Paenibacillus ginsengihumi (DSM 21568, JCM 14928, KCTC 13141)

Name: Paenibacillus ginsengihumi (DSM 21568, JCM 14928, KCTC 13141)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11632

Type strain

Culture col. no. DSM 21568 JCM 14928 KCTC 13141 DCY 16

NCBI tax ID(s) 1122919 431596

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- JCM <- D.-C. Yang; DCY16 JCM <-- D.-C. Yang DCY16. KCTC <- DC Yang, Kyunghee Univ.

Links

Paenibacillus ginsengihumi DSM 21568 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil of a ginseng field.

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

Name and taxonomic classification

SI-ID 406366

KCTC 13141,JCM 14928,DSM 21568

@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 ginsengihumi

Full scientific name Paenibacillus ginsengihumi Kim et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32362	positive	2.75 µm	0.65 µm	rod-shaped
67771				rod-shaped
67771	positive
125439					90.093

Pigmentation

32362

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15667	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)
15667	positive	growth	30
32362	positive	growth	25-42
32362	positive	optimum	37
67770	positive	growth	37
67771	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
32362	positive	growth	07-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32362	aerobe
67771	aerobe
125439	aerobe	96.297

Spore formation

@ref	Spore formation	Confidence
32362
125439		93.418
125438		91.328

Observation

@ref	Observation
67770	quinones: MK-7
67771	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32362	4853 ChEBI	esculin	+	hydrolysis
32362	17306 ChEBI	maltose	+	carbon source
32362	29864 ChEBI	mannitol	+	carbon source
32362	28053 ChEBI	melibiose	+	carbon source
32362	17632 ChEBI	nitrate	+	reduction
32362	17992 ChEBI	sucrose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32362	catalase	+	1.11.1.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
15667	soil of a ginseng field	Republic of Korea	KOR	Asia
67770	Soil of a ginseng field	Republic of Korea	KOR	Asia
67771	From soil	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF452662 (>99% sequence identity) for Paenibacillus ginsengihumi subclade from Microbeatlas

Aquatic Samples	195
Soil Samples	599
Animal Samples	258
Plant Samples	350
Total Samples	1402

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15667	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
67770	ASM38096v1 assembly for Paenibacillus ginsengihumi DSM 21568	scaffold	GCA_000380965	1122919.3	2521172661	1122919	47.58

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15667	Paenibacillus ginsengihumi strain DCY16 16S ribosomal RNA gene, partial sequence	EF452662	1512		1122919

GC content

@ref	GC-content (mol%)	Method
15667	50.9	high performance liquid chromatography (HPLC)
32362	50.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM38096v1 assembly for Paenibacillus ginsengihumi DSM 21568
NCBI: GCA_000380965

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.30	no
125439	gram_stain	BacteriaNetⓘ	variable	71.89	no
125439	spore_formation	BacteriaNetⓘ	yes	93.42	no
125439	motility	BacteriaNetⓘ	yes	90.09	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus ginsengihumi DSM 21568
PATRIC: 1122919.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	70.12	yes
125438	anaerobic	anaerobicⓘ	no	93.38	yes
125438	spore-forming	spore-formingⓘ	yes	91.33	yes
125438	aerobic	aerobicⓘ	yes	72.23	yes
125438	thermophilic	thermophileⓘ	no	88.64	no
125438	flagellated	motile2+ⓘ	yes	80.06	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	The Assembly of Bacteria Living in Natural Environments Shapes Neuronal Integrity and Behavioral Outputs in Caenorhabditis elegans.	Urquiza-Zurich S, Garcia-Angulo VA, Burdisso P, Palominos MF, Fernandez-Hubeid L, Harcha PA, Castillo JP, Calixto A.	mBio	10.1128/mbio.03402-22	2023
Phylogeny	Paenibacillus pueri sp. nov., isolated from Pu'er tea.	Kim BC, Jeong WJ, Kim DY, Oh HW, Kim H, Park DS, Park HM, Bae KS	Int J Syst Evol Microbiol	10.1099/ijs.0.002352-0	2009
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

#15667	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21568
#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 )
#28591	IJSEM 1164 2008 ( DOI 10.1099/ijs.0.65378-0 , PubMed 18450707 )
#32362	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 #28591
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 )

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Paenibacillus ginsengihumi (DSM 21568, JCM 14928, KCTC 13141)

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

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000380965

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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