Name: Sphingomonas insulae DS-28
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14257

Type strain:

Species: Sphingomonas insulae

Strain Designation: DS-28

Culture col. no.: DSM 21792, JCM 14603, KCTC 12872, CIP 110394

Strain history: CIP <- 2012, JCM <- 2007, J.H. Yoon: strain DS-28

NCBI tax ID(s): 424800 (species)

SI-ID 323998

JCM 14603, KCTC 12872, DSM 21792, CIP 110394

Section

Sphingomonas insulae DS-28 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

Gram-negative
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingomonas*
	Species	**Sphingomonas insulae**
	Full Scientific Name (LPSN)	Sphingomonas insulae Yoon et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32175]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #120141]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.966

[Ref.: #32175]	Cell length	3 µm

[Ref.: #32175]	Cell width	0.45 µm

[Ref.: #32175]	Cell shape	rod-shaped
[Ref.: #120141]	Cell shape	rod-shaped

[Ref.: #32175]	Motility	yes
[Ref.: #120141]	Motility	yes

[Ref.: #32175]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15956]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #15956]

Culture medium growth

[Ref.: #15956]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15956]

Culture medium composition

expand / minimize

[Ref.: #36905]

Culture medium

MEDIUM 328- for nutrient agar

[Ref.: #36905]

Culture medium growth

[Ref.: #36905]

Culture medium composition

expand / minimize

[Ref.: #120141]

Culture medium

CIP Medium 328

[Ref.: #120141]

Culture medium growth

[Ref.: #120141]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #15956]	growth	28 °C
[Ref.: #32175]	growth	04-34 °C
[Ref.: #32175]	optimum	25 °C
[Ref.: #36905]	growth	25 °C
[Ref.: #67770]	growth	25 °C
[Ref.: #67771]	growth	25 °C

[Ref.: #15956]	Temperature range	mesophilic
[Ref.: #32175]	Temperature range	mesophilic
[Ref.: #36905]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32175]			optimum	6.5
[Ref.: #32175]			growth	5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32175]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %96
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.988

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32175]		NaCl		growth	0-2	%
[Ref.: #32175]		NaCl		optimum	0.25	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32175]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32175]	cellobiose ChEBI	+	carbon source
[Ref.: #32175]	citrate ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32175]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #32175]	fructose ChEBI	+	carbon source
[Ref.: #32175]	galactose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32175]	glucose ChEBI	+	carbon source
[Ref.: #32175]	glycerol ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #32175]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #32175]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #32175]	mannose ChEBI	+	carbon source
[Ref.: #32175]	melibiose ChEBI	+	carbon source
[Ref.: #32175]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #32175]	raffinose ChEBI	+	carbon source
[Ref.: #32175]	rhamnose ChEBI	+	carbon source
[Ref.: #32175]	salicin ChEBI	+	carbon source
[Ref.: #32175]	sucrose ChEBI	+	carbon source
[Ref.: #32175]	trehalose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32175]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #32175]	acid phosphatase	+	3.1.3.2
[Ref.: #32175]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #32175]	catalase	+	1.11.1.6
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #15956]	23254	-	-	-	-	-	+	-	+	+	+	+	-	+	-	-	-	-	+	+	-	+

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

[Ref.: #15956]	Sample type/isolated from	soil
[Ref.: #15956]	Geographic location (country and/or sea, region)	Dokdo
[Ref.: #15956]	Country	Republic of Korea
[Ref.: #15956]	Country ISO 3 Code	KOR
[Ref.: #15956]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Dokdo
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #120141]	Sample type/isolated from	Environment, Soil
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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

[Ref.: #15956]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120141]	Biosafety level	1	Risk group (French classification)

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.: #15956]	Sphingomonas insulae strain DS-28 16S ribosomal RNA gene, partial sequence	EF363714	1447	ENA	424800 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Sphingomonas insulae DSM 21792	GCA_011762035	scaffold	GenBank	424800 tax ID
[Ref.: #66792]	Sphingomonas insulae KCTC 12872	GCA_010450875	complete	GenBank	424800 tax ID	*
[Ref.: #66792]	Sphingomonas insulae strain DSM 21792	424800.4	wgs	PATRIC	424800 tax ID	*
[Ref.: #66792]	Sphingomonas insulae strain KCTC 12872	424800.3	complete	PATRIC	424800 tax ID	*
[Ref.: #66792]	Sphingomonas insulae DSM 21792	2828333980	draft	JGI IMG/M	424800 tax ID	*

[Ref.: #32175]	GC-content	67 mol%
[Ref.: #67770]	GC-content	67 mol%	high performance liquid chromatography (HPLC)

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 insulae strain KCTC 12872 PATRIC: 424800.3
[Ref.: #69481]	spore-forming	no	96	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingomonas insulae KCTC 12872 NCBI: GCA_010450875.1
[Ref.: #69480]	motile	yes	81.383	yes
[Ref.: #69480]	flagellated	no	85.68	no
[Ref.: #69480]	gram-positive	no	97.091	yes
[Ref.: #69480]	anaerobic	no	99.347	yes
[Ref.: #69480]	aerobic	yes	94.717	no
[Ref.: #69480]	halophile	no	93.46	yes
[Ref.: #69480]	spore-forming	no	94.755	no
[Ref.: #69480]	glucose-util	yes	92.509	no
[Ref.: #69480]	thermophile	no	99.028	yes
[Ref.: #69480]	glucose-ferment	no	91.332	no

Availability in culture collections External links

[Ref.: #15956]

Culture collection no.

DSM 21792, JCM 14603, KCTC 12872, CIP 110394

[Ref.: #83416]

SI-ID 323998

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas cynarae sp. nov., a proteobacterium that produces an unusual type of sphingan.	Tala A, Lenucci M, Gaballo A, Durante M, Tredici SM, Debowles DA, Pizzolante G, Marcuccio C, Carata E, Piro G, Carpita NC, Mita G, Alifano P	Int J Syst Evol Microbiol	10.1099/ijs.0.032060-0	2012	*
Phylogeny	Sphingomonas insulae sp. nov., isolated from soil.	Yoon JH, Kang SJ, Lee SY, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.65075-0	2008	*

References

#15956

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21792

#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 )

#32175

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 #28417 (see below)

#36905 ; Curators of the CIP;

#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;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68369

Automatically annotated from API 20NE .

#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 )

#83416

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-ID323998.1 )

#120141 Collection of Institut Pasteur ; Curators of the CIP; CIP 110394

#28417

IJSEM 231 2008 ( DOI 10.1099/ijs.0.65075-0 , PubMed 18175714 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Sphingomonas insulae in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Sphingomonas insulae strain KCTC 12872

Sphingomonas insulae KCTC 12872

Change proposal

Change proposal