Daejeonella lutea (DSM 22385, KCTC 22699, N7d-4)

Name: Daejeonella lutea (DSM 22385, KCTC 22699, N7d-4)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24548

Type strain

Strain Designation N7d-4, P-2

Culture col. no. DSM 22385 KCTC 22699 N7d-4 JCM 16318 P-2

NCBI tax ID(s) 572036

Special Collections DSMZ JCM KCTC

Links

Daejeonella lutea N7d-4 is an aerobe, mesophilic, motile prokaryote that was isolated from soil of a potato field.

motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402387

KCTC 22699,DSM 22385

@ref 20215

Last LPSN update 2025-12-16 09:52:52

Domain Pseudomonadati

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Daejeonella

Species Daejeonella lutea

Full scientific name Daejeonella lutea (Oh et al. 2013) García-López et al. 2020

Synonyms (1)

Pedobacter luteus

Morphology

Cell morphology

@ref	Cell shape	Flagellum arrangement
67771	rod-shaped	gliding
67771
125438
125439

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20726	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)	Range
20726	positive	growth	25-30	mesophilic
67770	positive	growth	25	mesophilic
67771	positive	growth	25	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
67771	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.6

Observation

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

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	gluconeogenesis	100	8 of 8
66794	adipate degradation	100	2 of 2
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	CMP-KDO biosynthesis	100	4 of 4
66794	ethanol fermentation	100	2 of 2
66794	quinate degradation	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	cellulose degradation	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	pentose phosphate pathway	90.91	10 of 11
66794	starch degradation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	alanine metabolism	89.66	26 of 29
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	glycine betaine biosynthesis	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	pyrimidine metabolism	80	36 of 45
66794	peptidoglycan biosynthesis	80	12 of 15
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
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	degradation of sugar alcohols	75	12 of 16
66794	isoleucine metabolism	75	6 of 8
66794	purine metabolism	74.47	70 of 94
66794	proline metabolism	72.73	8 of 11
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	coenzyme M biosynthesis	70	7 of 10
66794	methionine metabolism	69.23	18 of 26
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	tryptophan metabolism	65.79	25 of 38
66794	lipid metabolism	64.52	20 of 31
66794	tyrosine metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	degradation of sugar acids	60	15 of 25
66794	arachidonate biosynthesis	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	glutathione metabolism	57.14	8 of 14
66794	lysine metabolism	57.14	24 of 42
66794	phenol degradation	55	11 of 20
66794	metabolism of disaccharids	54.55	6 of 11
66794	vitamin B1 metabolism	53.85	7 of 13
66794	degradation of pentoses	50	14 of 28
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	arginine metabolism	50	12 of 24
66794	selenocysteine biosynthesis	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	sulfate reduction	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	carotenoid biosynthesis	40.91	9 of 22
66794	glycine metabolism	40	4 of 10
66794	myo-inositol biosynthesis	40	4 of 10
66794	elloramycin biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	oxidative phosphorylation	31.87	29 of 91
66794	polyamine pathway	30.43	7 of 23
66794	mevalonate metabolism	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4

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	Latitude	Longitude
20726	soil of a potato field	Chungcheongbuk-do (36° 43' 00'' N 127° 26' 12'' E)	Republic of Korea	KOR	Asia	36.7167	127.437 36.7167/127.437
67770	Soil of a potato field		Republic of Korea	KOR	Asia
67771	From soil cultivating potatoes	Ochang	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence FJ377314 (>99% sequence identity) for Daejeonella lutea from Microbeatlas

Aquatic Samples	159
Soil Samples	220
Animal Samples	40
Plant Samples	18
Total Samples	437

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20726	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	IMG-taxon 2595698248 annotated assembly for Daejeonella lutea DSM 22385	scaffold	GCA_900168015	572036.3	2595698248	572036	76.35

Genome browser: GCA_900168015

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20726	Pedobacter luteus strain N7d-4 16S ribosomal RNA gene, partial sequence	FJ377314	1403		572036

GC content

@ref	GC-content (mol%)	Method
20726	48.5	high performance liquid chromatography (HPLC)
67770	42.3	genome sequence analysis
67771	48.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Daejeonella lutea DSM 22385
NCBI: GCA_900168015

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.60	no
125439	motility	BacteriaNetⓘ	no	74.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter luteus strain DSM 22385
PATRIC: 572036.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.98	yes
125438	anaerobic	anaerobicⓘ	no	97.05	yes
125438	spore-forming	spore-formingⓘ	no	86.00	no
125438	aerobic	aerobicⓘ	yes	85.36	yes
125438	thermophilic	thermophileⓘ	no	98.83	yes
125438	flagellated	motile2+ⓘ	no	85.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter mongoliensis sp. nov., isolated from grassland soil.	Yuan K, Cao M, Li J, Wang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.002637	2018
Phylogeny	Pedobacter luteus sp. nov., isolated from soil.	Oh HW, Kim BC, Park DS, Jeong WJ, Kim H, Lee KH, Kim SU	Int J Syst Evol Microbiol	10.1099/ijs.0.033134-0	2012

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 )
#20726	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22385
#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 .
#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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Daejeonella lutea (DSM 22385, KCTC 22699, N7d-4)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900168015

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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