Name: Sphingomonas prati W18RD
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132650

Type strain:

Species: Sphingomonas prati

Strain Designation: W18RD

Culture col. no.: DSM 103336, CGMCC 1.15645

Strain history: <- P. Manandhar and G. Zhang <- P. Manandhar, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China

NCBI tax ID(s): 1843237 (species)

SI-ID 405753

DSM 103336

Special Collections

Section

When using BacDive for research please cite our paper

Sphingomonas prati W18RD is an aerobe, chemoheterotroph, Gram-negative bacterium that forms circular colonies and was isolated from alpine meadow soil.

colony-forming
Gram-negative
rod-shaped
aerobe
chemoheterotroph
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingomonas*
	Species	**Sphingomonas prati**
	Full Scientific Name (LPSN)	Sphingomonas prati Manandhar et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24961]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %95.333
[Ref.: #125439]	Gram stain	negative Confidence in %99.9

[Ref.: #24961]	Cell length	1.1 µm

[Ref.: #24961]	Cell width	0.7 µm

[Ref.: #24961]	Cell shape	rod-shaped

[Ref.: #24961]	Motility	no

[Ref.: #24961]	Colony color	light orange
[Ref.: #24961]	Colony shape	circular
[Ref.: #24961]	Incubation period	4 days
[Ref.: #24961]	Cultivation medium used	R2A agar medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24961]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #24961]

Culture medium growth

[Ref.: #24439]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #24439]

Culture medium growth

[Ref.: #24439]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24439]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24439]	growth	28 °C
[Ref.: #24961]	growth	4-30 °C
[Ref.: #24961]	optimum	25 °C

	pH	Kind of pH		pH
[Ref.: #24961]			optimum	8
[Ref.: #24961]			growth	5.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24961]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %99.9

[Ref.: #24961]

Nutrition type

chemoheterotroph

[Ref.: #125439]

Ability of spore formation

no Confidence in %91.7

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24961]		NaCl		growth	0-1.0	%(w/v)
[Ref.: #24961]		NaCl		optimum	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24961]	4-nitrophenyl beta-D-glucopyranoside ChEBI	+	hydrolysis
[Ref.: #24961]	adipate ChEBI	-	assimilation
[Ref.: #68372]	amygdalin ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	arbutin ChEBI	+	assimilation	* from API 50CH assim
[Ref.: #68372]	cellobiose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	D-arabinose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	D-arabitol ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	D-fructose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	D-fucose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	D-galactose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	D-glucose ChEBI	-	assimilation
[Ref.: #68372]	D-glucose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	D-lyxose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	D-mannitol ChEBI	-	assimilation
[Ref.: #68372]	D-mannitol ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	D-mannose ChEBI	-	assimilation
[Ref.: #68372]	D-mannose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	D-ribose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	D-tagatose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	D-xylose ChEBI	+	assimilation	* from API 50CH assim
[Ref.: #24961]	decanoate ChEBI	-	assimilation
[Ref.: #68372]	erythritol ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	esculin ChEBI	+	hydrolysis
[Ref.: #68372]	esculin ChEBI	+	assimilation	* from API 50CH assim
[Ref.: #68372]	galactitol ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	gelatin ChEBI	-	hydrolysis
[Ref.: #68372]	gentiobiose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	gluconate ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	glucose ChEBI	-	fermentation
[Ref.: #68372]	glycerol ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	glycogen ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	inulin ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	L-arabinose ChEBI	-	assimilation
[Ref.: #68372]	L-arabinose ChEBI	+	assimilation	* from API 50CH assim
[Ref.: #68372]	L-arabitol ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	L-fucose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	L-rhamnose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	L-sorbose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	L-xylose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	lactose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	malate ChEBI	-	assimilation
[Ref.: #24961]	maltose ChEBI	-	assimilation
[Ref.: #68372]	maltose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	melezitose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	melibiose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	methyl alpha-D-glucopyranoside ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	methyl alpha-D-mannoside ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	methyl beta-D-xylopyranoside ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	myo-inositol ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #68372]	N-acetylglucosamine ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	nitrate ChEBI	-	reduction
[Ref.: #24961]	phenylacetate ChEBI	-	assimilation
[Ref.: #68372]	Potassium 2-ketogluconate ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	Potassium 5-ketogluconate ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	potassium gluconate ChEBI	-	assimilation
[Ref.: #68372]	raffinose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	ribitol ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	salicin ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	sodium citrate ChEBI	-	assimilation
[Ref.: #68372]	sorbitol ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	starch ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	sucrose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	trehalose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #24961]	tryptophan ChEBI	+	energy source
[Ref.: #68372]	turanose ChEBI	-	assimilation	* from API 50CH assim
[Ref.: #68372]	xylitol ChEBI	-	assimilation	* from API 50CH assim
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #24961]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #24961]		indole ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #24961]	acid phosphatase	+	3.1.3.2
[Ref.: #24961]	alkaline phosphatase	+	3.1.3.1
[Ref.: #24961]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #24961]	alpha-fucosidase	-	3.2.1.51
[Ref.: #24961]	alpha-galactosidase	+	3.2.1.22
[Ref.: #24961]	alpha-glucosidase	-	3.2.1.20
[Ref.: #24961]	alpha-mannosidase	-	3.2.1.24
[Ref.: #24961]	arginine dihydrolase	-	3.5.3.6
[Ref.: #24961]	beta-galactosidase	-	3.2.1.23
[Ref.: #24961]	beta-glucosidase	+	3.2.1.21
[Ref.: #24961]	beta-glucuronidase	-	3.2.1.31
[Ref.: #24961]	catalase	+	1.11.1.6
[Ref.: #24961]	cystine arylamidase	-	3.4.11.3
[Ref.: #24961]	cytochrome oxidase	+	1.9.3.1
[Ref.: #24961]	esterase (C 4)	+
[Ref.: #24961]	esterase lipase (C 8)	+
[Ref.: #24961]	leucine arylamidase	+	3.4.11.1
[Ref.: #24961]	lipase (C 14)	-
[Ref.: #24961]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #24961]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #24961]	trypsin	+	3.4.21.4
[Ref.: #24961]	tryptophan deaminase	+	4.1.99.1
[Ref.: #24961]	urease	-	3.5.1.5
[Ref.: #24961]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

API® 50CH assim:

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

	API ID	ControlQ	Assimilation of glycerolGLY	Assimilation of erythritolERY	Assimilation of D-arabinoseDARA	Assimilation of L-arabinoseLARA	Assimilation of D-riboseRIB	Assimilation of D-xyloseDXYL	Assimilation of L-xyloseLXYL	Assimilation of D-adonitolADO	Assimilation of methyl beta-D-xylopyranosideMDX	Assimilation of D-galactoseGAL	Assimilation of D-glucoseGLU	Assimilation of D-fructoseFRU	Assimilation of D-mannoseMNE	Assimilation of L-sorboseSBE	Assimilation of L-rhamnoseRHA	Assimilation of dulcitolDUL	Assimilation of inositolINO	Assimilation of D-mannitolMAN	Assimilation of sorbitolSOR	Assimilation of methyl alpha-D-mannopyranosideMDM	Assimilation of methyl alpha-D-glucopyranosideMDG	Assimilation of N-acetyl-glucosamineNAG	Assimilation of amygdalinAMY	Assimilation of arbutinARB	Assimilation of esculinESC	Assimilation of salicinSAL	Assimilation of cellobioseCEL	Assimilation of maltoseMAL	Assimilation of lactoseLAC	Assimilation of melibioseMEL	Assimilation of sucroseSAC	Assimilation of trehaloseTRE	Assimilation of inulinINU	Assimilation of melezitoseMLZ	Assimilation of raffinoseRAF	Assimilation of starchAMD	Assimilation of glycogenGLYG	Assimilation of xylitolXLT	Assimilation of gentiobioseGEN	Assimilation of turanoseTUR	Assimilation of D-lyxoseLYX	Assimilation of D-tagatoseTAG	Assimilation of D-fucoseDFUC	Assimilation of L-fucoseLFUC	Assimilation of D-arabitolDARL	Assimilation of L-arabitolLARL	Assimilation of gluconateGNT	Assimilation of 2-Ketogluconate2KG	Assimilation of 5-Ketogluconate5KG
[Ref.: #24439]	108	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #24439]	Sample type/isolated from	alpine meadow soil
[Ref.: #24439]	Geographic location (country and/or sea, region)	Qinghai-Tibetan Plateau, Tanggula mountain (33° 25.517' N 91° 55.855' E)
[Ref.: #24439]	Country	China
[Ref.: #24439]	Country ISO 3 Code	CHN
[Ref.: #24439]	Continent	Asia
[Ref.: #24439]	Geographic location	33.4253°/91.9309°
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Grassland
#Environmental	#Terrestrial	#Soil
#Climate	#Cold	#Alpine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU535675 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	81
Soil Samples	62
Animal Samples	48
Plant Samples	164
Total Samples	355

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

[Ref.: #24439]

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.: #24439]	Sphingomonas prati strain W18RD 16S ribosomal RNA gene, partial sequence	KU535675	1485	GenBank ENA	1843237 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomonas prati W18RD	GCA_009755805	scaffold	GenBank ENA	1843237 tax ID	*
[Ref.: #66792]	Sphingomonas prati CGMCC 1.15645	GCA_014643515	contig	GenBank ENA	1843237 tax ID	*
[Ref.: #66792]	Sphingomonas prati DSM 103336	GCA_014199405	scaffold	GenBank ENA	1843237 tax ID	*
[Ref.: #66792]	Sphingomonas prati strain CGMCC 1.15645	1843237.5	wgs	PATRIC	1843237 tax ID	*
[Ref.: #66792]	Sphingomonas prati strain DSM 103336	1843237.4	wgs	PATRIC	1843237 tax ID	*
[Ref.: #66792]	Sphingomonas prati DSM 103336	2828460860	draft	JGI IMG/M	1843237 tax ID	*

[Ref.: #24961]	GC-content	66.4 mol%
[Ref.: #24439]	GC-content	66.4 mol%	sequence analysis

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas prati W18RD NCBI: GCA_009755805.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	95.333	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.399	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	88.904	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	86.98	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.123	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	54.341	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas prati W18RD NCBI: GCA_009755805
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	91.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	56
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.9
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.9

Availability in culture collections External links

[Ref.: #24439]

Culture collection no.

DSM 103336, CGMCC 1.15645

[Ref.: #90963]

SI-ID 405753

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench.	Yang S, Li X, Xiao X, Zhuang G, Zhang Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.004235	2020	*
Phylogeny	Sphingomonas montana sp. nov., isolated from a soil sample from the Tanggula Mountain in the Qinghai Tibetan Plateau.	Manandhar P, Zhang G, Lama A, Liu F, Hu Y	Antonie Van Leeuwenhoek	10.1007/s10482-017-0915-6	2017	*
Phylogeny	Sphingomonas prati sp. nov., isolated from alpine meadow soil.	Manandhar P, Zhang G, Hu Y, Lama A, Gao F, Gu Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001346	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 )

#24439

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103336

#24961

P. Z. Manandhar, Gengxin,Hu, Yilun,Lama, Arun,Gao, Feng,Gu, Zhengquan: Sphingomonas prati sp. nov., isolated from alpine meadow soil. IJSEM 66: 4269 - 4275 2016 ( DOI 10.1099/ijsem.0.001346 , PubMed 27469025 )

#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) .

#68372

Automatically annotated from API 50CH assim .

#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 .

#90963

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-ID405753.1 )

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

* These data were automatically processed and therefore are not curated

Change proposal

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