Paenibacillus polymyxa (DSM 13815, CECT 5266, B.3)

Name: Paenibacillus polymyxa (DSM 13815, CECT 5266, B.3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11551

Type strain

Strain Designation B.3, B3

Culture col. no. DSM 13815 CECT 5266 B.3 CIP 107276 B3

NCBI tax ID(s) 114136

Special Collections DSMZ CIP

History <- DSMZ <- A. Ramos; B.3 CIP <- 2001, CECT <- 1999, A. Ramos-Cormenzana, strain: B3

Links

Paenibacillus polymyxa B.3 is a facultative anaerobe, mesophilic, Gram-negative prokaryote that was isolated from alpechin.

Gram-negative rod-shaped facultative anaerobe mesophilic 16S sequence

Name and taxonomic classification

SI-ID 87830

CECT 5266,DSM 13815,KCTC 13919,NCIMB 13897,CIP 107276,KACC 10925,BCRC 17350,CCRC 17350,LMG 21667

@ref 20215

Last LPSN update 2026-02-09 11:20:35

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus polymyxa

Full scientific name Paenibacillus polymyxa (Prazmowski 1880) Ash et al. 1994

Synonyms (4)

"Clostridium polymyxa"
Bacillus polymyxa
Paenibacillus jamilae
"Aerobacillus polymyxa"

BacDive ID	Other strains from **Paenibacillus polymyxa** (36)	Type strain
11487	P. polymyxa DSM 36, ATCC 842, BUCSAV 162, CCM 1459, JCM ... (type strain)
11480	P. polymyxa DSM 292, CCM 1609, CCUG 26011, LMG 6320, ...
11481	P. polymyxa 354, DSM 356, ATCC 8523, CCM 1465, CIP A45, ...
11482	P. polymyxa II, DSM 365
11483	P. polymyxa III, DSM 372
11484	P. polymyxa X16, DSM 740, ATCC 31325
11485	P. polymyxa V3, X18, DSM 741, ATCC 31326
11486	P. polymyxa TS3, X20, DSM 742
135868	P. polymyxa CIP 103698
136141	P. polymyxa NRS-279, 8277, CIP A39, ATCC 7070, NRRL B-368
136173	P. polymyxa CIP 103121, CN 2366
136174	P. polymyxa 11D2, CIP 103124
137194	P. polymyxa NRS-252, CIP 52.77, NRRL B-367, NRRL: B-367
137195	P. polymyxa CIP 52.78, ATCC 7047, NRRL B-366, NRRL: B-366
137949	P. polymyxa 239-86, CIP 102271
137957	P. polymyxa 263-86, CIP 102287
138780	P. polymyxa CIP A43, NCTC 1380, NRRL NRS-1238, NRRL: ...
138795	P. polymyxa CIP A48
139222	P. polymyxa CIP A40
139230	P. polymyxa CIP A46, NRRL B-465, NRRL: B-465
140662	P. polymyxa EG2,
141599	P. polymyxa CCUG 3378, IAM 12566
145818	P. polymyxa CCUG 29690 A
146828	P. polymyxa CCUG 32191
147439	P. polymyxa CCUG 33583
148295	P. polymyxa CCUG 35174, ATCC 43865
151953	P. polymyxa CCUG 45338
161991	P. polymyxa JCM 17240, FERM P-19158
162756	P. polymyxa JCM 20106, IAM 1210, IFO 3020, NBRC 3020
162907	P. polymyxa JCM 20385, ATCC 10401, BUCSAV 163, CCM 1460, ...
165732	P. polymyxa JCM 8035, IAM 19064
165733	P. polymyxa JCM 8036, IAM 19068
165734	P. polymyxa JCM 8037, IAM 19077
165735	P. polymyxa JCM 8038, IAM 19110
165736	P. polymyxa JCM 8039, IAM 19111
174355	P. polymyxa MVY-024, DSM 114788

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
120307	negative	rod-shaped

Colony morphology

120307

Hemolysis ability1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5172	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
33736	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120307	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5172	positive	growth	30	mesophilic
33736	positive	growth	30	mesophilic
120307	positive	growth	22-45
120307	negative	growth	10
120307	negative	growth	55

Culture pH

@ref	Ability	Type	PH
120307	positive	growth	6

Physiology and metabolism

Oxygen tolerance

120307

Oxygen tolerancefacultative anaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
120307	NaCl	positive	growth	0-4 %
120307	NaCl		growth	6 %
120307	NaCl		growth	8 %
120307	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
120307	16947 ChEBI	citrate	-	carbon source
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	17924 ChEBI	D-sorbitol	-	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
120307	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	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
120307	606565 ChEBI	hippurate	+	hydrolysis
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
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
120307	17632 ChEBI	nitrate	+	reduction
120307	17632 ChEBI	nitrate	+	respiration
120307	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		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	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	+	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
120307	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
120307	15688 ChEBI	acetoin	+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
120307	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
120307	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
120307	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120307	caseinase	+	3.4.21.50
120307	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
120307	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
120307	gamma-glutamyltransferase	-	2.3.2.2
120307	gelatinase	-
120307	lecithinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
120307	lipase	-
68382	lipase (C 14)	-		from API zym
120307	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
120307	ornithine decarboxylase	-	4.1.1.17
120307	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
120307	tween esterase	+
120307	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
120307	-	-	+	+	-	-	-	-	-	-	-	-	+	+	-	-	+	-	-	-

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
120307	not determinedn.d.	+	-	-	+	+	+	-	-	+/-	+	+	+	+	-	-	-	-	+	-	+/-	+	-	+	+	+	+	+	+	+	+	+	+	+/-	-	+	+	+	-	+	+	-	-	-	-	-	-	-	-	-

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
120307	not determinedn.d.	+	+	+	+	+	-	+	-	+	-	-	-	-	+	-	-	-	-	+	+	+	+	+	+	-	+	-	-	-	-	-	+	-	+	+	+	-	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	-	-	+	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Industrial wastewater

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
5172	alpechin	Spain	ESP	Europe
120307	Environment, Olive-mill wastewater	Spain	ESP	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5172	1	Risk group (German classification) According to TRBA 466
120307	1	Risk group (French classification) According to TRBA 466

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5172	Paenibacillus jamilae partial 16S rRNA gene, strain CECT 5266	AJ271157	1538		114136

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park.	Mead DA, Lucas S, Copeland A, Lapidus A, Cheng JF, Bruce DC, Goodwin LA, Pitluck S, Chertkov O, Zhang X, Detter JC, Han CS, Tapia R, Land M, Hauser LJ, Chang YJ, Kyrpides NC, Ivanova NN, Ovchinnikova G, Woyke T, Brumm C, Hochstein R, Schoenfeld T, Brumm P.	Stand Genomic Sci	10.4056/sigs.2605792	2012
	Noncontiguous finished genome sequences and descriptions of 'Paenibacillus bouchesdurhonensis,' 'Paenibacillus rubinfantis,' 'Paenibacillus senegalimassiliensis' and 'Paenibacillus tuaregi' identified by culturomics.	Pham TP, Tidjani Alou M, Traore SI, Brah S, Ali Diallo B, Diallo A, Sokhna C, Baptiste E, Levasseur A, Fournier PE, Cadoret F, Raoult D.	New Microbes New Infect	10.1016/j.nmni.2017.07.004	2017
	Microbial extracellular polymeric substances: central elements in heavy metal bioremediation.	Pal A, Paul AK.	Indian J Microbiol	10.1007/s12088-008-0006-5	2008
Stress	Heavy metals-resistant bacteria (HM-RB): Potential bioremediators of heavy metals-stressed Spinacia oleracea plant.	Desoky EM, Merwad AM, Semida WM, Ibrahim SA, El-Saadony MT, Rady MM	Ecotoxicol Environ Saf	10.1016/j.ecoenv.2020.110685	2020
Phylogeny	Genome-based reclassification of Paenibacillus jamilae Aguilera et al. 2001 as a later heterotypic synonym of Paenibacillus polymyxa (Prazmowski 1880) Ash et al. 1994.	Kwak MJ, Choi SB, Ha SM, Kim EH, Kim BY, Chun J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004140	2020
Biotechnology	Integrative application of heavy metal-resistant bacteria, moringa extracts, and nano-silicon improves spinach yield and declines its contaminant contents on a heavy metal-contaminated soil.	Eltahawy AMAE, Awad EAM, Ibrahim AH, Merwad AMA, Desoky EM	Front Plant Sci	10.3389/fpls.2022.1019014	2022
Genetics	Paenibacillus phocaensis sp. nov., isolated from the gut microbiota of a healthy infant.	Tidjani Alou M, Rathored J, Nguyen TT, Andrieu C, Couderc C, Brah S, Diallo BA, Fournier PE, Raoult D, Dubourg G.	New Microbes New Infect	10.1016/j.nmni.2016.12.001	2017
Phylogeny	Paenibacillus woosongensis sp. nov., a xylanolytic bacterium isolated from forest soil.	Lee JC, Yoon KH	Int J Syst Evol Microbiol	10.1099/ijs.0.65350-0	2008
Phylogeny	Paenibacillus jamilae sp. nov., an exopolysaccharide-producing bacterium able to grow in olive-mill wastewater.	Aguilera M, Monteoliva-Sanchez M, Suarez A, Guerra V, Lizama C, Bennasar A, Ramos-Cormenzana A	Int J Syst Evol Microbiol	10.1099/00207713-51-5-1687	2001
Phylogeny	Paenibacillus ottowii sp. nov. isolated from a fermentation system processing bovine manure.	Velazquez LF, Rajbanshi S, Guan S, Hinchee M, Welsh A	Int J Syst Evol Microbiol	10.1099/ijsem.0.003672	2020
Phylogeny	Paenibacillus beijingensis sp. nov., a nitrogen-fixing species isolated from wheat rhizosphere soil.	Wang LY, Li J, Li QX, Chen SF	Antonie Van Leeuwenhoek	10.1007/s10482-013-9974-5	2013

References

#5172	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13815
#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 )
#33736	; Curators of the CIP;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#120307	Collection of Institut Pasteur ; Curators of the CIP; CIP 107276
#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 polymyxa (DSM 13815, CECT 5266, B.3)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

16S sequences

Genome-based predictions

Literature

Literature

References

BacDive

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