Pseudomonas chlororaphis subsp. piscium (DSM 21509, NCIMB 14478, JF3835)

Name: Pseudomonas chlororaphis subsp. piscium (DSM 21509, NCIMB 14478, JF3835)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13181

Type strain

Strain Designation JF3835

Culture col. no. DSM 21509 NCIMB 14478 JF3835 CIP 110232

NCBI tax ID(s) 1513890

Special Collections DSMZ CIP

History CIP <- 2010, J. Frey, Bern Univ., Bern, Switzerland: strain JF3835 DSMZ <- S. E. Burr, Univ. Bern, Switzerland; JF3835 <- E. Goldschmitt-Clermont CIP <- 2010, J. Frey, Bern Univ., Bern, Switzerland: strain JF3835

Links

Pseudomonas chlororaphis subsp. piscium JF3835 is an obligate aerobe, Gram-negative, motile bacterium that was isolated from distal intestine of a European perch .

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

Name and taxonomic classification

SI-ID 374143

DSM 21509,NCIMB 14478,CIP 110232

@ref 20215

Last LPSN update 2026-05-29 08:27:59

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Pseudomonas

Species Pseudomonas chlororaphis subsp. piscium

Full scientific name Pseudomonas chlororaphis subsp. piscium Burr et al. 2010

Synonyms (1)

"Pseudomonas piscium"

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
118244	negative	rod-shaped
125439	negative		94.851
125438			91.973
125438	negative		98

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15754	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
37587	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118244	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
15754	positive	growth	28
37587	positive	growth	25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
118244	obligate aerobe
125438	aerobe	92.047

Spore formation

@ref	Spore formation	Confidence
125439		99.261

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
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	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
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
118244	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
118244	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
118244	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
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
68369	arginine dihydrolase	+	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
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
118244	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
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	+		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118244	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
118244	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
118244	-	+	+	+	-	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-

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
15754	+	-	-	+	-	-	+	-	+	-	+	+	+	-	+	+	-	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Fishes
#Host Body-Site	#Gastrointestinal tract

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
15754	distal intestine of a European perch (Perca fluviatilis L.)	Perca fluviatilis	Lake of Neuchatel	Switzerland	CHE	Europe
118244	European perch, distal intestine, Perca fluviatilis		Neuchâtel lake	Switzerland	CHE	Europe	2006

Taxonmaps

69479

Global distribution of 16S sequence FJ168539 (>99% sequence identity) for Pseudomonas from Microbeatlas

Aquatic Samples	1
Soil Samples	3
Animal Samples	6
Plant Samples	3
Total Samples	13

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15754	1	Risk group (German classification) According to TRBA 466
118244	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	ASM2874738v1 assembly for Pseudomonas chlororaphis DSM 21509	complete	GCA_028747385	587753.152	8088455273	587753	97.25
66792	ASM385034v1 assembly for Pseudomonas chlororaphis subsp. piscium DSM 21509	complete	GCA_003850345	1513890.7	2917064153	1513890	95.99
66792	IMG-taxon 2667528180 annotated assembly for Pseudomonas chlororaphis DSM 21509	chromosome	GCA_900104995	587753.26	2667528180	587753	87.51
66792	ASM126955v1 assembly for Pseudomonas chlororaphis subsp. piscium DSM 21509	contig	GCA_001269555	1513890.3	2917178910	1513890	70.71

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15754	Pseudomonas chlororaphis subsp. piscium strain JF3835 16S ribosomal RNA gene, partial sequence	FJ168539	1239		1513890

GC content

@ref	GC-content (mol%)	Method
15754	62.9	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: ASM2874738v1 assembly for Pseudomonas chlororaphis DSM 21509
NCBI: GCA_028747385

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	81.23	no
125439	gram_stain	BacteriaNetⓘ	negative	94.85	no
125439	spore_formation	BacteriaNetⓘ	no	99.26	no
125439	motility	BacteriaNetⓘ	yes	84.44	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas chlororaphis subsp. piscium DSM 21509
NCBI: GCA_003850345.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	no
125438	anaerobic	anaerobicⓘ	no	99.32	yes
125438	aerobic	aerobicⓘ	yes	92.05	no
125438	spore-forming	spore-formingⓘ	no	82.02	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	yes	91.97	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Potential of Subterranean Microbes: High-Throughput Screening for Industrially Relevant Enzymatic Activities in Dinaric Caves.	Babinskas J, Krutkevicius J, Bilela LL, Besta-Gajevic R, Matijosyte I.	Microbiologyopen	10.1002/mbo3.70146	2025
Phylogeny	Phenazines are involved in the antagonism of a novel subspecies of Pseudomonas chlororaphis strain S1Bt23 against Pythium ultimum.	Chi SI, Akuma M, Xu R, Plante V, Hadinezhad M, Tambong JT.	Sci Rep	10.1038/s41598-024-71418-y	2024
	Genome Mining Enabled by Biosynthetic Characterization Uncovers a Class of Benzoxazolinate-Containing Natural Products in Diverse Bacteria.	Shi YM, Crames JJ, Czech L, Bozhuyuk KAJ, Shi YN, Hirschmann M, Lamberth S, Claus P, Paczia N, Ruckert C, Kalinowski J, Bange G, Bode HB.	Angew Chem Int Ed Engl	10.1002/anie.202206106	2022
Genetics	Comprehensive genome analysis of Pseudomonas sp. SWRIQ11, a new plant growth-promoting bacterium that alleviates salinity stress in olive.	Zamanzadeh-Nasrabadi SM, Mohammadiapanah F, Sarikhan S, Shariati V, Saghafi K, Hosseini-Mazinani M.	3 Biotech	10.1007/s13205-023-03755-0	2023
	Global analysis of biosynthetic gene clusters reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria.	Shi YM, Hirschmann M, Shi YN, Ahmed S, Abebew D, Tobias NJ, Grun P, Crames JJ, Poschel L, Kuttenlochner W, Richter C, Herrmann J, Muller R, Thanwisai A, Pidot SJ, Stinear TP, Groll M, Kim Y, Bode HB.	Nat Chem	10.1038/s41557-022-00923-2	2022
Metabolism	Regulation of phenazine-1-carboxamide production by quorum sensing in type strains of Pseudomonas chlororaphis subsp. chlororaphis and Pseudomonas chlororaphis subsp. piscium.	Morohoshi T, Yabe N, Yaguchi N, Xie X, Someya N	J Biosci Bioeng	10.1016/j.jbiosc.2022.03.004	2022
	Plant growth promotion of the forage plant Lupinus albus Var. Orden Dorado using Pseudomonas agronomica sp. nov. and Bacillus pretiosus sp. nov. added over a valorized agricultural biowaste.	Robas Mora M, Fernandez Pastrana VM, Oliva LLG, Lobo AP, Jimenez Gomez PA.	Front Microbiol	10.3389/fmicb.2022.1046201	2022
Phylogeny	Pseudomonas chlororaphis subsp. piscium subsp. nov., isolated from freshwater fish.	Burr SE, Gobeli S, Kuhnert P, Goldschmidt-Clermont E, Frey J	Int J Syst Evol Microbiol	10.1099/ijs.0.011692-0	2010

References

#15754	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21509
#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 )
#37587	; 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) .
#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 .
#118244	Collection of Institut Pasteur ; Curators of the CIP; CIP 110232
#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 chlororaphis subsp. piscium (DSM 21509, NCIMB 14478, JF3835)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_028747385

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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