Pseudomonas oryzihabitans (DSM 6835, ATCC 43272, IAM 1568)

Name: Pseudomonas oryzihabitans (DSM 6835, ATCC 43272, IAM 1568)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13048

Type strain

Strain Designation KS0036, L-1, KS 0036

Culture col. no. DSM 6835 ATCC 43272 IAM 1568 JCM 2952 CCUG 12540 10 more

NCBI tax ID(s) 1215113 47885

Special Collections DSMZ CCUG JCM CIP

History <- ATCC (Flavimonas oryzihabitans) <- JCM <- K. Kodama; KS0036 <- Ajinomoto Co. Inc.; AJ 2197 <- K. Komagata; L-1 K. Kodama KS 0036 <-- AJ 2197 <-- K. Komagata L-1. CIP <- 1987, IAM <- JCM, Pseudomonas oryzihabitans <- K. Kodama: strain KS 0036 <- Ajinomoto Co. Inc.: strain AJ 2197 <- K. Komagata: strain L-1

Links

Pseudomonas oryzihabitans KS0036 is an obligate aerobe, Gram-negative, motile bacterium that was isolated from rice paddy.

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

Name and taxonomic classification

SI-ID 2812

LMG 7040,ATCC 43272,CCUG 12540,DSM 6835,IAM 1568,JCM 2952,LMG 8815,CIP 102996,NCIMB 12521,BCRC 16007,CCRC 16007,KACC 10797,NBRC 102199,CGMCC 1.3392,VTT E-032413

@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 oryzihabitans

Full scientific name Pseudomonas oryzihabitans Kodama et al. 1985

Synonyms (2)

Chryseomonas oryzihabitans
Flavimonas oryzihabitans

BacDive ID	Other strains from **Pseudomonas oryzihabitans** (51)	Type strain
134885	P. oryzihabitans 706-86, CIP 102685
134908	P. oryzihabitans 739-86, CIP 102739
136276	P. oryzihabitans Cor, CIP 104149
136277	P. oryzihabitans Man, CIP 104150
137866	P. oryzihabitans 904-85, CIP 101989
141211	P. oryzihabitans CCUG 203
141388	P. oryzihabitans CCUG 1366 A
141501	P. oryzihabitans CCUG 2415
141514	P. oryzihabitans CCUG 2503 A
141624	P. oryzihabitans CCUG 3993
141648	P. oryzihabitans CCUG 4329
141788	P. oryzihabitans CCUG 6826 A
141985	P. oryzihabitans CCUG 9468
142021	P. oryzihabitans CCUG 9987
142963	P. oryzihabitans CCUG 15934
143253	P. oryzihabitans CCUG 18069
143392	P. oryzihabitans CCUG 18848
143424	P. oryzihabitans CCUG 19081
143689	P. oryzihabitans CCUG 21017, NCTC 11851
144922	P. oryzihabitans CCUG 27098
145659	P. oryzihabitans CCUG 29166
146533	P. oryzihabitans CCUG 31383
146668	P. oryzihabitans CCUG 31756
147455	P. oryzihabitans CCUG 33606
148010	P. oryzihabitans CCUG 34662 B
148361	P. oryzihabitans CCUG 35283
149886	P. oryzihabitans CCUG 38613
150231	P. oryzihabitans CCUG 39334
152484	P. oryzihabitans CCUG 46912
153865	P. oryzihabitans CCUG 51429
153866	P. oryzihabitans CCUG 51430
156061	P. oryzihabitans CCUG 60244
164828	P. oryzihabitans JCM 3829, IAM 1601
164829	P. oryzihabitans JCM 3830, IAM 1611
164830	P. oryzihabitans JCM 3831, IAM 1620
164832	P. oryzihabitans JCM 3833, IAM 1580
164833	P. oryzihabitans JCM 3834, IAM 1591
164834	P. oryzihabitans JCM 3835, ATCC 43274, IAM 13017
164835	P. oryzihabitans JCM 3836, IAM 13018
164836	P. oryzihabitans JCM 3837, IAM 13019
164837	P. oryzihabitans JCM 3838, IAM 13020
164838	P. oryzihabitans JCM 3839, IAM 13021
164839	P. oryzihabitans JCM 3840, IAM 13022
164840	P. oryzihabitans JCM 3841, IAM 13023
164841	P. oryzihabitans JCM 3842, IAM 13024
164842	P. oryzihabitans JCM 3843, ATCC 43271, IAM 13025
164843	P. oryzihabitans JCM 3844, IAM 13026
164844	P. oryzihabitans JCM 3845, IAM 13027
164845	P. oryzihabitans JCM 3846, IAM 13028
164846	P. oryzihabitans JCM 3847, IAM 13029
174848	P. oryzihabitans 116517, DSM 116517

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
121455	negative	rod-shaped
125438	negative		97
125439	negative		95.3

Pigmentation

@ref	Production	Name
121455		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2845	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
2845	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
33754	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121455	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
2845	positive	growth	28
33754	positive	growth	30
67770	positive	growth	30
121455	positive	growth	10-41
121455	negative	growth	5

Physiology and metabolism

Oxygen tolerance

121455

Oxygen toleranceobligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121455	NaCl	positive	growth	0-4 %
121455	NaCl		growth	6 %
121455	NaCl		growth	8 %
121455	NaCl		growth	10 %

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
121455	16947 ChEBI	citrate	+	carbon source
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
121455	4853 ChEBI	esculin	-	hydrolysis
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	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
121455	17632 ChEBI	nitrate	-	reduction
121455	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
121455	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121455	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
121455	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
121455	alcohol dehydrogenase	-	1.1.1.1
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
121455	amylase	-
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
121455	beta-galactosidase	-	3.2.1.23
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
121455	caseinase	-	3.4.21.50
121455	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
121455	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121455	gelatinase	-
68369	gelatinase	-		from API 20NE
121455	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121455	lipase	-
68382	lipase (C 14)	-		from API zym
121455	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121455	ornithine decarboxylase	-	4.1.1.17
121455	oxidase	-
121455	protease	+
68382	trypsin	+	3.4.21.4	from API zym
121455	tryptophan deaminase	-
121455	tween esterase	+
121455	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	Entner Doudoroff pathway	100	10 of 10
66794	enterobactin biosynthesis	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	biotin biosynthesis	100	4 of 4
66794	ketogluconate metabolism	100	8 of 8
66794	starch degradation	100	10 of 10
66794	quinate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	formaldehyde oxidation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	taurine degradation	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	ubiquinone biosynthesis	100	7 of 7
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	NAD metabolism	94.44	17 of 18
66794	vitamin B12 metabolism	94.12	32 of 34
66794	glutamate and glutamine metabolism	92.86	26 of 28
66794	phenylalanine metabolism	92.31	12 of 13
66794	vitamin B6 metabolism	90.91	10 of 11
66794	proline metabolism	90.91	10 of 11
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	glutathione metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	purine metabolism	81.91	77 of 94
66794	glycine betaine biosynthesis	80	4 of 5
66794	vitamin K metabolism	80	4 of 5
66794	degradation of sugar acids	80	20 of 25
66794	peptidoglycan biosynthesis	80	12 of 15
66794	arginine metabolism	79.17	19 of 24
66794	citric acid cycle	78.57	11 of 14
66794	pyrimidine metabolism	77.78	35 of 45
66794	allantoin degradation	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	methionine metabolism	76.92	20 of 26
66794	vitamin B1 metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	histidine metabolism	75.86	22 of 29
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	lysine metabolism	73.81	31 of 42
66794	metabolism of disaccharids	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	oxidative phosphorylation	72.53	66 of 91
66794	alanine metabolism	72.41	21 of 29
66794	cysteine metabolism	72.22	13 of 18
66794	degradation of pentoses	71.43	20 of 28
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	non-pathway related	71.05	27 of 38
66794	lipid metabolism	70.97	22 of 31
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	octane oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	sulfoquinovose degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	sulfate reduction	61.54	8 of 13
66794	lipoate biosynthesis	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	tryptophan metabolism	57.89	22 of 38
66794	degradation of hexoses	55.56	10 of 18
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	polyamine pathway	52.17	12 of 23
66794	ribulose monophosphate pathway	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	arachidonic acid metabolism	50	9 of 18
66794	cyclohexanol degradation	50	2 of 4
66794	lactate fermentation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ascorbate metabolism	50	11 of 22
66794	coenzyme M biosynthesis	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	carotenoid biosynthesis	45.45	10 of 22
66794	phenol degradation	45	9 of 20
66794	nitrate assimilation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	glycine metabolism	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4

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
121455	-	+	+	+	-	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-

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
2845	-	-	-	-	-	-	-	-	+	+	+	+	-	+	+	+	-	+	+	-	-
2845	-	-	-	-	-	-	-	-	+	+/-	+	+	-	+/-	+	+	-	+	+	-	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
121455	not determinedn.d.	+	+	+	+	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	+	+	+	-	+	+	-	+	-	-	-	-	+	+	+	-	-	+	-	-	+	-	-	-	+	+	+	-	+	+	+	+	+	-	+	+	+	+	-	-	-	+	-	+	+	+	-	-	-	-	-	-	+	+	+	-	+	+	+	-	+	+	+	+	+	+	-	-	+	+	+	+	+	+	+	+	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
2845	rice paddy		Japan	JPN	Asia
45739	Normal rice paddy,Oryza sativa	Tokyo	Japan	JPN	Asia
121455	Plant, Rice		Japan	JPN	Asia	1963

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2845	2	Risk group (German classification) According to TRBA 466
121455	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
67770	ASM1298619v1 assembly for Pseudomonas oryzihabitans DSM 6835	contig	GCA_012986195	47885.39	8115116353	47885	74.34
66792	ASM73062v1 assembly for Pseudomonas oryzihabitans NBRC 102199	contig	GCA_000730625	1215113.3	2585427682	1215113	72.12
66792	ASM305773v2 assembly for Pseudomonas sp. RIT411	contig	GCA_003057735	47885.22		47885	70.49

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Pseudomonas oryzihabitans gene for 16S rRNA	D84004	1527	47885
20218	Pseudomonas oryzihabitans strain LMG 7040 16S ribosomal RNA gene, partial sequence	GQ250598	1527	47885
20218	Pseudomonas oryzihabitans gene for 16S rRNA, partial sequence, strain: NBRC 102199	AB681726	1463	47885
2845	Pseudomonas oryzihabitans partial 16S rRNA gene, type strain IAM 1568T	AM262973	1466	47885
124043	Pseudomonas oryzihabitans strain IAM 1568 16S ribosomal RNA gene, partial sequence.	OQ608823	422	47885
124043	Pseudomonas oryzihabitans strain IAM 1568 16S ribosomal RNA gene, partial sequence.	OQ875712	422	47885
124043	Pseudomonas oryzihabitans strain IAM 1568 16S ribosomal RNA gene, partial sequence.	OQ875742	1466	47885
124043	Pseudomonas oryzihabitans strain NBRC 102199 16S ribosomal RNA gene, partial sequence.	MH281747	1364	47885
124043	Pseudomonas oryzihabitans strain NBRC 102199 16S ribosomal RNA gene, partial sequence.	MN894061	1074	47885
124043	Pseudomonas oryzihabitans strain NBRC 102199 16S ribosomal RNA gene, partial sequence.	PQ524576	601	47885

GC content

@ref	GC-content (mol%)	Method
2845	65.1	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudomonas oryzihabitans NBRC 102199
NCBI: GCA_000730625

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	70.50	no
125439	gram_stain	BacteriaNetⓘ	negative	95.30	no
125439	motility	BacteriaNetⓘ	yes	80.00	no
125439	spore_formation	BacteriaNetⓘ	no	98.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas oryzihabitans NBRC 102199
PATRIC: 1215113.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	no
125438	anaerobic	anaerobicⓘ	no	99.22	no
125438	spore-forming	spore-formingⓘ	no	77.85	no
125438	aerobic	aerobicⓘ	yes	87.73	no
125438	thermophilic	thermophileⓘ	no	98.50	yes
125438	flagellated	motile2+ⓘ	yes	86.47	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Expanding the Pseudomonas diversity of the wheat rhizosphere: four novel species antagonizing fungal phytopathogens and with plant-beneficial properties.	Poli N, Keel CJ, Garrido-Sanz D.	Front Microbiol	10.3389/fmicb.2024.1440341	2024
	Validation List no. 219. Valid publication of new names and new combinations effectively published outside the IJSEM.	Oren A, Goker M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006452	2024
	Pseudomonas species prevalence, protein analysis, and antibiotic resistance: an evolving public health challenge.	Elbehiry A, Marzouk E, Aldubaib M, Moussa I, Abalkhail A, Ibrahem M, Hamada M, Sindi W, Alzaben F, Almuzaini AM, Algammal AM, Rawway M.	AMB Express	10.1186/s13568-022-01390-1	2022
Phylogeny	Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera.	Rudra B, Gupta RS.	Front Microbiol	10.3389/fmicb.2023.1273665	2023
Genetics	Genomic Insights into Cyanide Biodegradation in the Pseudomonas Genus.	Saez LP, Rodriguez-Caballero G, Olaya-Abril A, Cabello P, Moreno-Vivian C, Roldan MD, Luque-Almagro VM.	Int J Mol Sci	10.3390/ijms25084456	2024
Phylogeny	Epidemiological typing of Flavimonas oryzihabitans by PCR and pulsed-field gel electrophoresis.	Liu PY, Shi ZY, Lau YJ, Hu BS, Shyr JM, Tsai WS, Lin YH, Tseng CY.	J Clin Microbiol	10.1128/jcm.34.1.68-70.1996	1996
Enzymology	Rapid concentration and molecular enrichment approach for sensitive detection of Escherichia coli and Shigella species in potable water samples.	Maheux AF, Bissonnette L, Boissinot M, Bernier JL, Huppe V, Picard FJ, Berube E, Bergeron MG.	Appl Environ Microbiol	10.1128/aem.02337-10	2011
	Endophytic Seed-Associated Bacteria as Plant Growth Promoters of Cuban Rice (Oryza sativa L.).	Hernandez I, Taule C, Perez-Perez R, Battistoni F, Fabiano E, Villanueva-Guerrero A, Napoles MC, Herrera H.	Microorganisms	10.3390/microorganisms11092317	2023
Enzymology	Evaluation of Bioaerosol Bacterial Components of a Wastewater Treatment Plant Through an Integrate Approach and In Vivo Assessment.	Bruni E, Simonetti G, Bovone B, Casagrande C, Castellani F, Riccardi C, Pomata D, Di Filippo P, Federici E, Buiarelli F, Uccelletti D.	Int J Environ Res Public Health	10.3390/ijerph17010273	2019
	Halomonas sp. MC140, a polyhydroxyalkanoate (PHA) producer isolated from the Arctic environment.	Christensen M, Chiciudean I, Lascu I, Jablonski P, Shapaval V, Zimmermann B, Tanase AM, Hansen H.	Sci Rep	10.1038/s41598-025-06898-7	2025
Metabolism	Regulation of pyrimidine formation in Pseudomonas oryzihabitans.	West TP	J Basic Microbiol	10.1002/jobm.200710333	2007
	Biochemical Characterization and Genome Analysis of Pseudomonas loganensis sp. nov., a Novel Endophytic Bacterium	Karaman M, Yetiman A, Zhan J, Fidan O.	Microbiologyopen		2025
Phylogeny	Pseudomonas flavocrustae sp. nov., an endophyte with plant growth promoting traits isolated from Passiflora incarnata.	Cueva-Yesquen LG, Sartoratto A, da Silva Santos A, de Melo IS, Fantinatti-Garboggini F.	Sci Rep	10.1038/s41598-024-64349-1	2024
	Bactericidal Effect of Pseudomonas oryziphila sp. nov., a Novel Pseudomonas Species Against Xanthomonas oryzae Reduces Disease Severity of Bacterial Leaf Streak of Rice.	Yang R, Li S, Li Y, Yan Y, Fang Y, Zou L, Chen G.	Front Microbiol	10.3389/fmicb.2021.759536	2021
	Pseudomonas benzopyrenica sp. nov., isolated from soil, exhibiting high-efficiency degradation of benzo(a)pyrene.	Dong X, Rao Z, Wu S, Peng F, Xie Z, Long Y.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006034	2023
Phylogeny	Pseudomonas rhizoryzae sp. nov., isolated from rice.	Wang X, He SW, Guo HB, Thin KK, Gao JS, Wang Y, Zhang XX	Int J Syst Evol Microbiol	10.1099/ijsem.0.003852	2020

References

#2845	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6835
#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 )
#33754	; Curators of the CIP;
#45739	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 12540
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#121455	Collection of Institut Pasteur ; Curators of the CIP; CIP 102996
#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 oryzihabitans (DSM 6835, ATCC 43272, IAM 1568)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

API 20NE

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_012986195

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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