Pseudomonas parafulva (DSM 17004, AJ 2129, IFO 16636)

Name: Pseudomonas parafulva (DSM 17004, AJ 2129, IFO 16636)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13108

Type strain

Strain Designation CB-1

Culture col. no. DSM 17004 AJ 2129 IFO 16636 JCM 11244 NRIC 0501 4 more

NCBI tax ID(s) 1215114 157782

Special Collections DSMZ JCM CIP

History DSMZ <- M. Uchino,Tokyo University of Agriculture; NRIC 0501 JCM <-- M. Uchino <-- AJ 2129 <-- H. Iizuka and K. Komagata CB-1. CIP <- 2002, JCM <- M. Uchino <- AJ 2127 <- H. Iizuka and K. Komagata: strain CB-1

Links

Pseudomonas parafulva CB-1 is an obligate aerobe, Gram-negative, motile bacterium that was isolated from Oryza sativa.

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

Name and taxonomic classification

SI-ID 88072

IFO 16636,JCM 11244,CIP 107617,NBRC 16636,DSM 17004,LMG 24038,BCRC 17511,CCRC 17511

@ref 20215

Last LPSN update 2026-05-29 08:27:58

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Pseudomonas

Species Pseudomonas parafulva

Full scientific name Pseudomonas parafulva Uchino et al. 2002

BacDive ID	Other strains from **Pseudomonas parafulva** (1)	Type strain
161143	P. parafulva JCM 11245, IFO 16635, NBRC 16635

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
121557	negative	rod-shaped
125439	negative		94.407
125438	negative		99

Pigmentation

@ref	Production	Name
121557		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
39907	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
6684	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
121557	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6684	positive	growth	28
39907	positive	growth	30
67770	positive	growth	30
121557	positive	growth	10-37
121557	negative	growth	5
121557	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
121557	obligate aerobe
125438	aerobe	91.849
125439	obligate aerobe	90.686

Spore formation

@ref	Spore formation	Confidence
125439		99.622

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121557	NaCl	positive	growth	0-4 %
121557	NaCl		growth	6 %
121557	NaCl		growth	8 %
121557	NaCl		growth	10 %

Observation

67770

Observationquinones: Q-9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	+	hydrolysis	from API 20NE
121557	16947 ChEBI	citrate	+	carbon source
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
121557	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
121557	17632 ChEBI	nitrate	-	reduction
121557	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
121557	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121557	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
121557	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121557	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
121557	amylase	-
68369	arginine dihydrolase	+	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
121557	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121557	caseinase	-	3.4.21.50
121557	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
121557	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121557	gelatinase	-
68369	gelatinase	-		from API 20NE
121557	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121557	lipase	-
68382	lipase (C 14)	-		from API zym
121557	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
121557	ornithine decarboxylase	-	4.1.1.17
121557	oxidase	+
121557	protease	-
68382	trypsin	-	3.4.21.4	from API zym
121557	tryptophan deaminase	-
121557	tween esterase	-
121557	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

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
121557	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
6684	-	-	-	+	-	-	-	-	+	-	+	-	-	-	+	+	-	+	+	+	+
6684	-	-	+	+	-	-	-	-	+	-	+	-	-	-	+	+	-	+	+	+	+

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
121557	not determinedn.d.	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	+	+	-	-	+	-	-	+	-	-	-	+	+	+	+	+	-	-	-	-	-	+	+	+	+	-	+	+	+	+	+	+	+	-	+	+	-	-	-	+	+	+	+	+	+	+	-	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
6684	Oryza sativa	Oryza sativa	Japan	JPN	Asia
67770	Japanese rice paddy
121557	Food, Japanese rice paddy		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC507438 (>99% sequence identity) for Pseudomonas from Microbeatlas

Aquatic Samples	36
Soil Samples	47
Animal Samples	93
Plant Samples	74
Total Samples	250

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6684	1	Risk group (German classification) According to TRBA 466
121557	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
67770	ASM42576v1 assembly for Pseudomonas parafulva NBRC 16636 = DSM 17004	scaffold	GCA_000425765	1292029.3	2523533547	1215114	70.32
67770	ASM73064v1 assembly for Pseudomonas parafulva NBRC 16636 = DSM 17004	contig	GCA_000730645	1215114.3	2585427683	1215114	68.92

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
6684	Pseudomonas parafulva gene for 16S rRNA, partial sequence, strain: AJ 2129	AB060132	1484	1215114
67770	Pseudomonas parafulva JCM 11244 gene for 16S ribosomal RNA, partial sequence	LC507438	1459	157782
124043	Pseudomonas parafulva gene for 16S rRNA, partial sequence, strain: NBRC 16636.	AB681092	1462	1215114
124043	Pseudomonas parafulva NBRC 16636 = DSM 17004 strain C101 16S ribosomal RNA gene, partial sequence.	OR122184	1344	1215114
124043	Pseudomonas parafulva NBRC 16636 = DSM 17004 strain AJ 2129 16S ribosomal RNA gene, partial sequence.	MH613281	650	1215114
124043	Pseudomonas parafulva NBRC 16636 = DSM 17004 strain AJ 2129 16S ribosomal RNA gene, partial sequence.	MH620456	801	1215114

GC content

@ref	GC-content (mol%)	Method
67770	60	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: ASM42576v1 assembly for Pseudomonas parafulva NBRC 16636 = DSM 17004
BV-BRC: 1292029.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.69	no
125439	gram_stain	BacteriaNetⓘ	negative	94.41	no
125439	motility	BacteriaNetⓘ	yes	81.86	no
125439	spore_formation	BacteriaNetⓘ	no	99.62	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas parafulva DSM 17004
PATRIC: 1292029.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	99.38	no
125438	spore-forming	spore-formingⓘ	no	84.59	no
125438	aerobic	aerobicⓘ	yes	91.85	yes
125438	thermophilic	thermophileⓘ	no	98.49	yes
125438	flagellated	motile2+ⓘ	yes	86.37	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1.	Kumari K, Rawat V, Shadan A, Sharma PK, Deb S, Singh RP.	Front Microbiol	10.3389/fmicb.2023.1140249	2023
	The Indiscriminate Chemical Makeup of Secondary Metabolites Derived from Endophytes Harvested from Aloe barbadensis Miller in South Africa's Limpopo Region.	Nchabeleng MM, Fonkui TY, Ezekiel G.	Molecules	10.3390/molecules29061297	2024
Genetics	Draft genome sequence data of a 4-nitrophenol- degrading bacterium, Pseudomonas alloputida strain PNP.	Arora PK, Saroj RS, Mishra R, Omar RA, Kumari P, Srivastava A, Garg SK, Singh VP.	Data Brief	10.1016/j.dib.2021.107390	2021
	Bacterial Isolates Associated with Mortality Events in Brown Trout (Salmo trutta) Restocking Farms in Spain: A Descriptive Field Study.	Vargas-Gonzalez A, Barajas M, Perez-Sanchez T.	Animals (Basel)	10.3390/ani15172532	2025
	Antifungal Activity of Phyllospheric Bacteria Isolated from Coffea arabica against Hemileia vastatrix.	Ogata-Gutierrez K, Chumpitaz-Segovia C, Lirio-Paredes J, Zuniga-Davila D.	Microorganisms	10.3390/microorganisms12030582	2024
Phylogeny	Algal-bacterial bioremediation of cyanide-containing wastewater in a continuous stirred photobioreactor.	AbdelMageed MF, ElRakaiby MT.	World J Microbiol Biotechnol	10.1007/s11274-024-04230-5	2025
Genetics	Identification and specificity validation of unique and antimicrobial resistance genes to trace suspected pathogenic AMR bacteria and to monitor the development of AMR in non-AMR strains in the environment and clinical settings.	Rekadwad BN, Pramod N, Rao MPN, Hashem A, Avila-Quezada GD, Abd Allah EF.	Saudi J Biol Sci	10.1016/j.sjbs.2023.103869	2023
Phylogeny	Phylogenetic affiliation and determination of bioactive compounds of bacterial population associated with organs of mud crab, Scylla olivacea.	Zote J, Passari AK, Zothanpuia, Siddaiah CN, Kumar NS, Abd Allah EF, Hashem A, Alqarawi AA, Malik JA, Singh BP.	Saudi J Biol Sci	10.1016/j.sjbs.2018.08.025	2018
Genetics	High quality draft genome sequences of Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and Pseudomonas cremoricolorata DSM 17059(T) type strains.	Pena A, Busquets A, Gomila M, Mulet M, Gomila RM, Reddy TB, Huntemann M, Pati A, Ivanova N, Markowitz V, Garcia-Valdes E, Goker M, Woyke T, Klenk HP, Kyrpides N, Lalucat J	Stand Genomic Sci	10.1186/s40793-016-0178-2	2016
Phylogeny	Pseudomonas jilinensis sp. nov., Isolated from Oil Production Water of Jilin Oilfield in China.	Wang JW, Cai M, Nie Y, Hu B, Yang Y, Wu XL	Curr Microbiol	10.1007/s00284-019-01798-2	2019
Phylogeny	Pseudomonas pachastrellae sp. nov., isolated from a marine sponge.	Romanenko LA, Uchino M, Falsen E, Frolova GM, Zhukova NV, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.63176-0	2005
Phylogeny	Recharacterization of Pseudomonas fulva Iizuka and Komagata 1963, and proposals of Pseudomonas parafulva sp. nov. and Pseudomonas cremoricolorata sp. nov.	Uchino M, Shida O, Uchimura T, Komagata K	J Gen Appl Microbiol	10.2323/jgam.47.247	2001

References

#6684	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17004
#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 )
#39907	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#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 .
#121557	Collection of Institut Pasteur ; Curators of the CIP; CIP 107617
#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 .
#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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Pseudomonas parafulva (DSM 17004, AJ 2129, IFO 16636)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000425765

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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