Name: Sphingobium vermicomposti VC-230
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14193

Type strain:

Species: Sphingobium vermicomposti

Strain Designation: VC-230

Culture col. no.: DSM 21299, CCUG 55809

NCBI tax ID(s): 529005 (species)

SI-ID 399609

DSM 21299

Section

Sphingobium vermicomposti VC-230 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from homemade vermicompost from kitchen-waste.

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	*Sphingobium*
	Species	**Sphingobium vermicomposti**
	Full Scientific Name (LPSN)	Sphingobium vermicomposti Vaz-Moreira et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29097]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.991

[Ref.: #29097]	Cell length	0.95 µm

[Ref.: #29097]	Cell width	0.44 µm

[Ref.: #29097]	Cell shape	rod-shaped

[Ref.: #29097]	Motility	yes

[Ref.: #29097]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15424]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15424]

Culture medium growth

[Ref.: #15424]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15424]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15424]	growth	28 °C
[Ref.: #29097]	growth	15-37 °C
[Ref.: #29097]	optimum	30 °C

[Ref.: #15424]	Temperature range	mesophilic
[Ref.: #29097]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29097]			optimum	7
[Ref.: #29097]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29097]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29097]		NaCl		growth	01-01	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #29097]	arabinose ChEBI	+	carbon source
[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.: #29097]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #29097]	galactose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #29097]	glucose ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #29097]	lactose ChEBI	+	carbon source
[Ref.: #29097]	leucine ChEBI	+	carbon source
[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.: #29097]	rhamnose ChEBI	+	carbon source
[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.: #29097]	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.: #29097]	catalase	+	1.11.1.6
[Ref.: #29097]	cytochrome oxidase	+	1.9.3.1
[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.: #15424]	23249	-	-	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-	-	-	-	+

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

[Ref.: #15424]	Sample type/isolated from	homemade vermicompost from kitchen-waste
[Ref.: #15424]	Country	Portugal
[Ref.: #15424]	Country ISO 3 Code	PRT
[Ref.: #15424]	Continent	Europe

[Ref.: #60745]	Sample type/isolated from	Vermicompost,homemade from kitchen refuse
[Ref.: #60745]	Sampling date	2005
[Ref.: #60745]	Geographic location (country and/or sea, region)	Porto
[Ref.: #60745]	Country	Portugal
[Ref.: #60745]	Country ISO 3 Code	PRT
[Ref.: #60745]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Composting
#Engineered	#Waste	#Domestic waste

What are isolation sources categories?

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

[Ref.: #15424]

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.: #15424]	Sphingobium vermicomposti partial 16S rRNA gene, type strain VC-230T	AM998824	1451	ENA	529005 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobium vermicomposti DSM 21299	GCA_011762025	contig	GenBank	529005 tax ID	*
[Ref.: #66792]	Sphingobium vermicomposti strain DSM 21299	529005.3	wgs	PATRIC	529005 tax ID	*
[Ref.: #66792]	Sphingobium vermicomposti DSM 21299	2828330628	draft	JGI IMG/M	529005 tax ID	*

[Ref.: #15424]	GC-content	62 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29097]	GC-content	62 mol%

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: Sphingobium vermicomposti strain DSM 21299 PATRIC: 529005.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingobium vermicomposti strain DSM 21299 PATRIC: 529005.3
[Ref.: #69480]	gram-positive	no	97.614	yes
[Ref.: #69480]	anaerobic	no	98.852	yes
[Ref.: #69480]	halophile	no	91.961	yes
[Ref.: #69480]	spore-forming	no	94.899	no
[Ref.: #69480]	glucose-util	yes	80.969	yes
[Ref.: #69480]	motile	yes	68.127	yes
[Ref.: #69480]	flagellated	no	80.373	no
[Ref.: #69480]	aerobic	yes	93.736	yes
[Ref.: #69480]	thermophile	no	95.265	yes
[Ref.: #69480]	glucose-ferment	no	93.193	no

Availability in culture collections External links

[Ref.: #15424]

Culture collection no.

DSM 21299, CCUG 55809

[Ref.: #83353]

SI-ID 399609

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of Sphingobium psychrophilum sp. nov., a cold-adapted bacterium isolated from Arctic soil.	Dahal RH, Chaudhary DK, Kim DU, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004705	2021	*
Phylogeny	Sphingobium chungangianum sp. nov., isolated from rhizosphere of Pinus koraiensis.	Huq MA	Antonie Van Leeuwenhoek	10.1007/s10482-019-01266-8	2019	*
Phylogeny	Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov.	Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ, Tindall BJ, Sproer C, Overmann J	Int J Syst Evol Microbiol	10.1099/ijs.0.040105-0	2012	*
Phylogeny	Sphingobium wenxiniae sp. nov., a synthetic pyrethroid (SP)-degrading bacterium isolated from activated sludge in an SP-manufacturing wastewater treatment facility.	Wang BZ, Guo P, Zheng JW, Hang BJ, Li L, He J, Li SP	Int J Syst Evol Microbiol	10.1099/ijs.0.023309-0	2010	*
Phylogeny	Sphingobium vermicomposti sp. nov., isolated from vermicompost.	Vaz-Moreira I, Faria C, Lopes AR, Svensson L, Falsen E, Moore ER, Ferreira AC, Nunes OC, Manaia CM	Int J Syst Evol Microbiol	10.1099/ijs.0.006163-0	2009	*

References

#15424

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21299

#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 )

#29097

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 #25526 (see below)

#60745 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55809

#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) .

#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 )

#83353

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-ID399609.1 )

#25526

IJSEM 3145 2009 ( DOI 10.1099/ijs.0.006163-0 , PubMed 19643879 )

* These data were automatically processed and therefore are not curated

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Sphingobium vermicomposti strain DSM 21299

Sphingobium vermicomposti strain DSM 21299

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