Paenibacillus glycanilyticus (DSM 17608, CIP 107742, DS-1)

Name: Paenibacillus glycanilyticus (DSM 17608, CIP 107742, DS-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11590

Type strain

Strain Designation DS-1

Culture col. no. DSM 17608 CIP 107742 DS-1 JCM 11221 KCTC 3808 3 more

NCBI tax ID(s) 1220565 126569 2805379

Special Collections DSMZ JCM KCTC CIP

History DSMZ <- JCM <- A. Kobayashi, DS-1 JCM <-- A. Kobayashi DS-1. CIP <- 2002, JCM <- A. Kobayashi: strain DS-1

Links

Paenibacillus glycanilyticus DS-1 is an obligate aerobe, spore-forming, Gram-positive bacterium that was isolated from soil.

spore-forming Gram-positive motile rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 311030

JCM 11221,IFO 16618,NRRL B-23455,KCTC 3808,CIP 107742,NBRC 16618,DSM 17608,BCRC 17374,CCRC 17374,LMG 24743

@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 glycanilyticus

Full scientific name Paenibacillus glycanilyticus Dasman et al. 2002

BacDive ID	Other strains from **Paenibacillus glycanilyticus** (1)	Type strain
152649	P. glycanilyticus CCUG 47290

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
119697	positive	rod-shaped

Colony morphology

119697

Hemolysis ability0

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7081	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
39932	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119697	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7081	positive	growth	30
39932	positive	growth	30
67770	positive	growth	30
119697	positive	growth	22-45
119697	negative	growth	10
119697	negative	growth	55

Culture pH

@ref	Ability	Type	PH
119697	positive	growth	6

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
119697	obligate aerobe
125439	facultative anaerobe	92.359

Spore formation

@ref	Spore formation	Confidence
125438		92.23
125439		94.868
119697

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119697	NaCl	positive	growth	0-4 %
119697	NaCl		growth	6 %
119697	NaCl		growth	8 %
119697	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
119697	16947 ChEBI	citrate	-	carbon source
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
119697	4853 ChEBI	esculin	+	hydrolysis
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
119697	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	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
119697	17632 ChEBI	nitrate	+	reduction
119697	17632 ChEBI	nitrate	-	respiration
119697	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-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	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
119697	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
119697	15688 ChEBI	acetoin	-
119697	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
119697	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
119697	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
119697	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
119697	caseinase	-	3.4.21.50
119697	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
119697	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119697	gamma-glutamyltransferase	-	2.3.2.2
119697	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
119697	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
119697	ornithine decarboxylase	-	4.1.1.17
119697	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
119697	tween esterase	+
119697	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
119697	-	-	+	+	-	+	-	-	-	-	-	+	+	+	-	-	+	-	-	-

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
119697	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
119697	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
7081	soil	Osaka University Campus	Japan	JPN	Asia
67770	Soil sample from Osaka University Campus		Japan	JPN	Asia
119697	Environment, Soil		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB042938 (>99% sequence identity) for Paenibacillus from Microbeatlas

Aquatic Samples	439
Soil Samples	4491
Animal Samples	434
Plant Samples	2361
Total Samples	7725

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7081	1	Risk group (German classification) According to TRBA 466
119697	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
67770	ASM400080v1 assembly for Paenibacillus glycanilyticus NBRC 16618	contig	GCA_004000805	1220565.3	1220565	58.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7081	Paenibacillus sp. DS-1 gene for 16S rRNA	AB042938	1462		126569
67770	Paenibacillus glycanilyticus gene for 16S rRNA, partial sequence, strain: NBRC 16618	AB681087	1468		126569

GC content

@ref	GC-content (mol%)	Method
7081	50.5
67770	50.5	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM400080v1 assembly for Paenibacillus glycanilyticus NBRC 16618
BV-BRC: 1220565.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.36	no
125439	gram_stain	BacteriaNetⓘ	variable	74.53	no
125439	spore_formation	BacteriaNetⓘ	yes	94.87	no
125439	motility	BacteriaNetⓘ	yes	87.53	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus glycanilyticus NBRC 16618
PATRIC: 1220565.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	65.09	no
125438	anaerobic	anaerobicⓘ	no	94.96	yes
125438	spore-forming	spore-formingⓘ	yes	92.23	no
125438	aerobic	aerobicⓘ	yes	74.91	yes
125438	thermophilic	thermophileⓘ	no	96.83	yes
125438	flagellated	motile2+ⓘ	yes	84.46	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	A Comprehensive Analysis Using Colorimetry, Liquid Chromatography-Tandem Mass Spectrometry and Bioassays for the Assessment of Indole Related Compounds Produced by Endophytes of Selected Wheat Cultivars.	Kuzniar A, Wlodarczyk K, Sadok I, Staniszewska M, Wozniak M, Furtak K, Grzadziel J, Galazka A, Skorzynska-Polit E, Wolinska A.	Molecules	10.3390/molecules26051394	2021
Enzymology	Purification and properties of an enzyme capable of degrading the polysaccharide of the cyanobacterium, Nostoc commune.	Dasman, Kajiyama S, Okazawa A, Fukusaki E, Kobayashi A	Z Naturforsch C J Biosci	10.1515/znc-2002-11-1215	2002
Phylogeny	Paenibacillus glycanilyticus subsp. hiroshimensis subsp. nov., isolated from leaf soil collected in Japan.	Akita H, Itoiri Y, Takeda N, Matsushika A, Kimura ZI	Arch Microbiol	10.1007/s00203-020-02166-6	2021
Phylogeny	Paenibacillusliaoningensis sp. nov., isolated from soil.	Ai HX, Che YC, Wang L, Zhang L, Gu Y, Tan YN, Chang AK, Liu HS	Int J Syst Evol Microbiol	10.1099/ijsem.0.001159	2016
Phylogeny	Paenibacillus lupini sp. nov., isolated from nodules of Lupinus albus.	Carro L, Flores-Felix JD, Ramirez-Bahena MH, Garcia-Fraile P, Martinez-Hidalgo P, Igual JM, Tejedor C, Peix A, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijs.0.060830-0	2014
Phylogeny	Paenibacillus endophyticus sp. nov., isolated from nodules of Cicer arietinum.	Carro L, Flores-Felix JD, Cerda-Castillo E, Ramirez-Bahena MH, Igual JM, Tejedor C, Velazquez E, Peix A	Int J Syst Evol Microbiol	10.1099/ijs.0.050310-0	2013
Phylogeny	Paenibacillus catalpae sp. nov., isolated from the rhizosphere soil of Catalpa speciosa.	Zhang J, Wang ZT, Yu HM, Ma Y	Int J Syst Evol Microbiol	10.1099/ijs.0.040659-0	2012
Phylogeny	Paenibacillus algorifonticola sp. nov., isolated from a cold spring.	Tang QY, Yang N, Wang J, Xie YQ, Ren B, Zhou YG, Gu MY, Mao J, Li WJ, Shi YH, Zhang LX	Int J Syst Evol Microbiol	10.1099/ijs.0.025346-0	2010
Phylogeny	Paenibacillus prosopidis sp. nov., isolated from the nodules of Prosopis farcta.	Valverde A, Fterich A, Mahdhi M, Ramirez-Bahena MH, Caviedes MA, Mars M, Velazquez E, Rodriguez-Llorente ID	Int J Syst Evol Microbiol	10.1099/ijs.0.014241-0	2009
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 xinjiangensis sp. nov., isolated from Xinjiang province in China.	Lim JM, Jeon CO, Park DJ, Xu LH, Jiang CL, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64465-0	2006
Phylogeny	Paenibacillus glycanilyticus sp. nov., a novel species that degrades heteropolysaccharide produced by the cyanobacterium Nostoc commune.	Dasman, Kajiyama S, Kawasaki H, Yagi M, Seki T, Fukusaki E, Kobayashi A	Int J Syst Evol Microbiol	10.1099/00207713-52-5-1669	2002

References

#7081	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17608
#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 )
#39932	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#119697	Collection of Institut Pasteur ; Curators of the CIP; CIP 107742
#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 glycanilyticus (DSM 17608, CIP 107742, DS-1)

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_004000805

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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