Paenibacillus chondroitinus (DSM 5051, NRRL NRS-1351, CCUG 28527)

Name: Paenibacillus chondroitinus (DSM 5051, NRRL NRS-1351, CCUG 28527)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11467

Type strain

Strain Designation 1351

Culture col. no. DSM 5051 NRRL NRS-1351 CCUG 28527 1351 JCM 9072 9 more

NCBI tax ID(s) 1220560 59842

Special Collections DSMZ CCUG JCM KCTC CIP

History <- NRRL <- N.R. Smith, 1351 (Bacillus circulans) <- F.E. Clark NRRL NRS-1351 <-- N. R. Smith NRS-1351. CIP <- 1988, L.K. Nakamura, NRRL <- N.R. Smith: strain NRS-1351, Bacillus circulans <- F.E. Clark

Links

Paenibacillus chondroitinus 1351 is an obligate aerobe, Gram-negative, motile bacterium that was isolated from soil.

Gram-negative motile rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 10614

LMG 18040,ATCC 51184,DSM 5051,IFO 15376,JCM 9072,NCIMB 12518,NRRL NRS-1351,CCUG 28527,CIP 103123,NCIB 12518,CCM 4538,KCTC 3568,NBRC 15376,CFBP 4265,BCRC 15913,CCRC 15913,KCTC 3857,KACC 10841

@ref 20215

Last LPSN update 2026-02-09 11:20:33

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus chondroitinus

Full scientific name Paenibacillus chondroitinus (Nakamura 1987) Shida et al. 1997

Synonyms (1)

Bacillus chondroitinus

BacDive ID	Other strains from **Paenibacillus chondroitinus** (1)	Type strain
11468	P. chondroitinus DSM 13409, HSCC 612, NRRL B-14420

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
118255	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
35489	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
1915	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
118255	CIP Medium 3	Medium recipe at CIP
118255	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
1915	positive	growth	30
35489	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

118255

Oxygen toleranceobligate aerobe

Spore formation

@ref	Spore formation	Confidence
125438		91.003

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	+	fermentation	from API 20E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
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	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68368	16899 ChEBI	D-mannitol	-	fermentation	from API 20E
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	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68368	30849 ChEBI	L-arabinose	-	fermentation	from API 20E
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68368	28053 ChEBI	melibiose	+	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
118255	17632 ChEBI	nitrate	-	reduction
118255	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
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
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68368	17992 ChEBI	sucrose	+	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
118255	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	+		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

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
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	+	3.2.1.23	from API zym
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	+	3.2.1.31	from API zym
118255	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
68368	gelatinase	+		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
118255	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
118255	urease	-	3.5.1.5
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	-		from API zym

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
49272	+	-	-	-	-	-	-	-	-	+	+	+	-	-	-	-	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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
118255	-	-	+	+	-	+	-	-	-	-	+	+	-	+	+	+	-	-	-	-

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
49272	-	-	-	-	+	+	+	-	-	+	-	+	+	+	-	-	-	-	+	-	-	-	+	-	+	+	+	+	+	+	+	+	+	-	-	+	+	+	-	+	+	-	-	-	-	-	-	-	-	-
118255	not determinedn.d.	-	-	-	+/-	+/-	+/-	-	-	+/-	+/-	+/-	+/-	+/-	-	+/-	-	+/-	+/-	-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	-	+/-	+/-	-	-	-	+/-	+/-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type
1915	soil
49272	Soil
67770	Soil
118255	Environment, Soil

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1915	1	Risk group (German classification) According to TRBA 466
118255	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	ASM400076v1 assembly for Paenibacillus chondroitinus NBRC 15376	contig	GCA_004000765	1220560.3	1220560	56.91

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Paenibacillus chondroitinus partial 16S rRNA gene, isolate OS-213.a	AM237395	970	59842
20218	Paenibacillus chondroitinus DNA for 16S rRNA	D82064	1417	59842
20218	Paenibacillus chondroitinus gene for 16S rRNA, partial sequence	AB073206	1486	59842
20218	Paenibacillus chondroitinus gene for 16S rRNA, partial sequence, strain: NBRC 15376	AB680849	1461	59842

GC content

@ref	GC-content (mol%)	Method
1915	45.1-46.0
67770	47-48	Buoyant density centrifugation (BD)
67770	49	Buoyant density centrifugation (BD)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus chondroitinus NBRC 15376
NCBI: GCA_004000765

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	81.20	no
125439	motility	BacteriaNetⓘ	yes	73.70	no
125439	gram_stain	BacteriaNetⓘ	variable	80.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	87.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus chondroitinus NBRC 15376
PATRIC: 1220560.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	59.48	no
125438	anaerobic	anaerobicⓘ	no	91.96	yes
125438	spore-forming	spore-formingⓘ	yes	91.00	no
125438	aerobic	aerobicⓘ	yes	77.04	yes
125438	thermophilic	thermophileⓘ	no	94.70	yes
125438	flagellated	motile2+ⓘ	yes	79.38	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Development of quantitative real-time PCR assays for detection and quantification of surrogate biological warfare agents in building debris and leachate.	Saikaly PE, Barlaz MA, de Los Reyes FL.	Appl Environ Microbiol	10.1128/aem.00779-07	2007
Phylogeny	Differentiation of Paenibacillus larvae subsp. larvae, the cause of American foulbrood of honeybees, by using PCR and restriction fragment analysis of genes encoding 16S rRNA.	Alippi AM, Lopez AC, Aguilar OM.	Appl Environ Microbiol	10.1128/aem.68.7.3655-3660.2002	2002
	In vitro and in vivo production and split-intein mediated ligation (SIML) of circular bacteriocins.	Pena N, Bland MJ, Sevillano E, Munoz-Atienza E, Lafuente I, Bakkoury ME, Cintas LM, Hernandez PE, Gabant P, Borrero J.	Front Microbiol	10.3389/fmicb.2022.1052686	2022
Phylogeny	Paenibacillus alba nov., isolated from peat soil.	Kim HS, Srinivasan S, Lee SS	Curr Microbiol	10.1007/s00284-015-0795-9	2015
Genetics	Paenibacillus allorhizoplanae sp. nov. from the rhizoplane of a Zea mays root.	Kampfer P, Lipski A, Lamothe L, Clermont D, Criscuolo A, McInroy JA, Glaeser SP.	Arch Microbiol	10.1007/s00203-022-03225-w	2022
Phylogeny	Paenibacillus silvestris sp. nov., Isolated from Forest Soil.	Kim J, Jung HS, Baek JH, Chun BH, Khan SA, Jeon CO	Curr Microbiol	10.1007/s00284-020-02333-4	2021
Phylogeny	Paenibacillus anseongense sp. nov. a Silver Nanoparticle Producing Bacterium Isolated from Rhizospheric Soil.	Huq MA	Curr Microbiol	10.1007/s00284-020-02086-0	2020
Phylogeny	Paenibacillus aceris sp. nov., isolated from the rhizosphere of Acer okamotoanum, a plant native to Ulleungdo Island, Republic of Korea.	Hwang YJ, Ghim SY	Int J Syst Evol Microbiol	10.1099/ijsem.0.001748	2017
Phylogeny	Paenibacillus oryzisoli sp. nov., isolated from the rhizosphere of rice.	Zhang J, Ma XT, Gao JS, Zhang CW, Zhao JJ, Zhang RJ, Ma LA, Zhang XX	Antonie Van Leeuwenhoek	10.1007/s10482-016-0777-3	2016
Phylogeny	Paenibacillus ferrarius sp. nov., isolated from iron mineral soil.	Cao Y, Chen F, Li Y, Wei S, Wang G	Int J Syst Evol Microbiol	10.1099/ijs.0.063552-0	2014
Phylogeny	Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China.	Ming H, Nie GX, Jiang HC, Yu TT, Zhou EM, Feng HG, Tang SK, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-012-9738-7	2012
Phylogeny	Paenibacillus aestuarii sp. nov., isolated from an estuarine wetland.	Bae JY, Kim KY, Kim JH, Lee K, Cho JC, Cha CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.011544-0	2009
Phylogeny	Paenibacillus pectinilyticus sp. nov., isolated from the gut of Diestrammena apicalis.	Park DS, Jeong WJ, Lee KH, Oh HW, Kim BC, Bae KS, Park HY	Int J Syst Evol Microbiol	10.1099/ijs.0.002261-0	2009

References

#1915	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5051
#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 )
#35489	; Curators of the CIP;
#49272	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 28527
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#118255	Collection of Institut Pasteur ; Curators of the CIP; CIP 103123
#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 chondroitinus (DSM 5051, NRRL NRS-1351, CCUG 28527)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

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_004000765

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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