Paenibacillus harenae (DSM 16969, KCTC 3951, B519)

Name: Paenibacillus harenae (DSM 16969, KCTC 3951, B519)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11635

Type strain

Strain Designation B519, 22.101

Culture col. no. DSM 16969 KCTC 3951 B519 22.101

NCBI tax ID(s) 1122920 306543

Special Collections DSMZ KCTC Literature strains

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Paenibacillus harenae B519 is an aerobe, spore-forming, mesophilic prokaryote that was isolated from desert sand sample.

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

Name and taxonomic classification

SI-ID 232158

KCTC 3951,DSM 16969

@ref 20215

Last LPSN update 2025-12-16 09:49:38

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus harenae

Full scientific name Paenibacillus harenae Jeon et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32545	positive	3 µm	1 µm	rod-shaped
67771	positive
125439					94.6

Pigmentation

32545

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6584	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6584	positive	growth	30	mesophilic
32545	positive	growth	10-40
32545	positive	optimum	33.5	mesophilic
67771	positive	growth	35	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
32545	positive	optimum	6.75
32545	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32545	aerobe
67771	aerobe
125439	aerobe	96.4

Spore formation

@ref	Spore formation	Confidence
32545
125439		98
125438		93.322

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32545	NaCl	positive	growth	0-3 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32545	22599 ChEBI	arabinose	+	carbon source
32545	4853 ChEBI	esculin	+	hydrolysis
32545	28757 ChEBI	fructose	+	carbon source
32545	17234 ChEBI	glucose	+	carbon source
32545	17716 ChEBI	lactose	+	carbon source
32545	17306 ChEBI	maltose	+	carbon source
32545	37684 ChEBI	mannose	+	carbon source
32545	28053 ChEBI	melibiose	+	carbon source
32545	16634 ChEBI	raffinose	+	carbon source
32545	26546 ChEBI	rhamnose	+	carbon source
32545	17814 ChEBI	salicin	+	carbon source
32545	17992 ChEBI	sucrose	+	carbon source
32545	27082 ChEBI	trehalose	+	carbon source
32545	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32545	acid phosphatase	+	3.1.3.2
32545	alpha-galactosidase	+	3.2.1.22
32545	catalase	+	1.11.1.6
32545	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Sandy

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6584	desert sand sample	Gansu Province	China	CHN	Asia
67771	From soil		Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6584	1	Risk group (German 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	ASM42246v1 assembly for Paenibacillus harenae DSM 16969	scaffold	GCA_000422465	1122920.3	2523533617	1122920	71.59

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6584	Paenibacillus harenae strain B519 16S ribosomal RNA gene, partial sequence	AY839867	1523		306543

GC content

6584

GC-content (mol%)49.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus harenae DSM 16969
NCBI: GCA_000422465

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	98.00	no
125439	motility	BacteriaNetⓘ	yes	94.60	no
125439	gram_stain	BacteriaNetⓘ	variable	89.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus harenae DSM 16969 DSM 16969
NCBI: GCA_000422465.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	68.80	yes
125438	anaerobic	anaerobicⓘ	no	95.72	yes
125438	aerobic	aerobicⓘ	yes	75.59	yes
125438	spore-forming	spore-formingⓘ	yes	93.32	yes
125438	thermophilic	thermophileⓘ	no	92.47	yes
125438	flagellated	motile2+ⓘ	yes	86.46	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Complete Genome Sequences of Two Interactive Moderate Thermophiles, Paenibacillus napthalenovorans 32O-Y and Paenibacillus sp. 32O-W.	Butler RR, Wang J, Stark BC, Pombert JF.	Genome Announc	10.1128/genomea.01717-15	2016
Metabolism	Insights into the Unique Phosphorylation of the Lasso Peptide Paeninodin.	Zhu S, Hegemann JD, Fage CD, Zimmermann M, Xie X, Linne U, Marahiel MA.	J Biol Chem	10.1074/jbc.m116.722108	2016
Genetics	Mining biosynthetic gene clusters in Paenibacillus genomes to discover novel antibiotics	Kim M, Jeong D, Jang J, Jang J, Choi S.	BMC Microbiol		2024
Phylogeny	Paenibacillus harenae sp. nov., isolated from desert sand in China.	Jeon CO, Lim JM, Lee SS, Chung BS, Park DJ, Xu LH, Jiang CL, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65664-0	2009
Phylogeny	Paenibacillus vietnamensis sp. nov., isolated from the rhizosphere soil of Arachis hypogaea.	Nguyen MH, Dinh MTN, Lee KC, Kim JS, Nguyen TKN, Lee JS	Int J Syst Evol Microbiol	10.1099/ijsem.0.005537	2022
Phylogeny	Paenibacillus arenilitoris sp. nov., isolated from seashore sand and genome mining revealed the biosynthesis potential as antibiotic producer.	Deng N, Huang H, Hu Y, Wang X, Mo K	Antonie Van Leeuwenhoek	10.1007/s10482-022-01773-1	2022

References

#6584	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16969
#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 )
#32545	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 #28763 (see below)
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 harenae (DSM 16969, KCTC 3951, B519)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000422465

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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