Paenibacillus daejeonensis (DSM 15491, JCM 11236, KCTC 3745)

Name: Paenibacillus daejeonensis (DSM 15491, JCM 11236, KCTC 3745)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11561

Type strain

Strain Designation AP-20

Culture col. no. DSM 15491 JCM 11236 KCTC 3745 AP-20 CIP 107805 1 more

NCBI tax ID(s) 1122917 135193

Special Collections DSMZ JCM KCTC CIP

History <- K. S. Bae, Korea Research Inst. Bioscence and Biotechnol.; AP-20 J.-S. Lee AP-20. <- JS Lee, KRIBB CIP <- 2003, JCM <- 2001, Lee, strain AP-20

Links

Paenibacillus daejeonensis AP-20 is an aerobe, mesophilic, motile prokaryote that was isolated from soil.

motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 97892

KCTC 3745,JCM 11236,CIP 107805,DSM 15491,BCRC 17345,CCRC 17345

@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 daejeonensis

Full scientific name Paenibacillus daejeonensis Lee et al. 2002

BacDive ID	Other strains from **Paenibacillus daejeonensis** (1)	Type strain
161140	P. daejeonensis JCM 11237, KCTC 3750

Morphology

Cell morphology

@ref	Cell shape	Flagellum arrangement	Gram stain	Confidence
67771	rod-shaped	peritrichous
67771			variable
118844	rod-shaped		positive
125439				90.6

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5955	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
38232	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118844	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5955	positive	growth	30	mesophilic
38232	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic
118844	positive	growth	25-37	mesophilic
118844	negative	growth	10
118844	negative	growth	22
118844	negative	growth	45

Culture pH

@ref	Ability	Type	PH
118844	positive	growth	6

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
118844	obligate aerobe
125439	aerobe	94.8

Spore formation

@ref	Spore formation	Confidence
125438		92.249
125439		95.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
118844	NaCl	positive	growth	2 %
118844	NaCl		growth	0 %
118844	NaCl		growth	4 %
118844	NaCl		growth	6 %
118844	NaCl		growth	8 %
118844	NaCl		growth	10 %

Observation

@ref	Observation
67770	quinones: MK-7
67771	quinones: MK-7

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
118844	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	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	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
118844	4853 ChEBI	esculin	+	hydrolysis
68371	16813 ChEBI	galactitol	-	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
118844	606565 ChEBI	hippurate	+	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	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	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
118844	17632 ChEBI	nitrate	-	reduction
118844	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	15963 ChEBI	ribitol	-	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
118844	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
118844	15688 ChEBI	acetoin	-
118844	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
118844	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
118844	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
118844	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
118844	caseinase	-	3.4.21.50
118844	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
118844	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
118844	gamma-glutamyltransferase	-	2.3.2.2
118844	gelatinase	-
118844	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
118844	lipase	-
68382	lipase (C 14)	-		from API zym
118844	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
118844	ornithine decarboxylase	-	4.1.1.17
118844	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
118844	tryptophan deaminase	-
118844	tween esterase	-
118844	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
118844	-	-	+	+	-	+	-	-	-	-	-	+	-	+	-	-	+	-	-	-

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
118844	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
118844	not determinedn.d.	-	-	+	+	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	-	-	-	+	+	+	-	-	-	-	-	-	+	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5955	soil	Korea, Daejeon City	Republic of Korea	KOR	Asia
67770	Soil	Daejeon	Republic of Korea	KOR	Asia
67771	From soil	Daejeon	Republic of Korea	KOR	Asia
118844	Environment, Soil	Daejeon	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AF290916 (>99% sequence identity) for Paenibacillus daejeonensis subclade from Microbeatlas

Aquatic Samples
Soil Samples	5
Animal Samples
Plant Samples	9
Total Samples	14

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5955	1	Risk group (German classification) According to TRBA 466
118844	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	ASM37838v1 assembly for Paenibacillus daejeonensis DSM 15491	scaffold	GCA_000378385	1122917.3	2519103188	1122917	67.64

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Paenibacillus daejeonensis strain AP-20 16S ribosomal RNA gene, partial sequence	AF290916	1465		135193

GC content

@ref	GC-content (mol%)	Method
67770	53	high performance liquid chromatography (HPLC)
67771	53.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus daejeonensis DSM 15491
NCBI: GCA_000378385

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	95.50	no
125439	motility	BacteriaNetⓘ	yes	90.60	no
125439	gram_stain	BacteriaNetⓘ	variable	80.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	94.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus daejeonensis DSM 15491
PATRIC: 1122917.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	59.79	yes
125438	anaerobic	anaerobicⓘ	no	95.33	no
125438	spore-forming	spore-formingⓘ	yes	92.25	no
125438	aerobic	aerobicⓘ	yes	67.50	yes
125438	thermophilic	thermophileⓘ	no	94.66	yes
125438	flagellated	motile2+ⓘ	yes	83.72	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenetic analysis of the bacterial Pro-Pro-endopeptidase domain reveals a diverse family including secreted and membrane anchored proteins.	van Leeuwen HC, Roelofs D, Corver J, Hensbergen P.	Curr Res Microb Sci	10.1016/j.crmicr.2021.100024	2021
Phylogeny	Paenibacillus bryophyllum sp. nov., a nitrogen-fixing species isolated from Bryophyllum pinnatum.	Liu L, Yuan T, Yang F, Liu Z, Yang M, Peng G, Tan Z.	Antonie Van Leeuwenhoek	10.1007/s10482-018-1117-6	2018
Phylogeny	Paenibacillus selenii sp. nov., isolated from selenium mineral soil.	Xiang W, Wang G, Wang Y, Yao R, Zhang F, Wang R, Wang D, Zheng S.	Int J Syst Evol Microbiol	10.1099/ijs.0.063701-0	2014
Phylogeny	Paenibacillus brassicae sp. nov., isolated from cabbage rhizosphere in Beijing, China.	Gao M, Yang H, Zhao J, Liu J, Sun YH, Wang YJ, Sun JG.	Antonie Van Leeuwenhoek	10.1007/s10482-012-9849-1	2013
Phylogeny	Paenibacillus sophorae sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sophora japonica.	Jin HJ, Lv J, Chen SF.	Int J Syst Evol Microbiol	10.1099/ijs.0.021709-0	2011
Phylogeny	Paenibacillus forsythiae sp. nov., a nitrogen-fixing species isolated from rhizosphere soil of Forsythia mira.	Ma YC, Chen SF.	Int J Syst Evol Microbiol	10.1099/ijs.0.65238-0	2008
Phylogeny	Paenibacillus hispanicus sp. nov. isolated from Triticum aestivum roots.	Menendez E, Carro L, Tejedor C, Fernandez-Pascual M, Martinez-Molina E, Peix A, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijsem.0.001401	2016
Phylogeny	Paenibacillus tarimensis sp. nov., isolated from sand in Xinjiang, China.	Wang M, Yang M, Zhou G, Luo X, Zhang L, Tang Y, Fang C	Int J Syst Evol Microbiol	10.1099/ijs.0.65445-0	2008
Phylogeny	Paenibacillus daejeonensis sp. nov., a novel alkaliphilic bacterium from soil.	Lee JS, Lee KC, Chang YH, Hong SG, Oh HW, Pyun YR, Bae KS	Int J Syst Evol Microbiol	10.1099/00207713-52-6-2107	2002

References

#5955	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15491
#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 )
#38232	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#118844	Collection of Institut Pasteur ; Curators of the CIP; CIP 107805
#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 daejeonensis (DSM 15491, JCM 11236, KCTC 3745)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000378385

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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