Pseudomonas putida (DSM 50208, ATCC 17485, ICPB 2789-111)

Name: Pseudomonas putida (DSM 50208, ATCC 17485, ICPB 2789-111)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12922

Type strain

Strain Designation 53-2

Culture col. no. DSM 50208 ATCC 17485 ICPB 2789-111 53-2 NCIMB 12092 4 more

NCBI tax ID(s) 1295132 303

Special Collections DSMZ JCM KCTC

History <- ICPB <- W.R. Sistrom; 53-2 M. Tsuda <-- K. Furukawa <-- A. M. Chakrabarty <-- I. C. Gunsalus G7 <-- W. R. Sistrom 53-2.

Links

Pseudomonas putida 53-2 is a mesophilic human pathogen that was isolated from soil, enrichment with naphthalene.

mesophilic human pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 36668

ATCC 17485,JCM 6158,DSM 50208,CCRC 10461,KCTC 1642,NCIMB 12092,BCRC 10461

@ref 20215

Last LPSN update 2025-12-16 09:49:58

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Pseudomonas

Species Pseudomonas putida

Full scientific name Pseudomonas putida (Trevisan 1889) Migula 1895 (Approved Lists 1980)

Synonyms (2)

Arthrobacter siderocapsulatus
"Bacillus putidus"

BacDive ID	Other strains from **Pseudomonas putida** (130)	Type strain
12871	P. putida 90, A 3.12, DSM 291, ATCC 12633, DSM 50202, ... (type strain)
12872	P. putida 1593, DSM 295
12873	P. putida C-1, DSM 437, ATCC 23974, DSM 50253
12874	P. putida 77, DSM 1693, ATCC 8209, CCM 380, IFO 3738, ...
12875	P. putida 12/5, DSM 1868
12876	P. putida PaW 340, DSM 2112
12877	P. putida DSM 3226
12880	P. putida mt-2 PaW1, pWWO, DSM 3931, ATCC 33015, NCIB ...
12881	P. putida MT20, pWW20, DSM 3932, NCIB 12186
12882	P. putida MT15, pWW15, DSM 3936, NCIB 12184
12883	P. putida PaW611, pWW53-4, DSM 3937
12884	P. putida PaW701, pWW60-1, DSM 3938, NCIB 12198
12885	P. putida KF439, pKF439, DSM 4011
12886	P. putida PaW736, pWW60-22, DSM 4302, NCIB 12199
12887	P. putida MT53, pWW53, DSM 4303, NCIB 12187
12888	P. putida CAM, PpG1, DSM 4475
12889	P. putida NAH, PpG7, DSM 4476
12890	P. putida NIC, PpG25, DSM 4477
12891	P. putida PpG2100, SAL, DSM 4478
12892	P. putida PaW 130, DSM 5169
12893	P. putida PaW 95, DSM 5170
12894	P. putida CLB250, DSM 5232
12895	P. putida DSM 84, IMG 1513
12896	P. putida mt-2 KT2440, DSM 6125, ATCC 47054, CCUG 56301, ...
12898	P. putida S-832, DSM 6883
12899	P. putida S-313, DSM 6884
12900	P. putida BG1, DSM 6413
12901	P. putida DSM 6521, ATCC 11172, NCIB 8251, JCM 13061, ...
12902	P. putida pUTK9, DSM 6701, RB 1351
12903	P. putida US2, DSM 6755
12904	P. putida F1, PpF1, DSM 6899, ATCC 700007, JCM 31910, ...
12906	P. putida PS, DSM 7189
12907	P. putida Strain G, BKM-BN1123, DSM 7286, BKM BN-1123, ...
12908	P. putida Strain A, DSM 7314, NCIMB 11286, VKM B-1122, ...
12909	P. putida MM1, DSM 9278
12910	P. putida RW20-3b, DSM 11738
12911	P. putida GS1, DSM 12264
12912	P. putida 2-2L, DSM 12585
12913	P. putida PNP1, DSM 12448
12914	P. putida U, DSM 12735, ATCC 17514, NCIMB 10015, CCUG ...
12915	P. putida DSM 13624, IMI 358533
12918	P. putida TM1, DSM 16845
12919	P. putida 50-3-3, IBPM B-20, DSM 46608, CCEB 520, CIP ...
12920	P. putida Berlin 33/2, DSM 50026, CIP 103281
12921	P. putida cl-B, DSM 50198, ATCC 17453, ICPB 2563-77, ...
12924	P. putida DSM 50257, ATCC 6876, DSM 60118, NCPPB 244, ...
12925	P. putida MT-I1, DSM 21680
12926	P. putida WB, DSM 23849
100159	P. putida ST033293(HKI),
24382	P. putida 160, DSM 50194, ATCC 17529, ICPB 2440-133
24383	P. putida MS of E.E. Snell, DSM 50204, ATCC 17457, ...
24384	P. putida S16, DSM 28022
24385	P. putida B6-2, DSM 28064
130567	P. putida SQ1, DSM 100120
130999	P. putida Z2, DSM 16527
131000	P. putida TEC1, DSM 26234
131001	P. putida TEC1 407.1-delta 2, DSM 26250
131002	P. putida TEC1 407.3-delta2, DSM 26251
131003	P. putida TEC1 407-delta1, DSM 26252
131888	P. putida S13.1.2, DSM 102034
132784	P. putida TEC1 91-delta 1, DSM 26253
134429	P. putida AmMs 106, CIP 104063, ATCC 49128
134979	P. putida CIP 55.5, ATCC 795, IAM 1505, NCDO 754, NCIMB ...
135611	P. putida CIP 59.25, ATCC 12842, NCIMB 8865, JCM 13060, ...
135612	P. putida A3/9, CIP 59.26, NCIMB 8248
135753	P. putida CIP 108916, LMG 1246, ATCC 17430, NCIMB 10534, ...
135983	P. putida CIP 52.195
135984	P. putida CIP 52.196
136153	P. putida CIP 52.193
136154	P. putida CIP 52.197
136155	P. putida CIP 52.198
137196	P. putida CIP 52.194
137217	P. putida CIP 52.190
137776	P. putida 25300, 642-85, CIP 101794
137973	P. putida 340-86, CIP 102341
138643	P. putida 776.85, CIP 101936
138858	P. putida MD 7.3, CIP 59.19, NCIMB 8729
139223	P. putida CIP 52.189
141228	P. putida CCUG 264
141276	P. putida CCUG 553, LMG 2189
141504	P. putida CCUG 2471
141507	P. putida CCUG 2479
141521	P. putida CCUG 2525, NRRL B-2022
142893	P. putida CCUG 15619
143393	P. putida CCUG 18875
144913	P. putida CCUG 27052
145592	P. putida CCUG 28920
145805	P. putida CCUG 29643
146210	P. putida CCUG 30612
146426	P. putida CCUG 31110
146710	P. putida CCUG 32007
147231	P. putida CCUG 33113
147438	P. putida CCUG 33582
147515	P. putida CCUG 33721
147793	P. putida CCUG 34242
148510	P. putida CCUG 35570
149198	P. putida CCUG 37253
150737	P. putida CCUG 42126
153432	P. putida CCUG 49576
153483	P. putida CCUG 49716
153616	P. putida CCUG 50315
153618	P. putida CCUG 50317
154720	P. putida CCUG 54971
155478	P. putida CCUG 57833
156241	P. putida CCUG 60837
156461	P. putida CCUG 61918
161309	P. putida JCM 13062, ATCC 11250, CCM 3656, KCTC 1645, ...
161475	P. putida JCM 14351, ATCC 598, NRRL B-251
162298	P. putida JCM 18798
162685	P. putida JCM 20004, IAM 1002
162686	P. putida JCM 20005, IAM 1003
162700	P. putida JCM 20028, IAM 1049
162701	P. putida JCM 20029, IAM 1050
162713	P. putida JCM 20048, IAM 1094
162723	P. putida JCM 20066, IAM 1128
162741	P. putida JCM 20089, IAM 1177
162752	P. putida JCM 20102, IAM 1200
162760	P. putida JCM 20111, IAM 1218
162761	P. putida JCM 20112, ATCC 17464, IAM 1219
162768	P. putida JCM 20120, IAM 1235
162775	P. putida JCM 20129, IAM 1250
162804	P. putida JCM 20188, ATCC 4359, IAM 1506
162815	P. putida JCM 20228, IAM 1629
165987	P. putida JCM 9045
166071	P. putida JCM 9800
166073	P. putida JCM 9802
174606	P. putida Thor-Nr. 1021, DSM 115323
174607	P. putida 116234, DSM 116234
174608	P. putida 116510, DSM 116510
176535	P. putida NiuAA7, DSM 114486

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.4
125438	negative	99

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
12676	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
12676	positive	growth	26	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	91.028

Spore formation

@ref	Spore formation	Confidence
125439		98.2

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
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	+	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

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
12676	-	-	-	+	-	-	-	-	+	-	-	-	-	-	+	+	-	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type
12676	soil, enrichment with naphthalene
67770	Soil with naphthalene enrichment

Taxonmaps

69479

Global distribution of 16S sequence AF094739 (>99% sequence identity) for Pseudomonas from Microbeatlas

Aquatic Samples	421
Soil Samples	444
Animal Samples	802
Plant Samples	305
Total Samples	1972

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
12676			2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score	IMG accession
124043	ASM2322169v1 assembly for Pseudomonas putida G7	complete	GCA_023221695	303.984	303	69.97
66792	ASM131216v1 assembly for Pseudomonas putida JCM 18452	contig	GCA_001312165	1295132.3	1295132		2728369712

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Pseudomonas putida strain ATCC 17485 16S ribosomal RNA gene, partial sequence	AF094739	1449		303
20218	Pseudomonas putida 16S ribosomal RNA gene, strain: ATCC 17485, partial sequence	D85994	1329		303

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudomonas putida JCM 18452
NCBI: GCA_001312165

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.20	no
125439	motility	BacteriaNetⓘ	yes	85.30	no
125439	gram_stain	BacteriaNetⓘ	negative	98.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	85.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas putida JCM 18452
PATRIC: 1295132.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	97.72	no
125438	spore-forming	spore-formingⓘ	no	84.77	no
125438	aerobic	aerobicⓘ	yes	91.03	no
125438	thermophilic	thermophileⓘ	no	97.99	no
125438	flagellated	motile2+ⓘ	yes	84.92	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: implications for transcriptomics studies.	Ballerstedt H, Volkers RJ, Mars AE, Hallsworth JE, dos Santos VA, Puchalka J, van Duuren J, Eggink G, Timmis KN, de Bont JA, Wery J.	Appl Microbiol Biotechnol	10.1007/s00253-007-0914-z	2007
	Complete Genome Sequence of NAH7-Harboring Pseudomonas putida Strain G7.	Varner PM, Gunsch CK.	Microbiol Resour Announc	10.1128/mra.00394-22	2022
	An Evaluation of the Sensitivity and Applicability of a Droplet Digital Polymerase Chain Reaction Assay to Simultaneously Detect Pseudomonas aeruginosa and Pseudomonas fragi in Foods.	Huang J, Zhai L, Wang J, Sun X, Wang B, Wei Z.	Foods	10.3390/foods13101453	2024
	The effect of bacterial growth strategies on plasmid transfer and naphthalene degradation for bioremediation.	Varner PM, Allemann MN, Michener JK, Gunsch CK.	Environ Technol Innov	10.1016/j.eti.2022.102910	2022
Enzymology	Bioactive pregnane steroids from a South China Sea gorgonian Carijoa sp.	Zhao HY, Shao CL, Li ZY, Han L, Cao F, Wang CY.	Molecules	10.3390/molecules18033458	2013
Metabolism	Organization and evolution of naphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxychromene-2-carboxylate isomerase and trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid.	Eaton RW.	J Bacteriol	10.1128/jb.176.24.7757-7762.1994	1994
	Enhancement of Population Densities of Pseudomonas putida PpG7 in Agricultural Ecosystems by Selective Feeding with the Carbon Source Salicylate.	Colbert SF, Schroth MN, Weinhold AR, Hendson M.	Appl Environ Microbiol	10.1128/aem.59.7.2064-2070.1993	1993
	Enhanced growth and activity of a biocontrol bacterium genetically engineered to utilize salicylate.	Colbert SF, Hendson M, Ferri M, Schroth MN.	Appl Environ Microbiol	10.1128/aem.59.7.2071-2076.1993	1993
	Use of an Exotic Carbon Source To Selectively Increase Metabolic Activity and Growth of Pseudomonas putida in Soil.	Colbert SF, Isakeit T, Ferri M, Weinhold AR, Hendson M, Schroth MN.	Appl Environ Microbiol	10.1128/aem.59.7.2056-2063.1993	1993
	Anti-infective properties of bacteriocins: an update.	Hammami R, Fernandez B, Lacroix C, Fliss I.	Cell Mol Life Sci	10.1007/s00018-012-1202-3	2013
Enzymology	Construction of cloning cartridges for development of expression vectors in gram-negative bacteria.	Yen KM.	J Bacteriol	10.1128/jb.173.17.5328-5335.1991	1991
	Plasmid Involvement in Parathion Hydrolysis by Pseudomonas diminuta.	Serdar CM, Gibson DT, Munnecke DM, Lancaster JH.	Appl Environ Microbiol	10.1128/aem.44.1.246-249.1982	1982
	Action of a fluoranthene-utilizing bacterial community on polycyclic aromatic hydrocarbon components of creosote.	Mueller JG, Chapman PJ, Pritchard PH.	Appl Environ Microbiol	10.1128/aem.55.12.3085-3090.1989	1989
Enzymology	Development of a multiplex real-time PCR assay for the simultaneous detection of four bacterial pathogens causing pneumonia.	Lim HJ, Kang ER, Park MY, Kim BK, Kim MJ, Jung S, Roh KH, Sung N, Yang JH, Lee MW, Lee SH, Yang YJ.	PLoS One	10.1371/journal.pone.0253402	2021
Enzymology	Rapid identification of gram-negative bacteria with and without CTX-M extended-spectrum beta-lactamase from positive blood culture bottles by PCR followed by microchip gel electrophoresis.	Fujita S, Yosizaki K, Ogushi T, Uechi K, Takemori Y, Senda Y.	J Clin Microbiol	10.1128/jcm.01976-10	2011
	Critical Effect of H₂O₂ in the Agar Plate on the Growth of Laboratory and Environmental Strains.	Watanabe M, Igarashi K, Kato S, Kamagata Y, Kitagawa W.	Microbiol Spectr	10.1128/spectrum.03336-22	2022
Metabolism	ISC-like [2Fe-2S] ferredoxin (FdxB) dimer from Pseudomonas putida JCM 20004: structural and electron-nuclear double resonance characterization.	Iwasaki T, Kappl R, Bracic G, Shimizu N, Ohmori D, Kumasaka T.	J Biol Inorg Chem	10.1007/s00775-011-0793-8	2011
	Crystallization and preliminary X-ray diffraction studies of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004.	Iwasaki T, Ohmori D, Shimizu N, Kumasaka T.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309107045757	2007

References

#12676	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 50208
#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 )
#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 .
#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 .
#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 putida (DSM 50208, ATCC 17485, ICPB 2789-111)

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 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_023221695

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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