Pseudomonas borbori (CCUG 53773, DSM 17834, LMG 23199)

Name: Pseudomonas borbori (CCUG 53773, DSM 17834, LMG 23199)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13131

Type strain

Strain Designation R-20821

Culture col. no. CCUG 53773 DSM 17834 LMG 23199 R-20821 CIP 109375

NCBI tax ID(s) 289003

Special Collections DSMZ CCUG Literature strains CIP

History DSMZ <- B. Vanparys; R-20821 CIP <- 2006, DSMZ <- B. Vanparys, Ghent Univ., Ghent, Belgium: strain R-20821

Links

Pseudomonas borbori R-20821 is an aerobe, Gram-negative, motile bacterium that was isolated from nitrifying starting culture for the detoxification of aquaculture ponds and aquaria.

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

Name and taxonomic classification

SI-ID 94088

LMG 23199,DSM 17834,CCUG 53773,CIP 109375

@ref 20215

Last LPSN update 2026-05-29 08:27:58

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Pseudomonas

Species Pseudomonas borbori

Full scientific name Pseudomonas borbori Vanparys et al. 2006

BacDive ID	Other strains from **Pseudomonas borbori** (1)	Type strain
154478	P. borbori CCUG 53774, LMG 23200

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31765	negative	02-03 µm	1 µm	rod-shaped
116841	negative			rod-shaped
125439	negative				99.489
125439					92.201
125438	negative				99.5

Pigmentation

31765

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7205	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
37533	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
116841	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7205	positive	growth	28
31765	positive	growth	22-28
31765	positive	optimum	22-28
37533	positive	growth	30
60007	positive	growth	30

Culture pH

@ref	Ability	Type	PH
31765	positive	optimum	7
31765	positive	growth	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
31765	aerobe
60007	aerobe
116841	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
31765
125439		99.947

Observation

31765

Observationaggregates in chains

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
31765	24265 ChEBI	gluconate	+	carbon source
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
31765	17234 ChEBI	glucose	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
31765	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
116841	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
116841	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
116841	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
31765	catalase	+	1.11.1.6
116841	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31765	cytochrome oxidase	+	1.9.3.1
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
116841	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
116841	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
116841	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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
7205	+	-	-	-	-	-	-	-	+	-	-	-	-	+	+	+	-	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Aquaculture
#Engineered	#Laboratory	#Lab enrichment
#Environmental	#Aquatic	#Pond (small)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7205	nitrifying starting culture for the detoxification of aquaculture ponds and aquaria	Gent	Belgium	BEL	Europe
60007	A nitrifying inoculum
116841	Nitrifying inoculum	Ghent	Belgium	BEL	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7205	1	Risk group (German classification) According to TRBA 466
116841	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	IMG-taxon 2671180032 annotated assembly for Pseudomonas borbori DSM 17834	scaffold	GCA_900115555	289003.4	2671180032	289003	57.08

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7205	Pseudomonas borbori partial 16S rRNA gene, type strain R-20821T	AM114527	1494		289003

GC content

31765

GC-content (mol%)60.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2671180032 annotated assembly for Pseudomonas borbori DSM 17834
BV-BRC: 289003.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	84.59	no
125439	gram_stain	BacteriaNetⓘ	negative	99.49	no
125439	spore_formation	BacteriaNetⓘ	no	99.95	no
125439	motility	BacteriaNetⓘ	yes	92.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas borbori DSM 17834
NCBI: GCA_900115555.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	yes
125438	anaerobic	anaerobicⓘ	no	97.74	no
125438	aerobic	aerobicⓘ	yes	86.49	yes
125438	spore-forming	spore-formingⓘ	no	87.35	no
125438	thermophilic	thermophileⓘ	no	98.94	yes
125438	flagellated	motile2+ⓘ	yes	88.33	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudomonas tumuqii sp. nov., isolated from greenhouse soil.	Kong D, Li Q, Zhou Y, Wang Y, Jiang X, Wang Z, Ruan Z	Arch Microbiol	10.1007/s00203-022-02869-y	2022
Phylogeny	Pseudomonas composti sp. nov., isolated from compost samples.	Gibello A, Vela AI, Martin M, Mengs G, Alonso PZ, Garbi C, Fernandez-Garayzabal JF	Int J Syst Evol Microbiol	10.1099/ijs.0.027086-0	2011
Phylogeny	Pseudomonas marincola sp. nov., isolated from marine environments.	Romanenko LA, Uchino M, Tebo BM, Tanaka N, Frolova GM, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.65406-0	2008
Phylogeny	Pseudomonas peli sp. nov. and Pseudomonas borbori sp. nov., isolated from a nitrifying inoculum.	Vanparys B, Heylen K, Lebbe L, De Vos P	Int J Syst Evol Microbiol	10.1099/ijs.0.64224-0	2006

References

#7205	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17834
#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 )
#28038	IJSEM 1875 2006 ( DOI 10.1099/ijs.0.64224-0 , PubMed 16902024 )
#31765	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28038
#37533	; Curators of the CIP;
#60007	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53773
#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) .
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#116841	Collection of Institut Pasteur ; Curators of the CIP; CIP 109375
#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 borbori (CCUG 53773, DSM 17834, LMG 23199)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900115555

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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