Name: Sphingomonas japonica KC7
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14259

Type strain:

Species: Sphingomonas japonica

Strain Designation: KC7

Culture col. no.: DSM 22753, JCM 15438, KMM 3038, NRIC 0738, CIP 110395

Strain history: CIP <- 2012, JCM <- 2008, N. Tanaka: strain KC7

NCBI tax ID(s): 511662 (species)

SI-ID 362852

JCM 15438, CIP 110395

Special Collections

Section

Sphingomonas japonica KC7 is an aerobe, Gram-negative, motile bacterium that was isolated from marine crustacean specimen Paralithodes camtschatica.

Gram-negative
motile
rod-shaped
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 japonica**
	Full Scientific Name (LPSN)	Sphingomonas japonica Romanenko et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28989]	Gram stain	negative
[Ref.: #120316]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.078

[Ref.: #28989]	Cell length	1.65 µm

[Ref.: #28989]	Cell width	0.7 µm

[Ref.: #28989]	Cell shape	rod-shaped
[Ref.: #120316]	Cell shape	rod-shaped

[Ref.: #28989]	Motility	yes
[Ref.: #120316]	Motility	yes

[Ref.: #28989]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16495]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #16495]

Culture medium growth

[Ref.: #16495]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16495]

Culture medium composition

expand / minimize

[Ref.: #36629]

Culture medium

Marine agar (MA)

[Ref.: #36629]

Culture medium growth

[Ref.: #36629]

Culture medium composition

expand / minimize

[Ref.: #120316]

Culture medium

CIP Medium 13

[Ref.: #120316]

Culture medium growth

[Ref.: #120316]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #16495]	growth	28 °C
[Ref.: #28989]	growth	04-37 °C
[Ref.: #28989]	optimum	26.5 °C
[Ref.: #36629]	growth	25 °C
[Ref.: #67770]	growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28989]

Oxygen tolerance

aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %99

[Ref.: #28989]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* 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.: #28989]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #28989]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #28989]	tween 80 ChEBI	+	carbon source
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #28989]		hydrogen sulfide ChEBI	yes
[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.: #28989]	acid phosphatase	+	3.1.3.2
[Ref.: #28989]	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.: #28989]	catalase	+	1.11.1.6
[Ref.: #28989]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE
[Ref.: #28989]	gelatinase	+
[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.: #16495]	23263	-	-	-	-	-	+	-	+	+	+	-	-	-	+	-	-	-	-	-	-	-
[Ref.: #16495]	23156	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #16495]	Sample type/isolated from	marine crustacean specimen Paralithodes camtschatica
[Ref.: #16495]	Host species	Paralithodes camtschatica
[Ref.: #16495]	Geographic location (country and/or sea, region)	Sea of Japan, Peter the Great Bay
[Ref.: #16495]	Country	Russia
[Ref.: #16495]	Country ISO 3 Code	RUS
[Ref.: #16495]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Paralithodes camtschatica collected from Peter the Great Bay
[Ref.: #67770]	Host species	Paralithodes camtschatica
[Ref.: #67770]	Geographic location (country and/or sea, region)	Sea of Japan
[Ref.: #67770]	Country	Russia
[Ref.: #67770]	Country ISO 3 Code	RUS

[Ref.: #120316]	Sample type/isolated from	Paralithodes camtschatica collected from Peter the Great Bay
[Ref.: #120316]	Geographic location (country and/or sea, region)	Sea of Japan
[Ref.: #120316]	Country	Russian Federation
[Ref.: #120316]	Country ISO 3 Code	RUS
[Ref.: #120316]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Host	#Arthropoda	#Crustacea

What are isolation sources categories?

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

[Ref.: #16495]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120316]	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.: #16495]	Sphingomonas japonica gene for 16S rRNA, partial sequence, strain: KC7	AB428568	1480	GenBank ENA	511662 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Sphingomonas japonica DSM 22753	GCA_011762085	contig	GenBank ENA	511662 tax ID
[Ref.: #66792]	Sphingomonas japonica strain DSM 22753	511662.4	wgs	PATRIC	511662 tax ID	*
[Ref.: #66792]	Sphingomonas japonica DSM 22753	2828348002	draft	JGI IMG/M	511662 tax ID	*

[Ref.: #16495]

GC-content

66.7 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Sphingomonas japonica strain DSM 22753 PATRIC: 511662.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	99	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingomonas japonica strain DSM 22753 PATRIC: 511662.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.078	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	93.621	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.175	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.419	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.092	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	66.915	no

Availability in culture collections External links

[Ref.: #16495]

Culture collection no.

DSM 22753, JCM 15438, KMM 3038, NRIC 0738, CIP 110395

[Ref.: #83418]

SI-ID 362852

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas spermidinifaciens sp. nov., a novel bacterium containing spermidine as the major polyamine, isolated from an abandoned lead-zinc mine and emended descriptions of the genus Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica.	Feng GD, Yang SZ, Xiong X, Li HP, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001905	2017	*
Phylogeny	Sphingomonas japonica sp. nov., isolated from the marine crustacean Paralithodes camtschatica.	Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.003285-0	2009	*
Phylogeny	Sphingomonas baiyangensis sp. nov., isolated from water in Baiyang Lake.	Wei DW, Yang Y, Zeng Y, Wang C, Feng J	Int J Syst Evol Microbiol	10.1099/ijsem.0.005326	2022	*

References

#16495

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22753

#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 )

#28989

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 #25422 (see below)

#36629 ; 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;

#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 )

#83418

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-ID362852.1 )

#120316 Collection of Institut Pasteur ; Curators of the CIP; CIP 110395

#25422

IJSEM 1179 2009 ( DOI 10.1099/ijs.0.003285-0 , PubMed 19406815 )

* These data were automatically processed and therefore are not curated

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Sphingomonas japonica strain DSM 22753

Sphingomonas japonica strain DSM 22753

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