Panacibacter ginsenosidivorans (DSM 18138, JCM 31452, KCTC 12658)

Name: Panacibacter ginsenosidivorans (DSM 18138, JCM 31452, KCTC 12658)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132637

Type strain

Strain Designation GS 1550

Culture col. no. DSM 18138 JCM 31452 KCTC 12658 Gsoil 1550 GS 1550

NCBI tax ID(s) 1813871

Special Collections DSMZ JCM KCTC Literature strains

History <- S. T. Lee, KAIST; GSOIL 1550 <- D.-S. An; GS 1550 W.-T. Im; Hankyong Natl. Univ., South Korea; Gsoil 1550. <- ST Lee, KAIST

Links

Panacibacter ginsenosidivorans GS 1550 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil of a ginseng field.

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

Name and taxonomic classification

SI-ID 401940

KCTC 12658,JCM 31452,DSM 18138

@ref 20215

Last LPSN update 2026-02-09 11:31:45

Domain Bacteria

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Panacibacter

Species Panacibacter ginsenosidivorans

Full scientific name Panacibacter ginsenosidivorans Siddiqi et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
24911	negative	1.6-3.0 µm	0.5-1.2 µm	rod-shaped
67771				rod-shaped
67771	negative

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
24911	yellow	circular	2 days	R2A agar (Reasoner's 2A agar)

Pigmentation

@ref	Production	Name
24911		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24911	Reasoner's 2A agar (R2A)
24426	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)
24426	positive	growth	28
24911	positive	growth	10.0-37.0
24911	positive	optimum	30
24911	negative	growth	40
67770	positive	growth	30
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
24911	positive	optimum	6.0-7.0
24911	positive	growth	5.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
24911	aerobe
67771	aerobe

Spore formation

24911

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
24911	NaCl	positive	growth	0 %(w/v)

Observation

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
24911	16808 ChEBI	2-dehydro-D-gluconate	-	assimilation
24911	16193 ChEBI	3-hydroxybenzoate	-	assimilation
24911	37054 ChEBI	3-hydroxybutyrate	-	assimilation
24911	17879 ChEBI	4-hydroxybenzoate	-	assimilation
24911	355715 ChEBI	4-nitrophenyl beta-D-galactopyranoside	+	assimilation
24911	58143 ChEBI	5-dehydro-D-gluconate	+	assimilation
24911	17128 ChEBI	adipate	-	assimilation
24911	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
24911		casein	-	hydrolysis
24911	17634 ChEBI	D-glucose	-	assimilation
24911	16899 ChEBI	D-mannitol	-	assimilation
24911	16024 ChEBI	D-mannose	-	assimilation
24911	16988 ChEBI	D-ribose	+	assimilation
24911	17924 ChEBI	D-sorbitol	+	assimilation
24911	27689 ChEBI	decanoate	-	assimilation
24911	16991 ChEBI	dna	-	hydrolysis
24911	4853 ChEBI	esculin	+	hydrolysis
24911	5291 ChEBI	gelatin	-	hydrolysis
24911	28087 ChEBI	glycogen	+	assimilation
24911	17240 ChEBI	itaconate	-	assimilation
24911	16977 ChEBI	L-alanine	-	assimilation
24911	30849 ChEBI	L-arabinose	+	assimilation
24911	18287 ChEBI	L-fucose	-	assimilation
24911	15971 ChEBI	L-histidine	-	assimilation
24911	17203 ChEBI	L-proline	-	assimilation
24911	62345 ChEBI	L-rhamnose	+	assimilation
24911	17115 ChEBI	L-serine	-	assimilation
24911	24996 ChEBI	lactate	-	assimilation
24911	25115 ChEBI	malate	-	assimilation
24911	15792 ChEBI	malonate	-	assimilation
24911	17306 ChEBI	maltose	+	assimilation
24911	28053 ChEBI	melibiose	-	assimilation
24911	17268 ChEBI	myo-inositol	+	assimilation
24911	506227 ChEBI	N-acetylglucosamine	-	assimilation
24911	17632 ChEBI	nitrate	-	reduction
24911	18401 ChEBI	phenylacetate	-	assimilation
24911	32032 ChEBI	potassium gluconate	-	assimilation
24911	17272 ChEBI	propionate	-	assimilation
24911	17814 ChEBI	salicin	-	assimilation
24911	32954 ChEBI	sodium acetate	-	assimilation
24911	53258 ChEBI	sodium citrate	-	assimilation
24911	28017 ChEBI	starch	-	hydrolysis
24911	9300 ChEBI	suberic acid	-	assimilation
24911	17992 ChEBI	sucrose	+	assimilation
24911	53426 ChEBI	tween 80	-	hydrolysis
24911	31011 ChEBI	valerate	-	assimilation
24911	37166 ChEBI	xylan	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
24911	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
24911	acid phosphatase	+	3.1.3.2
24911	alkaline phosphatase	+	3.1.3.1
24911	alpha-chymotrypsin	-	3.4.21.1
24911	alpha-fucosidase	+	3.2.1.51
24911	alpha-galactosidase	+	3.2.1.22
24911	alpha-glucosidase	+	3.2.1.20
24911	alpha-mannosidase	+	3.2.1.24
24911	arginine dihydrolase	-	3.5.3.6
24911	beta-galactosidase	+	3.2.1.23
24911	beta-glucosidase	+	3.2.1.21
24911	beta-glucuronidase	+	3.2.1.31
24911	catalase	+	1.11.1.6
24911	cystine arylamidase	+	3.4.11.3
24911	cytochrome oxidase	-	1.9.3.1
24911	esterase (C 4)	+
24911	esterase lipase (C 8)	+
24911	leucine arylamidase	+	3.4.11.1
24911	lipase (C 14)	-
24911	N-acetyl-beta-glucosaminidase	+	3.2.1.52
24911	naphthol-AS-BI-phosphohydrolase	+
24911	trypsin	+	3.4.21.4
24911	urease	-	3.5.1.5
24911	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	quinate degradation	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	glycogen metabolism	100	5 of 5
66794	kanosamine biosynthesis II	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	CMP-KDO biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	palmitate biosynthesis	95.45	21 of 22
66794	NAD metabolism	94.44	17 of 18
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	heme metabolism	92.86	13 of 14
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
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	ketogluconate metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	purine metabolism	84.04	79 of 94
66794	pyrimidine metabolism	82.22	37 of 45
66794	threonine metabolism	80	8 of 10
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	serine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	lipid metabolism	77.42	24 of 31
66794	degradation of sugar acids	76	19 of 25
66794	alanine metabolism	75.86	22 of 29
66794	lactate fermentation	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	glycogen biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	acetate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	isoprenoid biosynthesis	73.08	19 of 26
66794	d-xylose degradation	72.73	8 of 11
66794	lysine metabolism	71.43	30 of 42
66794	propanol degradation	71.43	5 of 7
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	arginine metabolism	70.83	17 of 24
66794	histidine metabolism	68.97	20 of 29
66794	tryptophan metabolism	68.42	26 of 38
66794	degradation of pentoses	67.86	19 of 28
66794	octane oxidation	66.67	2 of 3
66794	sulfoquinovose degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	phenol degradation	65	13 of 20
66794	glycolysis	64.71	11 of 17
66794	citric acid cycle	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	degradation of hexoses	61.11	11 of 18
66794	cysteine metabolism	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	glycine betaine biosynthesis	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	myo-inositol biosynthesis	60	6 of 10
66794	factor 420 biosynthesis	60	3 of 5
66794	carotenoid biosynthesis	54.55	12 of 22
66794	vitamin B6 metabolism	54.55	6 of 11
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	grixazone biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	ascorbate metabolism	50	11 of 22
66794	ethanol fermentation	50	1 of 2
66794	oxidative phosphorylation	49.45	45 of 91
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	daunorubicin biosynthesis	44.44	4 of 9
66794	arachidonic acid metabolism	44.44	8 of 18
66794	3-phenylpropionate degradation	40	6 of 15
66794	arachidonate biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	vitamin B1 metabolism	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	cholesterol biosynthesis	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	vitamin E metabolism	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
24426	soil of a ginseng field	Pocheon Province	Republic of Korea	KOR	Asia
24911	soil samples collected near rhizosphere region of a ginseng plant					R2A agar (Reasoner's 2A agar)	7 days	30
67770	Soil of a ginseng field	Pocheon Province	Republic of Korea	KOR	Asia
67771	From soil, ginseng field		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KT950744 (>99% sequence identity) for Panacibacter ginsenosidivorans subclade from Microbeatlas

Aquatic Samples	5151
Soil Samples	26381
Animal Samples	1399
Plant Samples	3821
Total Samples	36752

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24426	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM797122v1 assembly for Panacibacter ginsenosidivorans Gsoil1550	complete	GCA_007971225	1813871.3	2883416032	1813871	96.78

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24426	Panacibacter ginsenosidivorans strain Gsoil 1550 16S ribosomal RNA gene, partial sequence	KT950744	1451		1813871

GC content

@ref	GC-content (mol%)	Method
24426	44.6	high performance liquid chromatography (HPLC)
67771	44.6

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Panacibacter microcysteis sp. nov., isolated from a eutrophic reservoir during the Microcystis bloom period.	Van Le V, Ko SR, Kang M, Lee SA, Oh HM, Ahn CY	Arch Microbiol	10.1007/s00203-022-02893-y	2022
Phylogeny	Limnovirga soli gen. nov., sp. nov., isolated from river sediment.	Yim KJ, Jung DH, Jang SW, Park S	Int J Syst Evol Microbiol	10.1099/ijsem.0.004891	2021
Phylogeny	Foetidibacter luteolus gen. nov., sp. nov., isolated from the rhizosphere of Salvia miltiorrhiza.	Pu Q, Zeng GH, Wang GW, Lu LE, Li A, Cheng XR, Wang XY, Li O, Sun C, Hu XF	Arch Microbiol	10.1007/s00203-020-02123-3	2021
Phylogeny	Ilyomonas limi gen. nov., sp. nov., a new member of the family Chitinophagaceae isolated from mud.	Chhetri G, Kim J, Kim H, Kim I, Kim MK, Seo T	Antonie Van Leeuwenhoek	10.1007/s10482-019-01300-9	2019
Phylogeny	Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field.	Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.001307	2016

References

#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 )
#24426	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18138
#24911	M. Z. M. S. Siddiqi, Siddiqi,Choi, Kang Duk,Im, Wan-Taek: Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field. IJSEM 66: 4039 - 4045 2016 ( DOI 10.1099/ijsem.0.001307 , PubMed 27412336 )
#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;
#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 .
#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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Panacibacter ginsenosidivorans (DSM 18138, JCM 31452, KCTC 12658)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_007971225

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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