Name: Sphingomonas yantingensis 1007
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24562

Type strain:

Species: Sphingomonas yantingensis

Strain Designation: 1007

Culture col. no.: DSM 27244, CCTCC AB 2013146, JCM 19201

Strain history: J. Huang and X. Sheng 1007.

NCBI tax ID(s): 1241761 (species)

SI-ID 408184

DSM 27244

Section

Sphingomonas yantingensis 1007 is a mesophilic, Gram-negative bacterium that was isolated from purple paddy soil.

Gram-negative
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 yantingensis**
	Full Scientific Name (LPSN)	Sphingomonas yantingensis Huang et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.988

Multimedia content

[Ref.: #20819]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20819]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #20819]

Culture medium growth

[Ref.: #20819]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20819]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #20819]			growth	28 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #20819]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.984

[Ref.: #67770]

Observation

quinones: Q-10

	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	+	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.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose 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.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[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.: #20819]	23276	-	-	-	-	-	+	-	+	+	+	+	-	+	+	-	-	-	+	-	-	-

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

[Ref.: #20819]	Sample type/isolated from	purple paddy soil
[Ref.: #20819]	Geographic location (country and/or sea, region)	Sichuan province, Yanting county, Linshan township (105° 27' E 31° 16' N, at an altitude of 420 m)
[Ref.: #20819]	Country	China
[Ref.: #20819]	Country ISO 3 Code	CHN
[Ref.: #20819]	Continent	Asia
[Ref.: #20819]	Geographic location	31.2667°/105.4500°

[Ref.: #67770]	Sample type/isolated from	Purplish soil in Yanting
[Ref.: #67770]	Geographic location (country and/or sea, region)	Sichuan
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JX566547 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	254
Soil Samples	73
Animal Samples	333
Plant Samples	63
Total Samples	723

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

[Ref.: #20819]

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.: #20819]	Sphingomonas yantingensis strain 1007 from China 16S ribosomal RNA gene, partial sequence	JX566547	1463	ENA	1241761 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomonas yantingensis DSM 27244	GCA_014199325	contig	GenBank	1241761 tax ID	*
[Ref.: #66792]	Sphingomonas yantingensis strain DSM 27244	1241761.3	wgs	PATRIC	1241761 tax ID	*
[Ref.: #66792]	Sphingomonas yantingensis DSM 27244	2828398746	draft	JGI IMG/M	1241761 tax ID	*

[Ref.: #20819]	GC-content	67 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	66.3-67.7 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 yantingensis strain DSM 27244 PATRIC: 1241761.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingomonas yantingensis strain DSM 27244 PATRIC: 1241761.3
[Ref.: #69480]	motile	yes	69.955	no
[Ref.: #69480]	gram-positive	no	97.042	no
[Ref.: #69480]	anaerobic	no	99.614	no
[Ref.: #69480]	aerobic	yes	95.967	no
[Ref.: #69480]	halophile	no	94.445	no
[Ref.: #69480]	spore-forming	no	94.061	no
[Ref.: #69480]	glucose-util	yes	90.686	yes
[Ref.: #69480]	flagellated	no	88.774	no
[Ref.: #69480]	thermophile	no	96.224	yes
[Ref.: #69480]	glucose-ferment	no	92.865	yes

Availability in culture collections External links

[Ref.: #20819]

Culture collection no.

DSM 27244, CCTCC AB 2013146, JCM 19201

[Ref.: #88416]

SI-ID 408184

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 yantingensis sp. nov., a mineral-weathering bacterium isolated from purplish paddy soil.	Huang J, Huang Z, Zhang ZD, He LY, Sheng XF	Int J Syst Evol Microbiol	10.1099/ijs.0.055954-0	2013	*

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 )

#20819

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27244

#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 .

#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 )

#88416

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-ID408184.1 )

* These data were automatically processed and therefore are not curated

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Sphingomonas yantingensis strain DSM 27244

Sphingomonas yantingensis strain DSM 27244

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