples	266
Plant Samples	37
Total Samples	1434

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3239	1	Risk group (German classification) According to TRBA 466
116332	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	ASM44499v1 assembly for Paracoccus aminophilus JCM 7686	complete	GCA_000444995	1367847.3	2547132467	1367847	98.01

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
3239	Paracoccus aminophilus gene for 16S rRNA, partial sequence, strain: NBRC 16710	AB681111	1388	34003
3239	Paracoccus aminophilus gene for 16S rRNA, strain: JCM 7686	D32239	1385	34003
3239	Paracoccus aminophilus 16S ribosomal RNA gene, partial sequence	AY014176	1458	34003

GC content

@ref	GC-content (mol%)	Method
3239	62.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM44499v1 assembly for Paracoccus aminophilus JCM 7686
BV-BRC: 1367847.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	95.69	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	86.73	no
125439	motility	BacteriaNetⓘ	no	60.39	no
125439	spore_formation	BacteriaNetⓘ	no	99.11	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paracoccus aminophilus JCM 7686 JCM 7686
NCBI: GCA_000444995.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.98	no
125438	anaerobic	anaerobicⓘ	no	94.73	yes
125438	aerobic	aerobicⓘ	yes	84.10	yes
125438	spore-forming	spore-formingⓘ	no	89.66	no
125438	thermophilic	thermophileⓘ	no	98.25	yes
125438	flagellated	motile2+ⓘ	yes	61.23	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-wide comparative analysis of clinical and environmental strains of the opportunistic pathogen Paracoccus yeei (Alphaproteobacteria).	Szuplewska M, Sentkowska D, Lasek R, Decewicz P, Halucha M, Funk L, Chmielowska C, Bartosik D.	Front Microbiol	10.3389/fmicb.2024.1483110	2024
	Characterization and genome sequence of N,N-dimethylformamide degradation in Paracoccus sulfuroxidans DM175A1-1 isolated from activated sludge of wastewater.	Zheng G, Su Y, Zhang W, Liu X, Shao L, Shen Z, Zhang D, Wang K, Miao Z.	Front Microbiol	10.3389/fmicb.2024.1419461	2024
Metabolism	Pigmentiphaga sp. Strain D-2 Uses a Novel Amidase To Initiate the Catabolism of the Neonicotinoid Insecticide Acetamiprid.	Yang H, Hu S, Wang X, Chuang S, Jia W, Jiang J.	Appl Environ Microbiol	10.1128/aem.02425-19	2020
	Differential Localization and Functional Specialization of parS Centromere-Like Sites in repABC Replicons of Alphaproteobacteria.	Czarnecki J, Chapkauskaitse E, Bos J, Sentkowska D, Wawrzyniak P, Wyszynska A, Szuplewska M, Bartosik D.	Appl Environ Microbiol	10.1128/aem.00207-22	2022
	Genome-Wide Discovery of Putative sRNAs in Paracoccus denitrificans Expressed under Nitrous Oxide Emitting Conditions.	Gaimster H, Chalklen L, Alston M, Munnoch JT, Richardson DJ, Gates AJ, Rowley G.	Front Microbiol	10.3389/fmicb.2016.01806	2016
Genetics	Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp.	Decewicz P, Golec P, Szymczak M, Radlinska M, Dziewit L.	Int J Mol Sci	10.3390/ijms21062096	2020
	Plasmid composition in Aeromonas salmonicida subsp. salmonicida 01-B526 unravels unsuspected type three secretion system loss patterns.	Tanaka KH, Vincent AT, Emond-Rheault JG, Adamczuk M, Frenette M, Charette SJ.	BMC Genomics	10.1186/s12864-017-3921-1	2017
Metabolism	In vivo creation of plasmid pCRT01 and its use for the construction of carotenoid-producing Paracoccus spp. strains that grow efficiently on industrial wastes.	Maj A, Dziewit L, Drewniak L, Garstka M, Krucon T, Piatkowska K, Gieczewska K, Czarnecki J, Furmanczyk E, Lasek R, Baj J, Bartosik D.	Microb Cell Fact	10.1186/s12934-020-01396-z	2020
Metabolism	Plasmids of carotenoid-producing Paracoccus spp. (Alphaproteobacteria) - structure, diversity and evolution.	Maj A, Dziewit L, Czarnecki J, Wlodarczyk M, Baj J, Skrzypczyk G, Giersz D, Bartosik D.	PLoS One	10.1371/journal.pone.0080258	2013
Genetics	Draft genomic sequence of a selenite-reducing bacterium, Paenirhodobacter enshiensis DW2-9(T).	Wang D, Zhu F, Zhu X, Zheng S, Wang R, Wang G.	Stand Genomic Sci	10.1186/s40793-015-0026-9	2015
Metabolism	Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway.	Lidbury I, Mausz MA, Scanlan DJ, Chen Y.	ISME J	10.1038/ismej.2017.31	2017
Metabolism	Benefits and Drawbacks of Harboring Plasmid pP32BP2, Identified in Arctic Psychrophilic Bacterium Psychrobacter sp. DAB_AL32B.	Ciok A, Cegielski A, Bartosik D, Dziewit L.	Int J Mol Sci	10.3390/ijms20082015	2019
Phylogeny	Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids.	Romaniuk K, Styczynski M, Decewicz P, Buraczewska O, Uhrynowski W, Fondi M, Wolosiewicz M, Szuplewska M, Dziewit L.	Genes (Basel)	10.3390/genes10110850	2019
Metabolism	Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome.	Decewicz P, Radlinska M, Dziewit L.	Viruses	10.3390/v9070161	2017
	Phasing of single DNA molecules by massively parallel barcoding.	Borgstrom E, Redin D, Lundin S, Berglund E, Andersson AF, Ahmadian A.	Nat Commun	10.1038/ncomms8173	2015
Metabolism	Conserved small mRNA with an unique, extended Shine-Dalgarno sequence.	Hahn J, Thalmann S, Migur A, von Boeselager RF, Kubatova N, Kubareva E, Schwalbe H, Evguenieva-Hackenberg E.	RNA Biol	10.1080/15476286.2016.1256534	2017
Metabolism	A novel siderophore system is essential for the growth of Pseudomonas aeruginosa in airway mucus.	Gi M, Lee KM, Kim SC, Yoon JH, Yoon SS, Choi JY.	Sci Rep	10.1038/srep14644	2015
	The SXT conjugative element and linear prophage N15 encode toxin-antitoxin-stabilizing systems homologous to the tad-ata module of the Paracoccus aminophilus plasmid pAMI2.	Dziewit L, Jazurek M, Drewniak L, Baj J, Bartosik D.	J Bacteriol	10.1128/jb.01610-06	2007
	Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals.	Dziewit L, Pyzik A, Szuplewska M, Matlakowska R, Mielnicki S, Wibberg D, Schluter A, Puhler A, Bartosik D.	Front Microbiol	10.3389/fmicb.2015.00152	2015
	Thermodynamic matchers for the construction of the cuckoo RNA family.	Reinkensmeier J, Giegerich R.	RNA Biol	10.1080/15476286.2015.1017206	2015
	Mobility and generation of mosaic non-autonomous transposons by Tn3-derived inverted-repeat miniature elements (TIMEs).	Szuplewska M, Ludwiczak M, Lyzwa K, Czarnecki J, Bartosik D.	PLoS One	10.1371/journal.pone.0105010	2014
Phylogeny	Characterization of Halomonas sp. ZM3 isolated from the Zelazny Most post-flotation waste reservoir, with a special focus on its mobile DNA.	Dziewit L, Pyzik A, Matlakowska R, Baj J, Szuplewska M, Bartosik D.	BMC Microbiol	10.1186/1471-2180-13-59	2013
	Coevolution of the ATPase ClpV, the sheath proteins TssB and TssC, and the accessory protein TagJ/HsiE1 distinguishes type VI secretion classes.	Forster A, Planamente S, Manoli E, Lossi NS, Freemont PS, Filloux A.	J Biol Chem	10.1074/jbc.m114.600510	2014
Metabolism	Engineering of an oleate hydratase for efficient C10-Functionalization of oleic acid.	Sun QF, Zheng YC, Chen Q, Xu JH, Pan J.	Biochem Biophys Res Commun	10.1016/j.bbrc.2020.12.039	2021
	Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study.	Zhu C, Li L-Y, Li C, Wu L, Zhang Y-Y, Yao Y, Yang J, Wang S-Y, Xing L-M, Zeng X-T, Fang C.	Microbiol Spectr	10.1128/spectrum.03376-24	2025
	Bacterial structure of aerobic granules is determined by aeration mode and nitrogen load in the reactor cycle.	Cydzik-Kwiatkowska A.	Bioresour Technol	10.1016/j.biortech.2015.01.101	2015
Metabolism	Exploration of the 1-deoxy-d-xylulose 5-phosphate synthases suitable for the creation of a robust isoprenoid biosynthesis system.	Kudoh K, Kubota G, Fujii R, Kawano Y, Ihara M.	J Biosci Bioeng	10.1016/j.jbiosc.2016.10.005	2017
	Prospects of formamide as nitrogen source in biotechnological production processes.	Schwardmann LS, Benninghaus L, Lindner SN, Wendisch VF.	Appl Microbiol Biotechnol	10.1007/s00253-023-12962-x	2024
	Characterization of an accessory plasmid of Sinorhizobium meliloti and its two replication-modules.	Luchetti A, Castellani LG, Toscani AM, Lagares A, Del Papa MF, Torres Tejerizo G, Pistorio M.	PLoS One	10.1371/journal.pone.0285505	2023
Genetics	Thermal Endurance by a Hot-Spring-Dwelling Phylogenetic Relative of the Mesophilic Paracoccus.	Mondal N, Roy C, Chatterjee S, Sarkar J, Dutta S, Bhattacharya S, Chakraborty R, Ghosh W.	Microbiol Spectr	10.1128/spectrum.01606-22	2022
Metabolism	A Central Small RNA Regulatory Circuit Controlling Bacterial Denitrification and N₂O Emissions.	Gaimster H, Hews CL, Griffiths R, Soriano-Laguna MJ, Alston M, Richardson DJ, Gates AJ, Rowley G.	mBio	10.1128/mbio.01165-19	2019
	Molecular, Physiological and Phenotypic Characterization of Paracoccus denitrificans ATCC 19367 Mutant Strain P-87 Producing Improved Coenzyme Q10.	Tokdar P, Sanakal A, Ranadive P, Khora SS, George S, Deshmukh SK.	Indian J Microbiol	10.1007/s12088-014-0506-4	2015
Metabolism	A New Catabolic Plasmid in Xanthobacter and Starkeya spp. from a 1,2-Dichloroethane-Contaminated Site.	Munro JE, Liew EF, Ly MA, Coleman NV.	Appl Environ Microbiol	10.1128/aem.01373-16	2016
Pathogenicity	Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance.	Loftie-Eaton W, Yano H, Burleigh S, Simmons RS, Hughes JM, Rogers LM, Hunter SS, Settles ML, Forney LJ, Ponciano JM, Top EM.	Mol Biol Evol	10.1093/molbev/msv339	2016
	A toxin-antitoxin system promotes the maintenance of an integrative conjugative element.	Wozniak RA, Waldor MK.	PLoS Genet	10.1371/journal.pgen.1000439	2009
Metabolism	A bioinformatic survey of distribution, conservation, and probable functions of LuxR solo regulators in bacteria.	Subramoni S, Florez Salcedo DV, Suarez-Moreno ZR.	Front Cell Infect Microbiol	10.3389/fcimb.2015.00016	2015
	Comparative genomic analysis of ten Streptococcus pneumoniae temperate bacteriophages.	Romero P, Croucher NJ, Hiller NL, Hu FZ, Ehrlich GD, Bentley SD, Garcia E, Mitchell TJ.	J Bacteriol	10.1128/jb.01272-08	2009
Metabolism	Unexpected diversity of bacteria capable of carbon monoxide oxidation in a coastal marine environment, and contribution of the Roseobacter-associated clade to total CO oxidation.	Tolli JD, Sievert SM, Taylor CD.	Appl Environ Microbiol	10.1128/aem.72.3.1966-1973.2006	2006
Metabolism	Diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents.	Teske A, Brinkhoff T, Muyzer G, Moser DP, Rethmeier J, Jannasch HW.	Appl Environ Microbiol	10.1128/aem.66.8.3125-3133.2000	2000
Metabolism	Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes.	Makarova KS, Wolf YI, Koonin EV.	Biol Direct	10.1186/1745-6150-4-19	2009
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	Enzymatic synthesis of 10-oxostearic acid in high space-time yield via cascade reaction of a new oleate hydratase and an alcohol dehydrogenase.	Wu YX, Pan J, Yu HL, Xu JH	J Biotechnol	10.1016/j.btecx.2019.100008	2019
	Genome-guided insight into the methylotrophy of Paracoccus aminophilus JCM 7686.	Dziewit L, Czarnecki J, Prochwicz E, Wibberg D, Schluter A, Puhler A, Bartosik D	Front Microbiol	10.3389/fmicb.2015.00852	2015
Genetics	Maintenance and genetic load of plasmid pKON1 of Paracoccus kondratievae, containing a highly efficient toxin-antitoxin module of the hipAB family.	Czarnecki J, Dziewit L, Kowalski L, Ochnio M, Bartosik D	Plasmid	10.1016/j.plasmid.2015.02.003	2015
Genetics	Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids.	Dziewit L, Czarnecki J, Wibberg D, Radlinska M, Mrozek P, Szymczak M, Schluter A, Puhler A, Bartosik D	BMC Genomics	10.1186/1471-2164-15-124	2014
Metabolism	Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilus JCM 7686.	Dziewit L, Kuczkowska K, Adamczuk M, Radlinska M, Bartosik D	FEMS Microbiol Lett	10.1111/j.1574-6968.2011.02388.x	2011
Enzymology	DIY series of genetic cassettes useful in construction of versatile vectors specific for Alphaproteobacteria.	Dziewit L, Adamczuk M, Szuplewska M, Bartosik D	J Microbiol Methods	10.1016/j.mimet.2011.04.016	2011
Metabolism	Plasmid pAMI2 of Paracoccus aminophilus JCM 7686 carries N,N-dimethylformamide degradation-related genes whose expression is activated by a LuxR family regulator.	Dziewit L, Dmowski M, Baj J, Bartosik D	Appl Environ Microbiol	10.1128/AEM.01926-09	2010
Phylogeny	Paracoccus lutimaris sp. nov., isolated from a tidal flat sediment.	Jung YT, Park S, Lee JS, Yoon JH.	Int J Syst Evol Microbiol	10.1099/ijs.0.064865-0	2014
Phylogeny	Paracoccus thiocyanatus sp. nov., a new species of thiocyanate-utilizing facultative chemolithotroph, and transfer of Thiobacillus versutus to the genus Paracoccus as Paracoccus versutus comb. nov. with emendation of the genus.	Katayama Y, Hiraishi A, Kuraishi H.	Microbiology (Reading)	10.1099/13500872-141-6-1469	1995
Phylogeny	Paracoccus cavernae sp. nov., isolated from a show cave.	Dominguez-Monino I, Jurado V, Hermosin B, Saiz-Jimenez C	Int J Syst Evol Microbiol	10.1099/ijsem.0.001018	2016
Phylogeny	Paracoccus zhejiangensis sp. nov., isolated from activated sludge in wastewater-treatment system.	Wu ZG, Zhang DF, Liu YL, Wang F, Jiang X, Li C, Li SP, Hong Q, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-013-9932-2	2013
Phylogeny	Paracoccus marinus sp. nov., an adonixanthin diglucoside-producing bacterium isolated from coastal seawater in Tokyo Bay.	Khan ST, Takaichi S, Harayama S	Int J Syst Evol Microbiol	10.1099/ijs.0.65103-0	2008
Phylogeny	Paracoccus aminophilus sp. nov. and Paracoccus aminovorans sp. nov., which utilize N,N-dimethylformamide.	Urakami T, Araki H, Oyanagi H, Suzuki K, Komagata K	Int J Syst Bacteriol	10.1099/00207713-40-3-287	1990

References

#3239	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 8538
#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 )
#34679	; 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 )
#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 .
#116332	Collection of Institut Pasteur ; Curators of the CIP; CIP 106077
#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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Paracoccus aminophilus (DSM 8538, ATCC 49673, IAM 14245)

Name and taxonomic classification

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Physiology and metabolism

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