Allopusillimonas ginsengisoli (DSM 25164, JCM 14767, KCTC 22046)

Name: Allopusillimonas ginsengisoli (DSM 25164, JCM 14767, KCTC 22046)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 364

Type strain

Culture col. no. DSM 25164 JCM 14767 KCTC 22046 DCY 25

NCBI tax ID(s) 453575

Special Collections DSMZ JCM KCTC Literature strains

History <- KCTC <- D.-C. Yang, Korean Ginseng Center and Ginseng Genetic Resource Bank, Gyeonggi-do D.-C. Yang DCY25. <- DC Yang, Kyunghee Univ.

Links

Allopusillimonas ginsengisoli DSM 25164 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from soil from ginseng field.

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

Name and taxonomic classification

SI-ID 399770

KCTC 22046,JCM 14767,DSM 25164

@ref 20215

Last LPSN update 2026-02-09 11:17:51

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Alcaligenaceae

Genus Allopusillimonas

Species Allopusillimonas ginsengisoli

Full scientific name Allopusillimonas ginsengisoli (Srinivasan et al. 2010) Babich et al. 2023

Synonyms (1)

Pusillimonas ginsengisoli

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
23278	negative	0.5-0.8 µm	0.3-0.6 µm	rod-shaped
67771	negative
125439	negative				98.3
125438	negative				97.313

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
23278	pale yellow	circular	5 days	nutrient agar

Multimedia

@ref:	17925
multimedia content:	DSM_25164.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_25164.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
17925	REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 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
17925	REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
23278	Nutrient agar (NA)

Culture temp

@ref	Growth	Type	Temperature (°C)
17925	positive	growth	28
23278	positive	growth	15-40
23278	negative	growth	4
23278	negative	growth	42
23278	positive	optimum	30
67770	positive	growth	30
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
23278	positive	optimum	7.0
23278	positive	growth	5.5-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
23278	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
23278
125439		96.2

Observation

@ref	Observation
67770	quinones: Q-8
67771	quinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23278	16808 ChEBI	2-dehydro-D-gluconate	-	growth
23278	16193 ChEBI	3-hydroxybenzoate	-	assimilation
23278	37054 ChEBI	3-hydroxybutyrate	+	assimilation
23278	17879 ChEBI	4-hydroxybenzoate	-	assimilation
23278	16724 ChEBI	4-hydroxybutyrate	+	assimilation
23278	17426 ChEBI	5-dehydro-D-gluconate	-	growth
23278	30089 ChEBI	acetate	+	growth
23278	17128 ChEBI	adipate	+	assimilation
23278	16947 ChEBI	citrate	+	assimilation
23278	8391 ChEBI	D-gluconate	-	assimilation
23278	17634 ChEBI	D-glucose	-	growth
23278	16899 ChEBI	D-mannitol	-	growth
23278	16024 ChEBI	D-mannose	-	growth
23278	16988 ChEBI	D-ribose	-	assimilation
23278	17924 ChEBI	D-sorbitol	-	assimilation
23278	27689 ChEBI	decanoate	-	assimilation
23278	4853 ChEBI	esculin	-	hydrolysis
23278	5291 ChEBI	gelatin	-	hydrolysis
23278	24265 ChEBI	gluconate	-	growth
23278	28087 ChEBI	glycogen	-	growth
23278	17240 ChEBI	itaconate	+	assimilation
23278	16977 ChEBI	L-alanine	+	assimilation
23278	30849 ChEBI	L-arabinose	-	growth
23278	18287 ChEBI	L-fucose	-	growth
23278	15971 ChEBI	L-histidine	-	assimilation
23278	17203 ChEBI	L-proline	+	assimilation
23278	62345 ChEBI	L-rhamnose	-	assimilation
23278	17115 ChEBI	L-serine	+	assimilation
23278	24996 ChEBI	lactate	+	growth
23278	25115 ChEBI	malate	+	assimilation
23278	15792 ChEBI	malonate	+	assimilation
23278	17306 ChEBI	maltose	-	assimilation
23278	17306 ChEBI	maltose	-	growth
23278	37684 ChEBI	mannose	-	assimilation
23278	28053 ChEBI	melibiose	-	growth
23278	17268 ChEBI	myo-inositol	-	assimilation
23278	506227 ChEBI	N-acetylglucosamine	-	growth
23278	18401 ChEBI	phenylacetate	+	assimilation
23278	17272 ChEBI	propionate	+	assimilation
23278	17814 ChEBI	salicin	-	growth
23278	28017 ChEBI	starch	-	hydrolysis
23278	9300 ChEBI	suberic acid	-	assimilation
23278	17992 ChEBI	sucrose	-	growth
23278	31011 ChEBI	valerate	+	assimilation

Enzymes

@ref	Value	Activity	Ec
23278	acid phosphatase	+	3.1.3.2
23278	alkaline phosphatase	+	3.1.3.1
23278	alpha-chymotrypsin	+	3.4.21.1
23278	alpha-fucosidase	-	3.2.1.51
23278	alpha-galactosidase	-	3.2.1.22
23278	alpha-glucosidase	-	3.2.1.20
23278	alpha-mannosidase	-	3.2.1.24
23278	arginine dihydrolase	-	3.5.3.6
23278	beta-galactosidase	-	3.2.1.23
23278	beta-glucosidase	-	3.2.1.21
23278	beta-glucuronidase	-	3.2.1.31
23278	catalase	+	1.11.1.6
23278	cystine arylamidase	+	3.4.11.3
23278	cytochrome oxidase	+	1.9.3.1
23278	esterase (C 4)	+
23278	esterase lipase (C 8)	+
23278	leucine arylamidase	+	3.4.11.1
23278	lipase (C 14)	-
23278	N-acetyl-beta-glucosaminidase	-	3.2.1.52
23278	naphthol-AS-BI-phosphohydrolase	+
23278	trypsin	+	3.4.21.4
23278	urease	-	3.5.1.5
23278	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	denitrification	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	ketogluconate metabolism	100	8 of 8
66794	threonine metabolism	100	10 of 10
66794	quinate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	enterobactin biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	butanoate fermentation	100	4 of 4
66794	ubiquinone biosynthesis	100	7 of 7
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CMP-KDO biosynthesis	100	4 of 4
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	starch degradation	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	cysteine metabolism	83.33	15 of 18
66794	vitamin B6 metabolism	81.82	9 of 11
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	lipoate biosynthesis	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	tryptophan metabolism	78.95	30 of 38
66794	heme metabolism	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	lipid A biosynthesis	77.78	7 of 9
66794	sulfate reduction	76.92	10 of 13
66794	degradation of sugar acids	76	19 of 25
66794	alanine metabolism	75.86	22 of 29
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	methionine metabolism	73.08	19 of 26
66794	proline metabolism	72.73	8 of 11
66794	glutathione metabolism	71.43	10 of 14
66794	tyrosine metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	oxidative phosphorylation	70.33	64 of 91
66794	purine metabolism	70.21	66 of 94
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	non-pathway related	68.42	26 of 38
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	cyanate degradation	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	d-mannose degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	glycolysis	64.71	11 of 17
66794	d-xylose degradation	63.64	7 of 11
66794	gluconeogenesis	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	pyrimidine metabolism	62.22	28 of 45
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	glycogen metabolism	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	degradation of sugar alcohols	56.25	9 of 16
66794	allantoin degradation	55.56	5 of 9
66794	phenol degradation	55	11 of 20
66794	metabolism of disaccharids	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	bile acid biosynthesis, neutral pathway	52.94	9 of 17
66794	polyamine pathway	52.17	12 of 23
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	carnitine metabolism	50	4 of 8
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	cyclohexanol degradation	50	2 of 4
66794	lactate fermentation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	degradation of pentoses	46.43	13 of 28
66794	nitrate assimilation	44.44	4 of 9
66794	aspartate and asparagine metabolism	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	ascorbate metabolism	40.91	9 of 22
66794	coenzyme M biosynthesis	40	4 of 10
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	carotenoid biosynthesis	36.36	8 of 22
66794	cholesterol biosynthesis	36.36	4 of 11
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	vitamin B12 metabolism	26.47	9 of 34
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	degradation of hexoses	22.22	4 of 18

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	Geographic location	Country	Country ISO 3 Code	Continent
17925	soil from ginseng field	near Daejeon	Republic of Korea	KOR	Asia
67770	Soil of a ginseng field near Daejeon City		Republic of Korea	KOR	Asia
67771	From soil, ginseng field		Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17925	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	ASM415345v1 assembly for Allopusillimonas ginsengisoli KCTC 22046	contig	GCA_004153455	453575.4	2891648259	453575	72.23

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17925	Pusillimonas ginsengisoli strain DCY25 16S ribosomal RNA gene, partial sequence	EF672088	1479		453575

GC content

@ref	GC-content (mol%)	Method
23278	57.3	high performance liquid chromatography (HPLC)
67771	57.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Allopusillimonas ginsengisoli KCTC 22046
NCBI: GCA_004153455

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.20	no
125439	motility	BacteriaNetⓘ	yes	77.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	80.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pusillimonas ginsengisoli strain KCTC 22046
PATRIC: 453575.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.31	yes
125438	anaerobic	anaerobicⓘ	no	98.38	yes
125438	spore-forming	spore-formingⓘ	no	88.77	yes
125438	aerobic	aerobicⓘ	yes	88.68	no
125438	thermophilic	thermophileⓘ	no	97.87	yes
125438	flagellated	motile2+ⓘ	yes	58.65	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pusillimonas maritima sp. nov., isolated from surface seawater.	Li J, Qi M, Lai Q, Dong C, Liu X, Wang G, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.004202	2020
Phylogeny	Pusillimonas caeni sp. nov., isolated from a sludge sample of a biofilm reactor.	Jin L, Ko SR, Cui Y, Lee CS, Oh HM, Ahn CY, Lee HG	Antonie Van Leeuwenhoek	10.1007/s10482-016-0782-6	2016
Phylogeny	Pusillimonas harenae sp. nov., isolated from a sandy beach, and emended description of the genus Pusillimonas.	Park MS, Park YJ, Jung JY, Lee SH, Park W, Lee K, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.029892-0	2011
Phylogeny	Pusillimonas soli sp. nov., isolated from farm soil.	Lee M, Woo SG, Chae M, Ten LN	Int J Syst Evol Microbiol	10.1099/ijs.0.020404-0	2009
Phylogeny	Pusillimonas ginsengisoli sp. nov., isolated from soil of a ginseng field.	Srinivasan S, Kim MK, Sathiyaraj G, Kim YJ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.018358-0	2009
Phylogeny	Paracandidimonas lactea sp. nov., a urea-utilizing bacterium isolated from landfill.	Zhang C, Pu Q, Ying JJ, Chen Y, Li CZ, Wu HT, Wang BJ, Zhang YH, Zeng GH, Li O, Hu XF, Sun C	Arch Microbiol	10.1007/s00203-022-03190-4	2022

References

#17925	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25164
#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 )
#23278	Sathiyaraj Srinivasan, Myung Kyum Kim, Gayathri Sathiyaraj, Yeon-Ju Kim,Deok-Chun Yang: Pusillimonas ginsengisoli sp. nov., isolated from soil of a ginseng field. IJSEM 60: 1783 - 1787 2010 ( DOI 10.1099/ijs.0.018358-0 , PubMed 19749028 )
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Allopusillimonas ginsengisoli (DSM 25164, JCM 14767, KCTC 22046)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004153455

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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