Paenibacillus elgii (DSM 22254, CIP 108552, KCTC 10016BP)

Name: Paenibacillus elgii (DSM 22254, CIP 108552, KCTC 10016BP)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11607

Type strain

Strain Designation LGC-32714SD17, SD17

Culture col. no. DSM 22254 CIP 108552 KCTC 10016BP NBRC 100335 LGC-32714SD17 2 more

NCBI tax ID(s) 1349776 189691

Special Collections DSMZ KCTC CIP Literature strains

History <- M. Miyashita, Natl. Inst. of Technol. and Evaluation (NITE), Japan <- D.-S. Kim; SD17 CIP <- 2004, NBRC <- Korea Res. Inst. Biosci. Biotec., K.S. Bae: strain SD17

Links

Paenibacillus elgii LGC-32714SD17 is a facultative anaerobe, spore-forming, Gram-variable bacterium that was isolated from roots of Perilla frutescens.

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

Name and taxonomic classification

SI-ID 134440

DSM 22254,NBRC 100335,CIP 108552,LMG 24465,CIP 108599

@ref 20215

Last LPSN update 2026-02-09 11:20:36

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus elgii

Full scientific name Paenibacillus elgii Kim et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29886	variable	4 µm	0.9 µm	rod-shaped
119007	positive			rod-shaped
125439					91.5

Colony morphology

119007

Hemolysis ability1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16236	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l MnSO4 0.01 g/l Distilled water
16236	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
33202	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
36889	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119007	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
16236	positive	growth	30
29886	positive	growth	20-45
29886	positive	optimum	32.5
33202	positive	growth	30
36889	positive	growth	30
119007	positive	growth	22-55
119007	negative	growth	10

Culture pH

@ref	Ability	Type	PH	PH range
29886	positive	optimum	7
29886	positive	growth	6-8.5	alkaliphile
119007	positive	growth	6

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29886	facultative anaerobe
119007	facultative anaerobe
125439	aerobe	92.4

Spore formation

@ref	Spore formation	Confidence
29886
119007
125439		95.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29886	NaCl	positive	growth	0-2 %
29886	NaCl	positive	optimum	1 %
119007	NaCl	positive	growth	0-2 %
119007	NaCl		growth	4 %
119007	NaCl		growth	6 %
119007	NaCl		growth	8 %
119007	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
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
29886	4853 ChEBI	esculin	+	hydrolysis
119007	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
29886	17234 ChEBI	glucose	+	carbon source
29886	17754 ChEBI	glycerol	+	carbon source
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
119007	606565 ChEBI	hippurate	+	hydrolysis
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	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	43943 ChEBI	methyl alpha-D-mannoside	+	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
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
29886	17632 ChEBI	nitrate	+	reduction
119007	17632 ChEBI	nitrate	+	reduction
119007	17632 ChEBI	nitrate	+	respiration
119007	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
29886	33942 ChEBI	ribose	+	carbon source
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
29886	53423 ChEBI	tween 40	+	carbon source
68371	17151 ChEBI	xylitol	+	builds acid from	from API 50CH acid
29886	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29886	35581 ChEBI	indole
119007	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
119007	15688 ChEBI	acetoin	-
119007	17234 ChEBI	glucose		-
29886	35581 ChEBI	indole			+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119007	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
119007	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
119007	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
119007	caseinase	+	3.4.21.50
29886	catalase	+	1.11.1.6
119007	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
119007	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119007	gamma-glutamyltransferase	-	2.3.2.2
119007	gelatinase	+
119007	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
119007	lipase	+
68382	lipase (C 14)	+		from API zym
119007	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
119007	ornithine decarboxylase	-	4.1.1.17
119007	oxidase	-
119007	protease	+
68382	trypsin	-	3.4.21.4	from API zym
119007	tween esterase	+
119007	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
119007	-	+	+	+	+	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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
119007	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
119007	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	+	-	+	-	+	-	+	-	+	-	+	+	-	-	-	+	-	-	-	-	+	+	+	+	+	+	-	-	-	-	+	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	+	+	-	-	-	-	+	-	-	+	+	+	-	+	+	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
16236	roots of Perilla frutescens	Perilla frutescens	Seocheon County	Republic of Korea	KOR	Asia
119007	Plant, Roots of Perilla frutescens		Seocheon County	Republic of Korea	KOR	Asia	1999

Taxonmaps

69479

Global distribution of 16S sequence AY090110 (>99% sequence identity) for Paenibacillus from Microbeatlas

Aquatic Samples	35
Soil Samples	257
Animal Samples	97
Plant Samples	15
Total Samples	404

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16236	1	Risk group (German classification) According to TRBA 466
119007	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	ASM400086v1 assembly for Paenibacillus elgii NBRC 100335	contig	GCA_004000865	1349776.3	2839866320	1349776	46.24

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Paenibacillus elgii gene for 16S rRNA, partial sequence, strain: NBRC 100335	AB681151	1459		189691
16236	Paenibacillus elgii strain SD17 16S ribosomal RNA gene, partial sequence	AY090110	1471		189691

GC content

16236

GC-content (mol%)51.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus elgii NBRC 100335
NCBI: GCA_004000865

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	95.20	no
125439	motility	BacteriaNetⓘ	yes	91.50	no
125439	gram_stain	BacteriaNetⓘ	variable	89.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	92.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus elgii NBRC 100335
PATRIC: 1349776.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	56.21	yes
125438	anaerobic	anaerobicⓘ	no	96.86	yes
125438	spore-forming	spore-formingⓘ	yes	88.62	yes
125438	aerobic	aerobicⓘ	yes	56.35	no
125438	thermophilic	thermophileⓘ	no	96.61	yes
125438	flagellated	motile2+ⓘ	yes	82.53	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Paenibacillus larvae-Directed Bacteriophage HB10c2 and Its Application in American Foulbrood-Affected Honey Bee Larvae.	Beims H, Wittmann J, Bunk B, Sproer C, Rohde C, Gunther G, Rohde M, von der Ohe W, Steinert M.	Appl Environ Microbiol	10.1128/aem.00804-15	2015
Phylogeny	Paenibacillus tianmuensis sp. nov., isolated from soil.	Wu X, Fang H, Qian C, Wen Y, Shen X, Li O, Gao H	Int J Syst Evol Microbiol	10.1099/ijs.0.024109-0	2010
Phylogeny	Paenibacillus elgii sp. nov., with broad antimicrobial activity.	Kim DS, Bae CY, Jeon JJ, Chun SJ, Oh HW, Hong SG, Baek KS, Moon EY, Bae KS	Int J Syst Evol Microbiol	10.1099/ijs.0.02414-0	2004

References

#16236	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22254
#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 )
#26259	IJSEM 2031 2004 ( DOI 10.1099/ijs.0.02414-0 , PubMed 15545429 )
#29886	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 #26259
#33202	; Curators of the CIP;
#36889	; Curators of the CIP;
#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 .
#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 .
#119007	Collection of Institut Pasteur ; Curators of the CIP; CIP 108599
#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 elgii (DSM 22254, CIP 108552, KCTC 10016BP)

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

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_004000865

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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