Name: Sphingomonas lutea JS5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133300

Type strain:

Species: Sphingomonas lutea

Strain Designation: JS5

Culture col. no.: KCTC 23642, JCM 18309, CCTCC AB 2017135

Strain history: C. N. Seong JS5.

NCBI tax ID(s): 1045317 (species)

Section

Sphingomonas lutea JS5 is an aerobe, Gram-negative bacterium that forms circular colonies and was isolated from freshwater of Juam reservoir.

colony-forming
Gram-negative
aerobe
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingomonas*
	Species	**Sphingomonas lutea**
	Full Scientific Name (LPSN)	Sphingomonas lutea Lee et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.666

[Ref.: #25055]	Colony size	0.5-1.0 mm
[Ref.: #25055]	Colony color	yellow
[Ref.: #25055]	Colony shape	circular
[Ref.: #25055]	Incubation period	5 days
[Ref.: #25055]	Cultivation medium used	R2A agar

[Ref.: #25055]	Pigment production	yes
[Ref.: #25055]	Pigment name	Carotenoid pigments
[Ref.: #25055]	Pigment production	no
[Ref.: #25055]	Pigment name	Flexirubin-type

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

NA (nutrient agar)

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Culture medium growth

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Culture medium

Marine agar (MA)

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Culture medium growth

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Culture medium

PCA (plate-count agar)

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Culture medium growth

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Culture medium

TSA (Trypticase soy agar)

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Culture medium growth

		Temperature
[Ref.: #25055]	growth	10-37 °C
[Ref.: #25055]	optimum	25-30 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #25055]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25055]			optimum	7
[Ref.: #25055]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25055]

Oxygen tolerance

aerobe

[Ref.: #25055]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.895

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25055]		NaCl		growth	0-0.5	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25055]	(-)-quinic acid ChEBI	-	respiration
[Ref.: #25055]	2,3-butanediol ChEBI	+/-	respiration
[Ref.: #25055]	2-hydroxybutyrate ChEBI	-	respiration
[Ref.: #25055]	2-oxobutanoate ChEBI	-	respiration
[Ref.: #25055]	2-oxoglutarate ChEBI	-	respiration
[Ref.: #25055]	2-oxopentanoate ChEBI	-	respiration
[Ref.: #25055]	3-hydroxybutyrate ChEBI	-	respiration
[Ref.: #25055]	4-hydroxy-L-proline ChEBI	-	respiration
[Ref.: #25055]	4-hydroxybutyrate ChEBI	-	respiration
[Ref.: #25055]	4-hydroxyphenylacetic acid ChEBI	-	respiration
[Ref.: #25055]	acetate ChEBI	-	respiration
[Ref.: #25055]	adipate ChEBI	-	assimilation
[Ref.: #25055]	alpha-cyclodextrin ChEBI	-	respiration
[Ref.: #25055]	alpha-D-glucose ChEBI	-	assimilation
[Ref.: #25055]	alpha-D-glucose ChEBI	-	respiration
[Ref.: #25055]	alpha-lactose ChEBI	-	respiration
[Ref.: #25055]	arabinose ChEBI	-	assimilation
[Ref.: #25055]	arginine ChEBI	-	hydrolysis
[Ref.: #25055]	beta-hydroxybutyrate ChEBI	+	respiration
[Ref.: #25055]	beta-hydroxybutyrate ChEBI	+	assimilation
[Ref.: #25055]	bromosuccinate ChEBI	-	respiration
[Ref.: #25055]	carnitine ChEBI	-	respiration
[Ref.: #25055]	casein	-	hydrolysis
[Ref.: #25055]	cellobiose ChEBI	-	respiration
[Ref.: #25055]	cellulose ChEBI	-	hydrolysis
[Ref.: #25055]	chitin ChEBI	-	hydrolysis
[Ref.: #25055]	cis-aconitate ChEBI	-	respiration
[Ref.: #25055]	citrate ChEBI	-	respiration
[Ref.: #25055]	D-alanine ChEBI	-	respiration
[Ref.: #25055]	D-arabitol ChEBI	-	respiration
[Ref.: #25055]	D-fructose ChEBI	-	respiration
[Ref.: #25055]	D-galactonic acid lactone ChEBI	-	respiration
[Ref.: #25055]	D-galactose ChEBI	-	assimilation
[Ref.: #25055]	D-galactose ChEBI	-	respiration
[Ref.: #25055]	D-galacturonic acid ChEBI	-	respiration
[Ref.: #25055]	D-glucarate ChEBI	-	respiration
[Ref.: #25055]	D-gluconate ChEBI	-	assimilation
[Ref.: #25055]	D-gluconate ChEBI	-	respiration
[Ref.: #25055]	D-glucosaminic acid ChEBI	-	respiration
[Ref.: #25055]	D-glucose 6-phosphate ChEBI	+/-	respiration
[Ref.: #25055]	D-glucuronate ChEBI	-	respiration
[Ref.: #25055]	D-mannitol ChEBI	-	respiration
[Ref.: #25055]	D-mannose ChEBI	-	respiration
[Ref.: #25055]	D-psicose ChEBI	-	respiration
[Ref.: #25055]	D-serine ChEBI	-	respiration
[Ref.: #25055]	D-sorbitol ChEBI	-	respiration
[Ref.: #25055]	decanoate ChEBI	-	assimilation
[Ref.: #25055]	dextrin ChEBI	-	respiration
[Ref.: #25055]	dna ChEBI	-	hydrolysis
[Ref.: #25055]	erythritol ChEBI	-	respiration
[Ref.: #25055]	esculin ChEBI	+	hydrolysis
[Ref.: #25055]	ethanolamine ChEBI	+/-	respiration
[Ref.: #25055]	formate ChEBI	-	respiration
[Ref.: #25055]	fructose ChEBI	-	builds acid from
[Ref.: #25055]	galactose ChEBI	-	builds acid from
[Ref.: #25055]	gamma-aminobutyric acid ChEBI	-	respiration
[Ref.: #25055]	gelatin ChEBI	-	hydrolysis
[Ref.: #25055]	gentiobiose ChEBI	-	assimilation
[Ref.: #25055]	gentiobiose ChEBI	-	respiration
[Ref.: #25055]	glucose ChEBI	-	assimilation
[Ref.: #25055]	glucose ChEBI	-	builds acid from
[Ref.: #25055]	glucose 1-phosphate ChEBI	+/-	respiration
[Ref.: #25055]	glucuronamide ChEBI	-	respiration
[Ref.: #25055]	glycerol ChEBI	-	respiration
[Ref.: #25055]	glycerol 1-phosphate ChEBI	+/-	respiration
[Ref.: #25055]	glycogen ChEBI	-	respiration
[Ref.: #25055]	glycyl L-aspartic acid ChEBI	-	assimilation
[Ref.: #25055]	glycyl L-aspartic acid ChEBI	-	respiration
[Ref.: #25055]	glycyl-l-glutamate ChEBI	+	respiration
[Ref.: #25055]	glycyl-l-glutamate ChEBI	+	assimilation
[Ref.: #25055]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #25055]	inosine ChEBI	-	respiration
[Ref.: #25055]	itaconate ChEBI	-	respiration
[Ref.: #25055]	L-alaninamide ChEBI	-	respiration
[Ref.: #25055]	L-alanine ChEBI	-	respiration
[Ref.: #25055]	L-alanylglycine ChEBI	-	respiration
[Ref.: #25055]	L-arabinose ChEBI	-	respiration
[Ref.: #25055]	L-asparagine ChEBI	-	respiration
[Ref.: #25055]	L-aspartate ChEBI	-	respiration
[Ref.: #25055]	L-fucose ChEBI	-	respiration
[Ref.: #25055]	L-glutamate ChEBI	+/-	respiration
[Ref.: #25055]	L-glutamate ChEBI	+/-	assimilation
[Ref.: #25055]	L-histidine ChEBI	-	assimilation
[Ref.: #25055]	L-histidine ChEBI	-	respiration
[Ref.: #25055]	L-leucine ChEBI	-	respiration
[Ref.: #25055]	L-ornithine ChEBI	-	respiration
[Ref.: #25055]	L-phenylalanine ChEBI	-	respiration
[Ref.: #25055]	L-proline ChEBI	+	respiration
[Ref.: #25055]	L-pyroglutamic acid ChEBI	-	respiration
[Ref.: #25055]	L-rhamnose ChEBI	-	respiration
[Ref.: #25055]	L-serine ChEBI	-	respiration
[Ref.: #25055]	L-threonine ChEBI	-	respiration
[Ref.: #25055]	lactate ChEBI	-	respiration
[Ref.: #25055]	lactose ChEBI	-	builds acid from
[Ref.: #25055]	lactulose ChEBI	-	respiration
[Ref.: #25055]	malate ChEBI	-	assimilation
[Ref.: #25055]	malonate ChEBI	-	respiration
[Ref.: #25055]	maltose ChEBI	-	assimilation
[Ref.: #25055]	maltose ChEBI	-	builds acid from
[Ref.: #25055]	maltose ChEBI	-	respiration
[Ref.: #25055]	mannitol ChEBI	-	assimilation
[Ref.: #25055]	mannitol ChEBI	-	builds acid from
[Ref.: #25055]	mannose ChEBI	-	assimilation
[Ref.: #25055]	mannose ChEBI	-	builds acid from
[Ref.: #25055]	melibiose ChEBI	-	assimilation
[Ref.: #25055]	melibiose ChEBI	-	respiration
[Ref.: #25055]	methyl beta-D-glucopyranoside ChEBI	-	respiration
[Ref.: #25055]	methyl pyruvate ChEBI	-	respiration
[Ref.: #25055]	monomethyl succinate ChEBI	-	respiration
[Ref.: #25055]	myo-inositol ChEBI	-	respiration
[Ref.: #25055]	N-acetylgalactosamine ChEBI	-	respiration
[Ref.: #25055]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #25055]	N-acetylglucosamine ChEBI	-	respiration
[Ref.: #25055]	nitrate ChEBI	-	reduction
[Ref.: #25055]	phenylacetate ChEBI	-	assimilation
[Ref.: #25055]	phenylethylamine ChEBI	-	respiration
[Ref.: #25055]	potassium gluconate ChEBI	-	assimilation
[Ref.: #25055]	propionate ChEBI	-	respiration
[Ref.: #25055]	putrescine ChEBI	+/-	respiration
[Ref.: #25055]	raffinose ChEBI	-	respiration
[Ref.: #25055]	rhamnose ChEBI	-	builds acid from
[Ref.: #25055]	ribitol ChEBI	-	respiration
[Ref.: #25055]	sebacic acid ChEBI	-	respiration
[Ref.: #25055]	sodium citrate ChEBI	-	assimilation
[Ref.: #25055]	starch ChEBI	-	hydrolysis
[Ref.: #25055]	succinamate ChEBI	-	respiration
[Ref.: #25055]	succinate ChEBI	-	assimilation
[Ref.: #25055]	succinate ChEBI	-	respiration
[Ref.: #25055]	sucrose ChEBI	-	builds acid from
[Ref.: #25055]	sucrose ChEBI	-	respiration
[Ref.: #25055]	thymidine ChEBI	+/-	respiration
[Ref.: #25055]	trehalose ChEBI	-	builds acid from
[Ref.: #25055]	trehalose ChEBI	-	assimilation
[Ref.: #25055]	trehalose ChEBI	-	respiration
[Ref.: #25055]	turanose ChEBI	-	assimilation
[Ref.: #25055]	turanose ChEBI	-	respiration
[Ref.: #25055]	tween 20 ChEBI	+	hydrolysis
[Ref.: #25055]	tween 40 ChEBI	-	assimilation
[Ref.: #25055]	tween 40 ChEBI	-	respiration
[Ref.: #25055]	tween 80 ChEBI	-	hydrolysis
[Ref.: #25055]	tween 80 ChEBI	-	respiration
[Ref.: #25055]	urea ChEBI	-	hydrolysis
[Ref.: #25055]	uridine ChEBI	+/-	respiration
[Ref.: #25055]	urocanic acid ChEBI	-	respiration
[Ref.: #25055]	xanthine ChEBI	-	hydrolysis
[Ref.: #25055]	xylan ChEBI	-	hydrolysis
[Ref.: #25055]	xylitol ChEBI	-	respiration
[Ref.: #25055]	xylose ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25055]		hydrogen sulfide ChEBI	no
[Ref.: #25055]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #25055]	acid phosphatase	+/-	3.1.3.2
[Ref.: #25055]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25055]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25055]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25055]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25055]	alpha-glucosidase	-	3.2.1.20
[Ref.: #25055]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25055]	beta-galactosidase	-	3.2.1.23
[Ref.: #25055]	beta-glucosidase	-	3.2.1.21
[Ref.: #25055]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25055]	catalase	+	1.11.1.6
[Ref.: #25055]	cystine arylamidase	-	3.4.11.3
[Ref.: #25055]	cytochrome oxidase	-	1.9.3.1
[Ref.: #25055]	esterase (C 4)	+
[Ref.: #25055]	esterase Lipase (C 8)	+
[Ref.: #25055]	leucine arylamidase	+	3.4.11.1
[Ref.: #25055]	lipase (C 14)	-
[Ref.: #25055]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25055]	naphthol-AS-BI-phosphohydrolase	+/-
[Ref.: #25055]	trypsin	-	3.4.21.4
[Ref.: #25055]	valine arylamidase	+/-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25055]

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	34.8
C16:0	16.4
C16:1ω7c / C16:1ω6c	16.3
C18:0	7.7
C17:1ω6c	5.2
C16:1ω5c	3.9
C18:1 2OH	3.4
11-Methyl C18:1ω7c	3.1
C18:1ω9c	3
C14:0	2.1

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

[Ref.: #25055]	Sample type/isolated from	freshwater of Juam reservoir
[Ref.: #25055]	Geographic location (country and/or sea, region)	Juam reservoir, Republic of Korea
[Ref.: #25055]	Country	Republic of Korea
[Ref.: #25055]	Country ISO 3 Code	KOR
[Ref.: #25055]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Freshwater of Juam reservoir
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Freshwater

What are isolation sources categories?

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.: #25055]	16S rRNA gene sequence	JF922305	1428	ENA	1045317 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomonas lutea KCTC 23642	GCA_014396785	complete	GenBank	1045317 tax ID	*
[Ref.: #66792]	Sphingomonas lutea strain KCTC 23642	1045317.3	complete	PATRIC	1045317 tax ID	*
[Ref.: #66792]	Sphingomonas lutea KCTC 23642	2896432115	complete	JGI IMG/M	1045317 tax ID	*
[Ref.: #66792]	Sphingomonas lutea KCTC 23642	GCA_021497585	chromosome	GenBank	1045317 tax ID	*

[Ref.: #67770]

GC-content

64.9 mol%

thermal denaturation, midpoint method (Tm)

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: Sphingomonas lutea KCTC 23642 NCBI: GCA_014396785.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingomonas lutea KCTC 23642 NCBI: GCA_014396785.1
[Ref.: #69480]	flagellated	no	97.776	no
[Ref.: #69480]	gram-positive	no	97.061	no
[Ref.: #69480]	anaerobic	no	98.668	yes
[Ref.: #69480]	aerobic	yes	83.287	no
[Ref.: #69480]	halophile	no	92.179	yes
[Ref.: #69480]	spore-forming	no	95.573	no
[Ref.: #69480]	thermophile	no	90.477	yes
[Ref.: #69480]	glucose-util	yes	66.109	yes
[Ref.: #69480]	motile	no	84.478	no
[Ref.: #69480]	glucose-ferment	no	89.194	no

Availability in culture collections External links

[Ref.: #25055]

Culture collection no.

KCTC 23642, JCM 18309, CCTCC AB 2017135

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas arenae sp. nov., isolated from desert soil.	Dong L, Li S, Lian WH, Wei QC, Mohamad OAA, Hozzein WN, Ahmed I, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.005195	2022	*
Phylogeny	Sphingomonas lutea sp. nov., isolated from freshwater of an artificial reservoir.	Lee JH, Kim DI, Kang JW, Seong CN	Int J Syst Evol Microbiol	10.1099/ijsem.0.001546	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 )

#25055

J. H. K. Lee, D. I.,Kang, J. W.,Seong, C. N.: Sphingomonas lutea sp. nov., isolated from freshwater of an artificial reservoir. IJSEM 66: 5493 - 5499 2016 ( DOI 10.1099/ijsem.0.001546 , PubMed 27902188 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

* These data were automatically processed and therefore are not curated

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Sphingomonas lutea KCTC 23642

Sphingomonas lutea KCTC 23642

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