Paenibacillus validus (DSM 3037, ATCC 43897, LMG 11161)

Name: Paenibacillus validus (DSM 3037, ATCC 43897, LMG 11161)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11488

Type strain

Culture col. no. DSM 3037 ATCC 43897 LMG 11161 NCIMB 12782 NRRL NRS-1000 12 more

NCBI tax ID(s) 1349783 44253

Special Collections DSMZ CCUG JCM KCTC CIP

History <- NRRL <- N.R. Smith, 1000 (Bacillus circulans) <- J.R. Porter <- G. Bredemann (Bacillus validus, 1) NRRL NRS-1000 <-- N. R. Smith NRS-1000 <-- J. R. Porter V1 <-- G. Bredemann. CIP <- 1988, L.K. Nakamura, Nat. Center Agri. Util. Res., Illinois, USA: strain NRS-1000, Bacillus validus

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Paenibacillus validus DSM 3037 is an obligate aerobe, mesophilic, Gram-positive prokaryote that was isolated from soil.

Gram-positive motile rod-shaped obligate aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 1210

LMG 11161,ATCC 43897,CIP 103120,DSM 3037,NCIMB 12782,CCUG 28520,NRRL B-14484,CCUG 27416,JCM 9077,CCM 3894,IFO 15382,KCTC 3401,CIP 106931,NBRC 15382,CFBP 4263,BCRC 15911,CCRC 15911,KCTC 3859,NRRL NRS-1000

@ref 20215

Last LPSN update 2026-02-09 11:20:34

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus validus

Full scientific name Paenibacillus validus (Nakamura 1984 ex Bredemann and Heigener 1935) Ash et al. 1994

Synonyms (3)

Paenibacillus gordonae
Bacillus gordonae
Bacillus validus

BacDive ID	Other strains from **Paenibacillus validus** (15)	Type strain
11489	P. validus Q1, DSM 5395, ATCC 29948, LMG 9817, NCIB ...
11490	P. validus Q13, DSM 6390
11491	P. validus Q12, DSM 6543, LMG 14664
11492	P. validus Pohb3, DSM 6544, LMG 14667
11493	P. validus DSM 6545, Tri 4
11494	P. validus Q2, DSM 6554
135182	P. validus CIP 103495
135258	P. validus CIP 103496
135259	P. validus CIP 103497
145015	P. validus CCUG 27416, NRRL NRS 1000
147965	P. validus CCUG 34590
153333	P. validus CCUG 49249
154069	P. validus CCUG 52230
154507	P. validus CCUG 53941
154677	P. validus CCUG 54819

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
123787	positive	rod-shaped
125439				93.6

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1279	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
34116	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
123787	CIP Medium 72	Medium recipe at CIP
123787	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1279	positive	growth	30	mesophilic
34116	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
123787	obligate aerobe
125439	aerobe	95.8

Spore formation

@ref	Spore formation	Confidence
125439		96
125438		90.837

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
123787	17632 ChEBI	nitrate	+	reduction
123787	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123787	35581 ChEBI	indole

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
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
123787	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
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
123787	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
123787	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
123787	-	-	+	-	-	+	-	-	-	-	-	+	-	-	-	-	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type
1279	soil
123787	Environment, Soil

Taxonmaps

69479

Global distribution of 16S sequence AB073203 (>99% sequence identity) for Paenibacillus validus subclade from Microbeatlas

Aquatic Samples	577
Soil Samples	2020
Animal Samples	722
Plant Samples	483
Total Samples	3802

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1279	1	Risk group (German classification) According to TRBA 466
123787	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	ASM400098v1 assembly for Paenibacillus validus NBRC 15382	contig	GCA_004000985	1349783.3	8117258880	1349783	48.04

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Paenibacillus validus strain DSM3037 DNA for 16S ribosomal RNA, partial sequence	D78320	1424	44253
20218	Paenibacillus validus gene for 16S rRNA, partial sequence	AB073203	1487	44253
20218	Paenibacillus validus gene for 16S rRNA, partial sequence, strain: NBRC 15382	AB680854	1466	44253
20218	Paenibacillus validus ribosomal RNA small subunit ribosomal RNA gene, complete sequence	M77489	1418	44253

GC content

@ref	GC-content (mol%)	Method
1279	53.9
67770	54	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 validus NBRC 15382
NCBI: GCA_004000985

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	96.00	no
125439	motility	BacteriaNetⓘ	yes	93.60	no
125439	gram_stain	BacteriaNetⓘ	variable	88.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	95.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus validus NBRC 15382
PATRIC: 1349783.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	58.10	no
125438	anaerobic	anaerobicⓘ	no	94.78	no
125438	spore-forming	spore-formingⓘ	yes	90.84	no
125438	aerobic	aerobicⓘ	yes	76.42	yes
125438	thermophilic	thermophileⓘ	no	89.86	yes
125438	flagellated	motile2+ⓘ	yes	80.24	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Isolation from the Sorghum bicolor mycorrhizosphere of a bacterium compatible with arbuscular mycorrhiza development and antagonistic towards soilborne fungal pathogens.	Budi SW, van Tuinen D, Martinotti G, Gianinazzi S.	Appl Environ Microbiol	10.1128/aem.65.11.5148-5150.1999	1999
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
Metabolism	Uncovering the protocatechuate 2,3-cleavage pathway genes.	Kasai D, Fujinami T, Abe T, Mase K, Katayama Y, Fukuda M, Masai E.	J Bacteriol	10.1128/jb.00840-09	2009
Metabolism	The bacterium Paenibacillus validus stimulates growth of the arbuscular mycorrhizal fungus Glomus intraradices up to the formation of fertile spores.	Hildebrandt U, Ouziad F, Marner FJ, Bothe H	FEMS Microbiol Lett	10.1111/j.1574-6968.2005.00027.x	2006
Metabolism	Isolation and characterization of a gene cluster for dibenzofuran degradation in a new dibenzofuran-utilizing bacterium, Paenibacillus sp. strain YK5.	Iida T, Nakamura K, Izumi A, Mukouzaka Y, Kudo T	Arch Microbiol	10.1007/s00203-005-0045-9	2005
Enzymology	Paenibacillus (formerly Bacillus) gordonae (Pichinoty et al. 1986) Ash et al. 1994 is a later subjective synonym of Paenibacillus (formerly Bacillus) validus (Nakamura 1984) Ash et al. 1994: emended description of P. validus.	Heyndrickx M, Vandemeulebroecke K, Scheldeman P, Hoste B, Kersters K, De Vos P, Logan NA, Aziz AM, Ali N, Berkeley RC	Int J Syst Bacteriol	10.1099/00207713-45-4-661	1995
	Paenibacillus agilis sp. nov., Paenibacillus cremeus sp. nov. and Paenibacillus terricola sp. nov., isolated from rhizosphere soils.	Kim J, Chhetri G, Kim I, So Y, Seo T.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005640	2022
Phylogeny	Paenibacillus xylanisolvens sp. nov., a xylan-degrading bacterium from soil.	Khianngam S, Tanasupawat S, Akaracharanya A, Kim KK, Lee KC, Lee JS	Int J Syst Evol Microbiol	10.1099/ijs.0.022269-0	2010
Phylogeny	Paenibacillus ginsengihumi sp. nov., a bacterium isolated from soil in a ginseng field.	Kim MK, Kim YA, Park MJ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.65378-0	2008

References

#1279	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3037
#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 )
#34116	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#123787	Collection of Institut Pasteur ; Curators of the CIP; CIP 103120
#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 validus (DSM 3037, ATCC 43897, LMG 11161)

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

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004000985

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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