Name: Edaphovirga cremea SYP-B2100
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159199

Type strain:

Species: Edaphovirga cremea

Strain Designation: SYP-B2100

Culture col. no.: DSM 105170, CGMCC 1.5857, KCTC 62024

Strain history: <- Yi-Xuan Zhang, Shenyang Pharmaceutical Univ.

NCBI tax ID(s): 2267246 (species)

Section

Edaphovirga cremea SYP-B2100 is an aerobe, mesophilic, motile bacterium that was isolated from rhizospheric soil of Codonopsis clematidea.

motile
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	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Enterobacteriaceae*
	Genus	"Edaphovirga"
	Species	"Edaphovirga cremea"
	Full Scientific Name (LPSN)	Edaphovirga cremea Xue et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.806

[Ref.: #69480]	Motility	yes Confidence in %97.886

Multimedia content

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Caption:

DSM 105170 on medium 535 at 28 °C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #66022]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #66022]			growth	28 °C
[Ref.: #67771]			growth	28 °C

[Ref.: #66022]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %96.565
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	sorbitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	+	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	yes	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	-		* from API 20E
[Ref.: #68368]		indole ChEBI		+	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E

API® 20E:

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

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #66022]	17731	+	-	-	-	-	-	-	-	+	-	-	+	+	-	+	+	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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

[Ref.: #66022]	Sample type/isolated from	rhizospheric soil of Codonopsis clematidea
[Ref.: #66022]	Host species	Codonopsis clematidea
[Ref.: #66022]	Geographic location (country and/or sea, region)	Xinjiang uygur autonomous region (43° 31' N, 85° 08' E)
[Ref.: #66022]	Country	China
[Ref.: #66022]	Country ISO 3 Code	CHN
[Ref.: #66022]	Continent	Asia
[Ref.: #66022]	Geographic location	43.5167°/85.1333°

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Xinjiang Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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.: #66022]	Edaphovirga cremea 16S ribosomal RNA gene, partial sequence	KY009921	1564	ENA	2267246 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Edaphovirga cremea DSM 105170	GCA_003332275	scaffold	GenBank	2267246 tax ID	*
[Ref.: #66792]	Rahnella sp. DSM 105170	2267246.3	wgs	PATRIC	2267246 tax ID	*
[Ref.: #66792]	Edaphovirga cremea DSM 105170	2852103415	draft	JGI IMG/M	2267246 tax ID	*

[Ref.: #66022]

GC-content

50.3 mol%

sequence analysis

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: Edaphovirga cremea DSM 105170 NCBI: GCA_003332275.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Edaphovirga cremea DSM 105170 NCBI: GCA_003332275.1
[Ref.: #69480]	motile	yes	90.309	no
[Ref.: #69480]	flagellated	no	58.047	no
[Ref.: #69480]	gram-positive	no	97.915	no
[Ref.: #69480]	anaerobic	no	96.913	yes
[Ref.: #69480]	aerobic	yes	69.675	no
[Ref.: #69480]	halophile	no	92.546	no
[Ref.: #69480]	spore-forming	no	93.738	no
[Ref.: #69480]	glucose-util	yes	95.662	no
[Ref.: #69480]	thermophile	no	99.416	yes
[Ref.: #69480]	glucose-ferment	yes	92.89	yes

Availability in culture collections External links

[Ref.: #66022]

Culture collection no.

DSM 105170, CGMCC 1.5857, KCTC 62024

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Edaphovirga cremea gen. nov., sp. nov., isolated from the rhizospheric soil of Codonopsis clematidea.	Xue JY, Zhang MY, Zhang Y, Cheng J, Liu LC, Wu YY, Zhang TY, Zhang YX	J Microbiol	10.1007/s12275-019-8408-0	2019	*

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 )

#66022

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105170

#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) .

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

#68368

Automatically annotated from API 20E .

#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 )

* These data were automatically processed and therefore are not curated

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Edaphovirga cremea DSM 105170

Edaphovirga cremea DSM 105170

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