Lysobacter soli (DSM 24712, KCTC 22011, LMG 24126)

Name: Lysobacter soli (DSM 24712, KCTC 22011, LMG 24126)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17498

Type strain

Culture col. no. DSM 24712 KCTC 22011 LMG 24126 DCY 21

NCBI tax ID(s) 453783

Special Collections DSMZ KCTC Literature strains

History <- KCTC <- S. Srinivasan, Korean Ginseng Center and Ginseng Genetic Resource Bank, Gyeonggi; DCY21 <- DC Yang, Kyunghee Univ.

Links

Lysobacter soli DSM 24712 is an aerobe, Gram-negative, motile bacterium that was isolated from soil of ginseng field.

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

Name and taxonomic classification

SI-ID 307677

LMG 24126,KCTC 22011,DSM 24712

@ref 20215

Last LPSN update 2026-02-09 11:22:14

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Lysobacter

Species Lysobacter soli

Full scientific name Lysobacter soli Srinivasan et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
29584	negative	0.6-0.9 µm	0.2-0.5 µm	rod-shaped	gliding
67771	negative
125439	negative					96.9
125438	negative					98.235

Pigmentation

29584

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17735	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)
17735	positive	growth	28
29584	positive	growth	04-42
29584	positive	optimum	30
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
29584	positive	optimum	7-7.5
29584	positive	growth	05-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29584	aerobe
67771	aerobe
125439	obligate aerobe	100

Spore formation

@ref	Spore formation	Confidence
125439		95.9
125438		90.41

Observation

@ref	Observation
29584	aggregates in chains
67771	quinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29584	30089 ChEBI	acetate	+	carbon source
29584	22599 ChEBI	arabinose	+	carbon source
29584	33984 ChEBI	fucose	+	carbon source
29584	17234 ChEBI	glucose	+	carbon source
29584	17306 ChEBI	maltose	+	carbon source
29584	37684 ChEBI	mannose	+	carbon source
29584	17632 ChEBI	nitrate	+	reduction

Enzymes

@ref	Value	Activity	Ec
29584	catalase	+	1.11.1.6
29584	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	formaldehyde oxidation	100	3 of 3
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	methylglyoxal degradation	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	denitrification	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	pentose phosphate pathway	90.91	10 of 11
66794	propionate fermentation	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	purine metabolism	84.04	79 of 94
66794	NAD metabolism	83.33	15 of 18
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	tryptophan metabolism	78.95	30 of 38
66794	citric acid cycle	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	heme metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	alanine metabolism	75.86	22 of 29
66794	histidine metabolism	75.86	22 of 29
66794	acetate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	pyrimidine metabolism	73.33	33 of 45
66794	methionine metabolism	73.08	19 of 26
66794	d-xylose degradation	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	starch degradation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	vitamin B1 metabolism	69.23	9 of 13
66794	acetoin degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	cyanate degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	glycolysis	64.71	11 of 17
66794	lipid metabolism	64.52	20 of 31
66794	glutathione metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	vitamin B6 metabolism	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	ketogluconate metabolism	62.5	5 of 8
66794	lysine metabolism	61.9	26 of 42
66794	glycine betaine biosynthesis	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	D-cycloserine biosynthesis	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	non-pathway related	57.89	22 of 38
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	degradation of sugar alcohols	56.25	9 of 16
66794	degradation of sugar acids	56	14 of 25
66794	d-mannose degradation	55.56	5 of 9
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	ribulose monophosphate pathway	50	1 of 2
66794	catecholamine biosynthesis	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of pentoses	50	14 of 28
66794	quinate degradation	50	1 of 2
66794	phenol degradation	50	10 of 20
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	coenzyme A metabolism	50	2 of 4
66794	sulfate reduction	46.15	6 of 13
66794	ascorbate metabolism	45.45	10 of 22
66794	metabolism of disaccharids	45.45	5 of 11
66794	arachidonic acid metabolism	44.44	8 of 18
66794	vitamin B12 metabolism	41.18	14 of 34
66794	oxidative phosphorylation	40.66	37 of 91
66794	bacilysin biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	polyamine pathway	39.13	9 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	alginate biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	4-hydroxymandelate 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)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17735	soil of ginseng field	Daejeon City	Republic of Korea	KOR	Asia
67771	From soil, ginseng field		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF623862 (>99% sequence identity) for Lysobacter from Microbeatlas

Aquatic Samples	78
Soil Samples	1232
Animal Samples	69
Plant Samples	230
Total Samples	1609

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17735	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	ASM338228v1 assembly for Lysobacter soli KCTC 22011	contig	GCA_003382285	453783.3	2838987433	453783	65.87

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17735	Lysobacter sp. DCY21T 16S ribosomal RNA gene, partial sequence	EF623862	1496		453783

GC content

17735

GC-content (mol%)65.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Lysobacter soli KCTC 22011
NCBI: GCA_003382285

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.90	no
125439	motility	BacteriaNetⓘ	yes	60.70	no
125439	gram_stain	BacteriaNetⓘ	negative	96.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	100.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lysobacter soli strain KCTC 22011
PATRIC: 453783.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.24	yes
125438	anaerobic	anaerobicⓘ	no	98.25	yes
125438	spore-forming	spore-formingⓘ	no	90.41	no
125438	aerobic	aerobicⓘ	yes	85.36	yes
125438	thermophilic	thermophileⓘ	no	96.98	no
125438	flagellated	motile2+ⓘ	yes	65.66	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lysobacter prati sp. nov., isolated from a plateau meadow sample.	Fang BZ, Xie YG, Zhou XK, Zhang XT, Liu L, Jiao JY, Xiao M, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-020-01386-6	2020
Phylogeny	Lysobacter tabacisoli sp. nov., isolated from rhizosphere soil of Nicotiana tabacum L.	Xiao M, Zhou XK, Chen X, Duan YQ, Alkhalifah DHM, Im WT, Hozzein WN, Chen W, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003164	2018
Phylogeny	Lysobacter silvisoli sp. nov., isolated from forest soil.	Zhang XJ, Yao Q, Wang YH, Yang SZ, Feng GD, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003105	2018
Phylogeny	Lysobacter pedocola sp. nov., a novel species isolated from Korean soil.	Jang JH, Lee D, Seo T	J Microbiol	10.1007/s12275-018-8046-y	2018
Phylogeny	Lysobacter cavernae sp. nov., a novel bacterium isolated from a cave sample.	Chen W, Zhao YL, Cheng J, Zhou XK, Salam N, Fang BZ, Li QQ, Hozzein WN, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-016-0704-7	2016
Phylogeny	Lysobacter panacisoli sp. nov., isolated from ginseng soil.	Choi JH, Seok JH, Cha JH, Cha CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.062034-0	2014
Phylogeny	Lysobacter soli sp. nov., isolated from soil of a ginseng field.	Srinivasan S, Kim MK, Sathiyaraj G, Kim HB, Kim YJ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.016428-0	2009

References

#17735	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24712
#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 )
#25976	IJSEM 1543 2010 ( DOI 10.1099/ijs.0.016428-0 , PubMed 19684312 )
#29584	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 #25976
#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 )

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Lysobacter soli (DSM 24712, KCTC 22011, LMG 24126)

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

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003382285

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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