Paenibacillus urinalis (DSM 22281, CCUG 53521, CIP 109357)

Name: Paenibacillus urinalis (DSM 22281, CCUG 53521, CIP 109357)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11630

Type strain

Strain Designation 5402403

Culture col. no. DSM 22281 CCUG 53521 CIP 109357 5402403

NCBI tax ID(s) 521520

Special Collections DSMZ CCUG CIP Literature strains

History CIP <- 2006, V. Roux, Timone Hosp., Marseille, France: strain 5402403 DSMZ <- CCUG; CCUG 53521 <- V. Roux; Timone hospital, Marseille, France; 5402403 CIP <- 2006, V. Roux, Timone Hosp., Marseille, France: strain 5402403

Links

Paenibacillus urinalis 5402403 is a facultative anaerobe, spore-forming, Gram-negative bacterium that was isolated from Human urine, 36-yr-old woman.

spore-forming Gram-negative motile rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 343460

CCUG 53521,CIP 109357,DSM 22281

@ref 20215

Last LPSN update 2026-05-29 08:27:36

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus urinalis

Full scientific name Paenibacillus urinalis Roux et al. 2008

BacDive ID	Other strains from **Paenibacillus urinalis** (3)	Type strain
131166	P. urinalis T3_4, DSM 31034
132097	P. urinalis D3_2, DSM 103743
154862	P. urinalis CCUG 55452

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32267	negative	3.2 µm	1 µm	rod-shaped
123753	positive			rod-shaped
125439					92.539

Pigmentation

32267

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16176	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l MnSO4 0.01 g/l Distilled water
37526	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123753	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
16176	positive	growth	35
32267	positive	growth	30-37
32267	positive	optimum	33.5
37526	positive	growth	37
59923	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32267	facultative anaerobe
59923	aerobe
123753	facultative anaerobe
125439	facultative anaerobe	95.478

Spore formation

@ref	Spore formation	Confidence
32267
125439		96.92
125438		92.534

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32267	NaCl	positive	growth	5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
32267	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
32267	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	builds acid from	from API 50CH acid
32267	17234 ChEBI	glucose	+	carbon source
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	+	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	+	builds acid from	from API 50CH acid
32267	17306 ChEBI	maltose	+	carbon source
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
32267	29864 ChEBI	mannitol	+	carbon source
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	+	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
32267	506227 ChEBI	N-acetylglucosamine	+	carbon source
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
123753	17632 ChEBI	nitrate	-	reduction
123753	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123753	35581 ChEBI	indole

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
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
32267	catalase	+	1.11.1.6
123753	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
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
123753	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
123753	urease	+	3.5.1.5
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
123753	-	-	+	+	-	+	-	-	-	+	-	+	+	+	-	-	+	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
123753	not determinedn.d.	-	-	-	+	+	+	-	-	+	+	+	+	+	-	+	-	-	+	+/-	+/-	+/-	+	+	+	+	+	+	+	+	+	+	+/-	-	+/-	+	+	-	-	+/-	+/-	-	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	#Female
#Host Body Product	#Fluids	#Urine

Isolation

@ref	Sample type	Host species	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
16176	Human urine, 36-yr-old woman	Homo sapiens		Timone hospital, Marseille	France	FRA	Europe
59923	Human urine,36-yr-old woman	Homo sapiens	2005-11-01	Marseille,Timone hospital	France	FRA	Europe
123753	Human, Urine	Homo sapiens		Marseille	France	FRA	Europe	2005

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
16176	yes, in single cases	1	Risk group (German classification) According to TRBA 466
123753		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	IMG accession	NCBI tax ID	Score	BV-BRC accession	INSDC accession
66792	Paenibacillus urinalis DSM 22281	complete	2901084651	521520	95.75
66792	Paenibacillus urinalis strain DSM 22281	contig		521520	75.03	521520.3
124043	ASM4267882v1 assembly for Paenibacillus urinalis CCUG 53521	scaffold		521520	73.79		GCA_042678825

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16176	Paenibacillus urinalis strain 5402403 16S ribosomal RNA gene, partial sequence	EF212892	1403		1204727

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus urinalis strain DSM 22281
BV-BRC: 521520.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	95.48	no
125439	gram_stain	BacteriaNetⓘ	variable	69.84	no
125439	motility	BacteriaNetⓘ	yes	92.54	no
125439	spore_formation	BacteriaNetⓘ	yes	96.92	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus urinalis strain DSM 22281
PATRIC: 521520.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	58.36	yes
125438	anaerobic	anaerobicⓘ	no	96.19	yes
125438	spore-forming	spore-formingⓘ	yes	92.53	no
125438	aerobic	aerobicⓘ	yes	57.22	no
125438	thermophilic	thermophileⓘ	no	91.63	no
125438	flagellated	motile2+ⓘ	yes	83.15	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus shunpengii sp. nov., isolated from farmland soil.	Yang YJ, Zhang YT, Chen GQ, Cheng D, Qiu JG, He Q, He J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002484	2017
Phylogeny	Paenibacillus insulae sp. nov., isolated from soil.	Cho SJ, Cho SH, Kim TS, Park SH, Kim SB, Lee GH	J Microbiol	10.1007/s12275-015-4610-x	2015
Phylogeny	Paenibacillus provencensis sp. nov., isolated from human cerebrospinal fluid, and Paenibacillus urinalis sp. nov., isolated from human urine.	Roux V, Fenner L, Raoult D	Int J Syst Evol Microbiol	10.1099/ijs.0.65228-0	2008

References

#16176	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22281
#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 )
#28508	IJSEM 682 2008 ( DOI 10.1099/ijs.0.65228-0 , PubMed 18319478 )
#32267	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 #28508
#37526	; Curators of the CIP;
#59923	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53521
#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) .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#123753	Collection of Institut Pasteur ; Curators of the CIP; CIP 109357
#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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Paenibacillus urinalis (DSM 22281, CCUG 53521, CIP 109357)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042678825

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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