Name: Daejeonella lutea N7d-4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24548

Type strain:

Species: Daejeonella lutea

Strain Designation: N7d-4, P-2

Culture col. no.: DSM 22385, KCTC 22699, JCM 16318

Strain history: <- KS Bae, KRIBB

NCBI tax ID(s): 572036 (species)

SI-ID 402387

DSM 22385

Section

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

motile
rod-shaped
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Daejeonella*
	Species	**Daejeonella lutea**
	Full Scientific Name (LPSN)	Daejeonella lutea (Oh et al. 2013) García-López et al. 2020

Synonym

Pedobacter luteus

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.992

[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #67771]	Motility	yes

[Ref.: #67771]	Flagellum arrangement	gliding

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20726]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #20726]

Culture medium growth

[Ref.: #20726]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20726]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20726]	growth	25-30 °C
[Ref.: #67770]	growth	25 °C
[Ref.: #67771]	growth	25 °C

[Ref.: #20726]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.987

[Ref.: #67770]	Observation	quinones: MK-7
[Ref.: #67771]	Observation	quinones: MK-7

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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #20726]	Sample type/isolated from	soil of a potato field
[Ref.: #20726]	Geographic location (country and/or sea, region)	Chungcheongbuk-do (36° 43' 00'' N 127° 26' 12'' E)
[Ref.: #20726]	Country	Republic of Korea
[Ref.: #20726]	Country ISO 3 Code	KOR
[Ref.: #20726]	Continent	Asia
[Ref.: #20726]	Geographic location	36.7167°/127.4370°

[Ref.: #67770]	Sample type/isolated from	Soil of a potato field
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil cultivating potatoes
[Ref.: #67771]	Geographic location (country and/or sea, region)	Ochang
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #20726]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20726]	Pedobacter luteus strain N7d-4 16S ribosomal RNA gene, partial sequence	FJ377314	1403	ENA	572036 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Daejeonella lutea DSM 22385	GCA_900168015	scaffold	GenBank	572036 tax ID
[Ref.: #66792]	Pedobacter luteus strain DSM 22385	572036.3	wgs	PATRIC	572036 tax ID	*
[Ref.: #66792]	Pedobacter luteus DSM 22385	2595698248	draft	JGI IMG/M	572036 tax ID	*

[Ref.: #20726]	GC-content	48.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	42.3 mol%	genome sequence analysis
[Ref.: #67771]	GC-content	48.5 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Daejeonella lutea DSM 22385 NCBI: GCA_900168015.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pedobacter luteus strain DSM 22385 PATRIC: 572036.3
[Ref.: #69480]	gram-positive	no	97.511	yes
[Ref.: #69480]	anaerobic	no	99.198	no
[Ref.: #69480]	halophile	no	94.384	no
[Ref.: #69480]	spore-forming	no	94.903	no
[Ref.: #69480]	glucose-util	yes	81.892	no
[Ref.: #69480]	flagellated	no	97.532	yes
[Ref.: #69480]	aerobic	yes	85.193	no
[Ref.: #69480]	thermophile	no	96.023	yes
[Ref.: #69480]	motile	no	90.883	no
[Ref.: #69480]	glucose-ferment	no	89.701	no

Availability in culture collections External links

[Ref.: #20726]

Culture collection no.

DSM 22385, KCTC 22699, JCM 16318

[Ref.: #88403]

SI-ID 402387

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

#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 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#88403

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID402387.1 )

* These data were automatically processed and therefore are not curated

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Daejeonella lutea DSM 22385

Pedobacter luteus strain DSM 22385

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