Pseudomonas synxantha (DSM 18928, ATCC 9890, CIP 59.22)

Name: Pseudomonas synxantha (DSM 18928, ATCC 9890, CIP 59.22)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13065

Type strain

Culture col. no. DSM 18928 ATCC 9890 CIP 59.22 LMG 2335 NCDO 757 11 more

NCBI tax ID(s) 1215118 47883

Special Collections DSMZ CCUG JCM CIP

History <- CIP <- NCIB (P. fluorescens) <- ATCC <- R.S. Breed, Cornell Univ. (Flavobacterium synthaxum) IFO 3913 <-- ATCC 9890 <-- R. S. Breed <-- B. W. Hammer. CIP <- 1959, NCIB, Pseudomonas fluorescens <- 1950 ATCC, R.S. Breed, Cornell Univ., New-York, USA, Flavobacterium synthaxum

Links

Pseudomonas synxantha DSM 18928 is an aerobe, Gram-negative, motile bacterium that was isolated from cream.

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

Name and taxonomic classification

SI-ID 92404

LMG 2190,ATCC 9890,IAM 12356,IFO 3906,IFO 3913,LMG 2335,NCDO 757,NCIB 8178,NCTC 10696,NRRL B-780,NCIMB 8178,CIP 59.22,JCM 11599,NBRC 3913,CFBP 5591,NBRC 3906,BCRC 11022,CCRC 11022,CCUG 50208,CCUG 561,KCTC 12499,NRRL B-1645,DSM 18928,CGMCC 1.3353

@ref 20215

Last LPSN update 2026-02-09 11:21:01

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Pseudomonas

Species Pseudomonas synxantha

Full scientific name Pseudomonas synxantha (Ehrenberg 1840) Holland 1920 (Approved Lists 1980)

Synonyms (1)

"Vibrio synxanthus"

BacDive ID	Other strains from **Pseudomonas synxantha** (2)	Type strain
13064	P. synxantha G, DSM 13080
154583	P. synxantha CCUG 54472

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
123400	negative	rod-shaped
125438			90.818
125438	negative		97
125439	negative		97.1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7789	REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37601	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
123400	CIP Medium 3	Medium recipe at CIP
123400	CIP Medium 72	Medium recipe at CIP
7789	PSEUDOMONAS AGAR F (DSMZ Medium 907)	Medium recipe at MediaDive	Name: PSEUDOMONAS AGAR F (DSMZ Medium 907) Composition: Agar 15.0 g/l Glycerol 10.0 g/l Proteose peptone 10.0 g/l Tryptone 10.0 g/l MgSO4 1.5 g/l K2HPO4 1.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7789	positive	growth	28
37601	positive	growth	30
58786	positive	growth	28
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
58786	aerobe
123400	obligate aerobe
125438	aerobe	92.799

Spore formation

@ref	Spore formation	Confidence
123400
125439		95.2

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
123400	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
123400	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
123400	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
123400	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
123400	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
123400	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
123400	-	+	+	+	-	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-

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
7789	+	-	-	+	-	-	+	-	+	+	+	+	+	-	+	+	-	+	+	-	+
7789	+	-	-	+	-	-	+	-	+	+	+	+	+	-	+	+	-	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Dairy product

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7789	cream	Iowa	USA	USA	North America
58786	Cream
67770	Cream
123400	Food, Milk	Iowa	United States of America	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence D84025 (>99% sequence identity) for Pseudomonas from Microbeatlas

Aquatic Samples	1631
Soil Samples	874
Animal Samples	3216
Plant Samples	2451
Total Samples	8172

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7789	1	Risk group (German classification) According to TRBA 466
123400	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	45076_A01 assembly for Pseudomonas synxantha NCTC10696	complete	GCA_901482615	47883.23	8116416863	47883	97.87
67770	IMG-taxon 2667527385 annotated assembly for Pseudomonas synxantha LMG 2190	chromosome	GCA_900105675	47883.6	2667527385	47883	89.09
67770	G8689 assembly for Pseudomonas synxantha DSM 18928	contig	GCA_001439725	47883.4	2660238513	47883	66.52
67770	ASM209179v1 assembly for Pseudomonas synxantha NBRC 3913	contig	GCA_002091795	1215118.3	2969229168	1215118	64

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
7789	Pseudomonas synxantha 16S rRNA gene, complete sequence	D84025	1527	47883
67770	Pseudomonas synxantha gene for 16S rRNA, partial sequence, strain: NBRC 3913	AB680171	1462	47883
124043	Pseudomonas synxantha culture DSM:18928 16S ribosomal RNA gene, partial sequence.	KX186990	1431	47883
124043	Pseudomonas synxantha strain NBRC 3913 16S ribosomal RNA gene, partial sequence.	OP164715	1441	47883

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudomonas synxantha NCTC10696
NCBI: GCA_901482615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	87.10	no
125439	gram_stain	BacteriaNetⓘ	negative	97.10	no
125439	motility	BacteriaNetⓘ	yes	79.30	no
125439	spore_formation	BacteriaNetⓘ	no	95.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas synxantha NCTC10696
NCBI: GCA_901482615.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	no
125438	anaerobic	anaerobicⓘ	no	98.86	yes
125438	aerobic	aerobicⓘ	yes	92.80	yes
125438	spore-forming	spore-formingⓘ	no	80.79	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	yes	90.82	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genome assembly of Pseudomonas sp. strain SED1^T, a psychrotolerant bacterium isolated from Deception Glacier (Washington, USA).	Shain DH, Klein EA.	Microbiol Resour Announc	10.1128/mra.00125-24	2024
	Simultaneous quantification of the most common and proteolytic Pseudomonas species in raw milk by multiplex qPCR.	Maier C, Hofmann K, Huptas C, Scherer S, Wenning M, Lucking G.	Appl Microbiol Biotechnol	10.1007/s00253-021-11109-0	2021
Biotechnology	Sourdough authentication: quantitative PCR to detect the lactic acid bacterial microbiota in breads.	Pontonio E, Di Cagno R, Mahony J, Lanera A, De Angelis M, van Sinderen D, Gobbetti M.	Sci Rep	10.1038/s41598-017-00549-2	2017
	Isolation, characterization, and genetic manipulation of cold-tolerant, manganese-oxidizing Pseudomonas sp. strains.	Jones I, Vermillion D, Tracy C, Denton R, Davis R, Geszvain K.	Appl Environ Microbiol	10.1128/aem.00510-24	2024
Enzymology	NADP(+)-dependent D-threonine dehydrogenase from Pseudomonas cruciviae IFO 12047.	Misono H, Kato I, Packdibamrung K, Nagata S, Nagasaki S.	Appl Environ Microbiol	10.1128/aem.59.9.2963-2968.1993	1993
	New Insights into Pseudomonas spp.-Produced Antibiotics: Genetic Regulation of Biosynthesis and Implementation in Biotechnology.	Baukova A, Bogun A, Sushkova S, Minkina T, Mandzhieva S, Alliluev I, Jatav HS, Kalinitchenko V, Rajput VD, Delegan Y.	Antibiotics (Basel)	10.3390/antibiotics13070597	2024
Enzymology	Superiority of molecular techniques for identification of gram-negative, oxidase-positive rods, including morphologically nontypical Pseudomonas aeruginosa, from patients with cystic fibrosis.	Wellinghausen N, Kothe J, Wirths B, Sigge A, Poppert S.	J Clin Microbiol	10.1128/jcm.43.8.4070-4075.2005	2005
Metabolism	Regulation of pyrimidine nucleotide biosynthesis in Pseudomonas synxantha.	West TP	Antonie Van Leeuwenhoek	10.1007/s10482-007-9164-4	2007
Phylogeny	Pseudomonas lactucae sp. nov., a pathogen causing bacterial rot of lettuce in Japan.	Sawada H, Fujikawa T, Satou M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004917	2021
Phylogeny	Pseudomonas haemolytica sp. nov., isolated from raw milk and skimmed milk concentrate.	Hofmann K, Huptas C, Doll EV, Scherer S, Wenning M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004043	2020
Phylogeny	Pseudomonas carnis sp. nov., isolated from meat.	Lick S, Krockel L, Wibberg D, Winkler A, Blom J, Bantleon A, Goesmann A, Kalinowski J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003928	2020

References

#7789	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18928
#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 )
#37601	; Curators of the CIP;
#58786	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 50208
#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;
#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 .
#123400	Collection of Institut Pasteur ; Curators of the CIP; CIP 59.22
#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 synxantha (DSM 18928, ATCC 9890, CIP 59.22)

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_901482615

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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