Pseudomonas japonica (DSM 22348, IAM 15071, JCM 21532)

Name: Pseudomonas japonica (DSM 22348, IAM 15071, JCM 21532)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13165

Type strain

Strain Designation WL

Culture col. no. DSM 22348 IAM 15071 JCM 21532 NBRC 103040 TISTR 1526 1 more

NCBI tax ID(s) 1215104 256466

Special Collections DSMZ JCM

History <- NBRC <- W. Pungrasmi, Univ. Tokyo, Japan IAM 15071 <-- W. Pungrasmi.

Links

Pseudomonas japonica WL is a bacterium that was isolated from activated sludge from sewage treatment plant.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 132666

IAM 15071,JCM 21532,NBRC 103040,TISTR 1526,DSM 22348,CCUG 59024,CCUG 59367

@ref 20215

Last LPSN update 2026-02-09 11:21:03

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Pseudomonas

Species Pseudomonas japonica

Full scientific name Pseudomonas japonica Pungrasmi et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.5
125439	negative	98.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16305	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)
16305	positive	growth	28
67770	positive	growth	30

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		99.2

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
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
16305	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	+	-	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Water treatment plant

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16305	activated sludge from sewage treatment plant	Odaii, Adachi-ku, Tokyo	Japan	JPN	Asia
67770	Activated sludge from sewage treatment plant	Odaii, Adachi-ku, Tokyo	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16305	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM4268532v1 assembly for Pseudomonas japonica TISTR 1526	scaffold	GCA_042685325			256466	63.23
67770	IMG-taxon 2700988710 annotated assembly for Pseudomonas japonica DSM 22348	scaffold	GCA_900188455	256466.3	2700988710	256466	61.98
67770	ASM73058v1 assembly for Pseudomonas japonica NBRC 103040 = DSM 22348	contig	GCA_000730585	1215104.3	2585427681	1215104	46.16

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Pseudomonas japonica gene for 16S rRNA, partial sequence, strain: NBRC 103040	AB681920	1462	1215104
16305	Pseudomonas japonica gene for 16S rRNA, partial sequence	AB126621	1498	1215104
124043	Pseudomonas japonica NBRC 103040 = DSM 22348 16S ribosomal RNA gene, partial sequence.	KT825519	1450	1215104

GC content

16305

GC-content (mol%)66.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudomonas japonica DSM 22348
NCBI: GCA_900188455

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	73.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.50	no
125439	motility	BacteriaNetⓘ	yes	88.90	no
125439	spore_formation	BacteriaNetⓘ	no	99.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas japonica NBRC 103040 = DSM 22348
PATRIC: 1215104.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	96.99	no
125438	spore-forming	spore-formingⓘ	no	86.50	no
125438	aerobic	aerobicⓘ	yes	85.71	no
125438	thermophilic	thermophileⓘ	no	97.79	yes
125438	flagellated	motile2+ⓘ	yes	89.45	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column.	Pathak A, Stothard P, Chauhan A.	Microorganisms	10.3390/microorganisms9030490	2021
	Isolation and molecular characterization of biofouling bacteria and profiling of quorum sensing signal molecules from membrane bioreactor activated sludge.	Lade H, Paul D, Kweon JH.	Int J Mol Sci	10.3390/ijms15022255	2014
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
Phylogeny	[Reactivating factor of Luteococcus japonicus subsp. casei: isolation and characterization].	Vorob'eva LI, Rogozhin EA, Khodzhaev EIu, Nikolaev IV, Turova TP.	Prikl Biokhim Mikrobiol	10.7868/s0555109914060166	2015
Genetics	Genomic analysis of siderophore beta-hydroxylases reveals divergent stereocontrol and expands the condensation domain family.	Reitz ZL, Hardy CD, Suk J, Bouvet J, Butler A.	Proc Natl Acad Sci U S A	10.1073/pnas.1903161116	2019
	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
	Interspecies Interaction of Bacteria Listeria monocytogenes, Yersinia pseudotuberculosis, and Marine Saprotrophs during Long-Term Culturing in Biofilms.	Eskova AI, Yakovlev AA, Obuhova VS, Bynina MP, Kim AV, Shchelkanov MY.	Bull Exp Biol Med	10.1007/s10517-024-06167-z	2024
	Draft genome sequences of Pseudomonas strains zfem001-005 isolated from the intestine of larval zebrafish Danio rerio.	Simbassa SB, Clark J, Salazar K, Maresso A, Krachler AM.	Microbiol Resour Announc	10.1128/mra.00934-23	2024
Genetics	Taxonomic, metabolic traits and species description of aromatic compound degrading Indian soil bacterium Pseudomonas bharatica CSV86^T.	Mohapatra B, Phale PS.	J Environ Sci Health A Tox Hazard Subst Environ Eng	10.1080/10934529.2023.2204805	2023
	Genomics for the characterization of the mechanisms of microbial strains in degrading petroleum pollutants.	Sui X, Wang X, Yu L, Ji H.	Environ Sci Pollut Res Int	10.1007/s11356-022-23685-3	2023
Genetics	Echoes in the Deep: Revealing Influenza A Viruses' Persistence and Microbial Associations in Aquatic Ecosystems.	Chen W, Yang P, Hu J, Liu X, Jiang C, Wu H, Wang Y, Yan Q, Lu S, Xiong J, Huang X, Pan Y, He F, Chen Q, Hu S, Chen M, Xiong C.	Transbound Emerg Dis	10.1155/tbed/5586400	2025
	MALDI-TOF Mass Spectrometry Characterization of Culturable Microbiota Associated with the Skin of Amphibians from the Southern Andes Mountains of Ecuador.	Salazar J, Gonzalez J, Riofrio R, Siavichay F, Carrera M, Mogrovejo A, Barrera-Galicia G, Valdez-Tenezaca A.	Microb Ecol	10.1007/s00248-025-02555-8	2025
	Influence of Pseudomonas japonica and organic amendments on the growth and metal tolerance of Celosia argentea L.	Iqbal A, Mushtaq MU, Khan AHA, Nawaz I, Yousaf S, Zeshan, Iqbal M.	Environ Sci Pollut Res Int	10.1007/s11356-019-06181-z	2020
Enzymology	Open and closed structures of L-arginine oxidase by cryo-electron microscopy and X-ray crystallography.	Yamaguchi H, Takahashi K, Numoto N, Suzuki H, Tatsumi M, Kamegawa A, Nishikawa K, Asano Y, Mizukoshi T, Miyano H, Fujiyoshi Y, Sugiki M.	J Biochem	10.1093/jb/mvae070	2025
Metabolism	Rapid Detection of Phosphate-Solubilizing Bacteria from Agricultural Areas in Erzurum.	Alaylar B, Gulluce M, Karadayi M, Isaoglu M.	Curr Microbiol	10.1007/s00284-019-01688-7	2019
	Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions.	Ramirez-Hernandez MDC, Gaytan-Cervantes J, Gonzalez-Torres C, Loyola-Cruz MA, Garcia-Mendiola RE, Cruz-Cruz C, Cortes-Ortiz IA, Garcia-Moncada E, Lopez-Flores T, Duran-Manuel EM, Gomez-Mancilla N, Oviedo-Lopez MF, Jimenez-Zamarripa CA, Rojas-Bernabe A, Garcia-Hernandez OA, Puente-Rivera J, Lopez-Ornelas A, Nieto-Velazquez NG, Blanco-Hernandez DMR, Castaneda-Ortega JC, Hernandez-Castellanos B, Anaya-Saavedra G, Calzada-Mendoza CC, Bello-Lopez JM.	Microorganisms	10.3390/microorganisms13092121	2025
	The Mexican giant maize of Jala landrace harbour plant-growth-promoting rhizospheric and endophytic bacteria.	Rios-Galicia B, Villagomez-Garfias C, De la Vega-Camarillo E, Guerra-Camacho JE, Medina-Jaritz N, Arteaga-Garibay RI, Villa-Tanaca L, Hernandez-Rodriguez C.	3 Biotech	10.1007/s13205-021-02983-6	2021
	Horizontal Transfer of Virulence Factors by Pathogenic Enterobacteria to Marine Saprotrophic Bacteria during Co-Cultivation in Biofilm.	Eskova AI, Andryukov BG, Yakovlev AA, Kim AV, Ponomareva AL, Obuhova VS.	BioTech (Basel)	10.3390/biotech11020017	2022
	The influence of benzene on the composition, diversity and performance of the anodic bacterial community in glucose-fed microbial fuel cells.	Tyszkiewicz N, Truu J, Mlynarz P, Pasternak G.	Front Microbiol	10.3389/fmicb.2024.1384463	2024
Biotechnology	Insights into the microbial composition and potential efficiency of selected commercial biofertilisers.	Raimi A, Roopnarain A, Chirima GJ, Adeleke R.	Heliyon	10.1016/j.heliyon.2020.e04342	2020
	Zinc solubilization characteristics of efficient siderophore-producing soil bacteria.	Eshaghi E, Nosrati R, Owlia P, Malboobi MA, Ghaseminejad P, Ganjali MR.	Iran J Microbiol	10.18502/ijm.v11i5.1961	2019
	New Insights into Cockroach Control: Using Functional Diversity of Blattella germanica Symbionts.	Pan X, Wang X, Zhang F.	Insects	10.3390/insects11100696	2020
Phylogeny	New Insights Into Culturable and Unculturable Bacteria Across the Life History of Medicinal Maggots Lucilia sericata (Meigen) (Diptera: Calliphoridae).	Maleki-Ravasan N, Ahmadi N, Soroushzadeh Z, Raz AA, Zakeri S, Dinparast Djadid N.	Front Microbiol	10.3389/fmicb.2020.00505	2020
	Appraisal of diversity and functional attributes of thermotolerant wheat associated bacteria from the peninsular zone of India.	Verma P, Yadav AN, Khannam KS, Mishra S, Kumar S, Kumar S, Saxena AK, Suman A.	Saudi J Biol Sci	10.1016/j.sjbs.2016.01.042	2019
Phylogeny	Methylobrevis albus sp. nov., isolated from freshwater lake sediment.	Zou QH, Feng X, Wang TJ, Du ZJ.	Arch Microbiol	10.1007/s00203-021-02442-z	2021
	Pseudomonas palmensis sp. nov., a Novel Bacterium Isolated From Nicotiana glauca Microbiome: Draft Genome Analysis and Biological Potential for Agriculture.	Gutierrez-Albanchez E, Garcia-Villaraco A, Lucas JA, Horche I, Ramos-Solano B, Gutierrez-Manero FJ.	Front Microbiol	10.3389/fmicb.2021.672751	2021
Phylogeny	Pseudomonas mangrovi sp. nov., isolated from mangrove soil.	Ye Y, Chen C, Ren Y, Wang R, Zhang C, Han S, Ju Z, Zhao Z, Sun C, Wu M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003141	2019
Phylogeny	Paenibacillus albidus sp. nov., isolated from grassland soil.	Zhuang J, Xin D, Zhang YQ, Guo J, Zhang J.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002356	2017
Phylogeny	Luteococcus sediminum sp. nov., isolated from deep subseafloor sediment of the South Pacific Gyre.	Fan X, Zhang Z, Li Z, Zhang XH.	Int J Syst Evol Microbiol	10.1099/ijs.0.058529-0	2014
Phylogeny	Kangiella sediminilitoris sp. nov., isolated from a tidal flat sediment.	Lee SY, Park S, Oh TK, Yoon JH.	Int J Syst Evol Microbiol	10.1099/ijs.0.040691-0	2013
Phylogeny	Tetrasphaera remsis sp. nov., isolated from the Regenerative Enclosed Life Support Module Simulator (REMS) air system.	Osman S, Moissl C, Hosoya N, Briegel A, Mayilraj S, Satomi M, Venkateswaran K.	Int J Syst Evol Microbiol	10.1099/ijs.0.65137-0	2007
	Functional genome mining and taxono-genomics reveal eco-physiological traits and species distinctiveness of aromatic-degrading Pseudomonas bharatica sp. nov.	Mohapatra B, Nain S, Sharma R, Phale PS.	Environ Microbiol Rep	10.1111/1758-2229.13066	2022
Phylogeny	Pseudomonas brassicae sp. nov., a pathogen causing head rot of broccoli in Japan.	Sawada H, Fujikawa T, Horita H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004412	2020
Phylogeny	Pseudomonas qingdaonensis sp. nov., an aflatoxin-degrading bacterium, isolated from peanut rhizospheric soil.	Wang MQ, Wang Z, Yu LN, Zhang CS, Bi J, Sun J	Arch Microbiol	10.1007/s00203-019-01636-w	2019
Phylogeny	Pseudomonas japonica sp. nov., a novel species that assimilates straight chain alkylphenols.	Pungrasmi W, Lee HS, Yokota A, Ohta A	J Gen Appl Microbiol	10.2323/jgam.54.61	2008

References

#16305	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22348
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#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 japonica (DSM 22348, IAM 15071, JCM 21532)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042685325

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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