Name: Pseudomonas japonica WL
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13165

Type strain:

Species: Pseudomonas japonica

Strain Designation: WL

Culture col. no.: DSM 22348, IAM 15071, JCM 21532, NBRC 103040, TISTR 1526

Strain history: IAM 15071 <-- W. Pungrasmi.

NCBI tax ID(s): 1215104 (strain), 256466 (species)

SI-ID 132666

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

Section

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

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Pseudomonadales*
	Family	*Pseudomonadaceae*
	Genus	*Pseudomonas*
	Species	**Pseudomonas japonica**
	Full Scientific Name (LPSN)	Pseudomonas japonica Pungrasmi et al. 2008

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16305]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)

[Ref.: #16305]

Culture medium growth

[Ref.: #16305]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16305]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #16305]			growth	28 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #16305]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67770]

Observation

quinones: Q-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	+	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #16305]	22908	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	+	-	+	+	+	+

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #16305]	Sample type/isolated from	activated sludge from sewage treatment plant
[Ref.: #16305]	Geographic location (country and/or sea, region)	Odaii, Adachi-ku, Tokyo
[Ref.: #16305]	Country	Japan
[Ref.: #16305]	Country ISO 3 Code	JPN
[Ref.: #16305]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Activated sludge from sewage treatment plant
[Ref.: #67770]	Geographic location (country and/or sea, region)	Odaii, Adachi-ku, Tokyo
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Water treatment plant

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #16305]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16305]	Pseudomonas japonica gene for 16S rRNA, partial sequence	AB126621	1498	ENA	1215104 tax ID
[Ref.: #20218]	Pseudomonas japonica gene for 16S rRNA, partial sequence, strain: NBRC 103040	AB681920	1462	ENA	1215104 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pseudomonas japonica NBRC 103040 = DSM 22348	GCA_000730585	contig	GenBank	1215104 tax ID
[Ref.: #67770]	Pseudomonas japonica DSM 22348	GCA_900188455	scaffold	GenBank	256466 tax ID
[Ref.: #66792]	Pseudomonas japonica NBRC 103040 = DSM 22348	1215104.3	wgs	PATRIC	1215104 tax ID	*
[Ref.: #66792]	Pseudomonas japonica strain DSM 22348	256466.3	wgs	PATRIC	256466 tax ID	*
[Ref.: #66792]	Pseudomonas japonica NBRC 103040	2585427681	draft	JGI IMG/M	1215104 tax ID	*
[Ref.: #66792]	Pseudomonas japonica DSM 22348	2700988710	draft	JGI IMG/M	256466 tax ID	*

[Ref.: #16305]

GC-content

66.0 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudomonas japonica NBRC 103040 = DSM 22348 PATRIC: 1215104.3
[Ref.: #69480]	motile	yes	89.387	no
[Ref.: #69480]	gram-positive	no	98.063	no
[Ref.: #69480]	anaerobic	no	98.623	no
[Ref.: #69480]	aerobic	yes	96.277	no
[Ref.: #69480]	halophile	no	86.55	no
[Ref.: #69480]	spore-forming	no	96.015	no
[Ref.: #69480]	thermophile	no	99.862	no
[Ref.: #69480]	glucose-util	yes	90.73	no
[Ref.: #69480]	flagellated	yes	82.279	no
[Ref.: #69480]	glucose-ferment	no	87.131	no

Availability in culture collections External links

[Ref.: #16305]

Culture collection no.

DSM 22348, IAM 15071, JCM 21532, NBRC 103040, TISTR 1526

[Ref.: #82373]

SI-ID 132666

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#82373

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID132666.1 )

* These data were automatically processed and therefore are not curated

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Pseudomonas japonica NBRC 103040 = DSM 22348

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