"Paenibacillus donghaensis" (DSM 22278, KCTC 13049, LMG 23780)

BacDive ID 11638

Type strain

Strain Designation JH8

Culture col. no. DSM 22278 KCTC 13049 LMG 23780 JH8

NCBI tax ID(s) 414771

Special Collections DSMZ KCTC

History <- LMG; LMG 23780 <- D.-H. Roh, Chungbuk Natl. Univ., Dept. Microbiol. and Biotechnol. Res. Inst., Korea; JH8 <- DH Roh, Chungbuk Natl. Univ.

Links

"Paenibacillus donghaensis" JH8 is an aerobe, motile, rod-shaped bacterium that was isolated from Sediment, East Sea.

motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 292640

LMG 23780,DSM 22278,KCTC 13049

@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 donghaensis"

Full scientific name Paenibacillus donghaensis Choi et al. 2008

Morphology

Cell morphology

@ref	Cell shape	Flagellum arrangement	Gram stain	Confidence
67771	rod-shaped	peritrichous
67771			positive
125439				90.2

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16174	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

Culture temp

@ref	Growth	Type	Temperature (°C)
16174	positive	growth	25
67771	positive	growth	20-25

Physiology and metabolism

Oxygen tolerance

67771

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		95.5
125438		91.805

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	valine metabolism	100	9 of 9
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	pentose phosphate pathway	100	11 of 11
66794	glycogen metabolism	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	adipate degradation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	palmitate biosynthesis	100	22 of 22
66794	L-lactaldehyde degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	ribulose monophosphate pathway	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	NAD metabolism	100	18 of 18
66794	cellulose degradation	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	sulfopterin metabolism	100	4 of 4
66794	glutathione metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	vitamin B1 metabolism	92.31	12 of 13
66794	starch degradation	90	9 of 10
66794	alanine metabolism	89.66	26 of 29
66794	pyrimidine metabolism	88.89	40 of 45
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	peptidoglycan biosynthesis	80	12 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	vitamin K metabolism	80	4 of 5
66794	lipoate biosynthesis	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	heme metabolism	78.57	11 of 14
66794	degradation of pentoses	78.57	22 of 28
66794	allantoin degradation	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	degradation of hexoses	77.78	14 of 18
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	degradation of aromatic, nitrogen containing compounds	75	9 of 12
66794	degradation of sugar alcohols	75	12 of 16
66794	gluconeogenesis	75	6 of 8
66794	methionine metabolism	73.08	19 of 26
66794	propanol degradation	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	non-pathway related	71.05	27 of 38
66794	glycolysis	70.59	12 of 17
66794	oxidative phosphorylation	68.13	62 of 91
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	lysine metabolism	64.29	27 of 42
66794	degradation of sugar acids	64	16 of 25
66794	proline metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	leucine metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	factor 420 biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	citric acid cycle	57.14	8 of 14
66794	tryptophan metabolism	55.26	21 of 38
66794	histidine metabolism	55.17	16 of 29
66794	metabolism of disaccharids	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	polyamine pathway	52.17	12 of 23
66794	selenocysteine biosynthesis	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	tyrosine metabolism	50	7 of 14
66794	quinate degradation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	lactate fermentation	50	2 of 4
66794	phenol degradation	50	10 of 20
66794	kanosamine biosynthesis II	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	3-phenylpropionate degradation	40	6 of 15
66794	propionate fermentation	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	carnitine metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	arachidonic acid metabolism	33.33	6 of 18
66794	coenzyme M biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16174	Sediment, East Sea	Donghae	Republic of Korea	KOR	Asia
67771	From deep-sea sediment	the East Sea	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF079062 (>99% sequence identity) for Paenibacillus donghaensis subclade from Microbeatlas

Aquatic Samples	8
Soil Samples	22
Animal Samples	7
Plant Samples	4
Total Samples	41

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM219241v1 assembly for Paenibacillus donghaensis KCTC 13049	complete	GCA_002192415	414771.3	2757320370	414771	97.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16174	Paenibacillus donghaensis strain JH8 16S ribosomal RNA gene, partial sequence	EF079062	1434		414771

GC content

16174

GC-content (mol%)53.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus donghaensis strain KCTC 13049
PATRIC: 414771.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	95.50	no
125439	motility	BacteriaNetⓘ	yes	90.20	no
125439	gram_stain	BacteriaNetⓘ	variable	86.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	77.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus donghaensis KCTC 13049
NCBI: GCA_002192415.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	69.26	yes
125438	anaerobic	anaerobicⓘ	no	93.36	yes
125438	aerobic	aerobicⓘ	yes	51.91	no
125438	spore-forming	spore-formingⓘ	yes	91.81	no
125438	thermophilic	thermophileⓘ	no	92.78	yes
125438	flagellated	motile2+ⓘ	yes	85.67	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes.	Teber R, Asakawa S.	Int J Mol Sci	10.3390/ijms25052566	2024
Genetics	Genome sequencing to develop Paenibacillus donghaensis strain JH8(T) (KCTC 13049(T)=LMG 23780(T)) as a microbial fertilizer and correlation to its plant growth-promoting phenotype.	Jung BK, Hong SJ, Jo HW, Jung Y, Park YJ, Park CE, Kim MC, Ibal JC, Roh DH, Shin JH	Mar Genomics	10.1016/j.margen.2017.11.006	2017
Phylogeny	Newly Isolated Paenibacillus monticola sp. nov., a Novel Plant Growth-Promoting Rhizobacteria Strain From High-Altitude Spruce Forests in the Qilian Mountains, China.	Li HP, Gan YN, Yue LJ, Han QQ, Chen J, Liu QM, Zhao Q, Zhang JL	Front Microbiol	10.3389/fmicb.2022.833313	2022
Phylogeny	Paenibacillus donghaensis sp. nov., a xylan-degrading and nitrogen-fixing bacterium isolated from East Sea sediment.	Choi JH, Im WT, Yoo JS, Lee SM, Moon DS, Kim HJ, Rhee SK, Roh DH	J Microbiol Biotechnol	7155	2008

References

#16174	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22278
#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 )
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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 )

Rate our new design

Content

About us

"Paenibacillus donghaensis" (DSM 22278, KCTC 13049, LMG 23780)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_002192415

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media