Name: Staphylococcus edaphicus P5085
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 157258

Type strain:

Species: Staphylococcus edaphicus

Strain Designation: P5085

Culture col. no.: DSM 104441, CCM 8730, CCUG 72269, CIP 111603

Strain history: CIP <- 2018, CCM <- 2016, I. Sedlacek, Mazaryk Univ., Brno, Czech Republic

NCBI tax ID(s): 1955013 (species)

SI-ID 401196

DSM 104441

Special Collections

Section

Staphylococcus edaphicus P5085 is an aerobe, Gram-positive bacterium that was isolated from Fragments of black porus stone.

Gram-positive
aerobe
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Staphylococcaceae*
	Genus	*Staphylococcus*
	Species	**Staphylococcus edaphicus**
	Full Scientific Name (LPSN)	Staphylococcus edaphicus Pant??ek et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #118996]	Gram stain	negative

[Ref.: #118996]	Cell shape	coccus-shaped

[Ref.: #118996]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #64323]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #64323]

Culture medium growth

[Ref.: #64323]

Culture medium link

Medium recipe at MediaDive

[Ref.: #64323]

Culture medium composition

expand / minimize

[Ref.: #64323]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #64323]

Culture medium growth

[Ref.: #64323]

Culture medium link

Medium recipe at MediaDive

[Ref.: #64323]

Culture medium composition

expand / minimize

[Ref.: #118996]

Culture medium

CIP Medium 72

[Ref.: #118996]

Culture medium growth

[Ref.: #118996]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #63798]			growth	37 °C
[Ref.: #64323]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #63798]

Oxygen tolerance

aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %99

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68375]	arabinose ChEBI	-	fermentation	* from API ID32STA
[Ref.: #68375]	arginine ChEBI	-	hydrolysis	* from API ID32STA
[Ref.: #68375]	cellobiose ChEBI	-	fermentation	* from API ID32STA
[Ref.: #68375]	D-fructose ChEBI	+	fermentation	* from API ID32STA
[Ref.: #68375]	D-glucose ChEBI	+	fermentation	* from API ID32STA
[Ref.: #68375]	D-mannitol ChEBI	+	fermentation	* from API ID32STA
[Ref.: #68375]	D-ribose ChEBI	-	fermentation	* from API ID32STA
[Ref.: #68375]	esculin ChEBI	-	hydrolysis	* from API ID32STA
[Ref.: #68375]	lactose ChEBI	-	fermentation	* from API ID32STA
[Ref.: #68375]	maltose ChEBI	+	fermentation	* from API ID32STA
[Ref.: #68375]	N-acetylglucosamine ChEBI	+	fermentation	* from API ID32STA
[Ref.: #68375]	nitrate ChEBI	+	reduction	* from API ID32STA
[Ref.: #68375]	ornithine ChEBI	-	degradation	* from API ID32STA
[Ref.: #68375]	raffinose ChEBI	-	fermentation	* from API ID32STA
[Ref.: #68375]	sucrose ChEBI	+	fermentation	* from API ID32STA
[Ref.: #68375]	trehalose ChEBI	-	fermentation	* from API ID32STA
[Ref.: #68375]	turanose ChEBI	-	fermentation	* from API ID32STA
[Ref.: #68375]	urea ChEBI	+	hydrolysis	* from API ID32STA
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic resistance	Concentration
[Ref.: #68375]		novobiocin ChEBI	yes	1.8	µg	* from API ID32STA

	Metabolite production	Metabolite	Production
[Ref.: #68375]		acetoin ChEBI	no	* from API ID32STA

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #68375]		acetoin ChEBI	-	* from API ID32STA

	Enzyme	Enzyme activity	EC number
[Ref.: #68375]	alkaline phosphatase	-	3.1.3.1	* from API ID32STA
[Ref.: #68375]	arginine dihydrolase	-	3.5.3.6	* from API ID32STA
[Ref.: #68375]	beta-galactosidase	-	3.2.1.23	* from API ID32STA
[Ref.: #68375]	beta-glucosidase	-	3.2.1.21	* from API ID32STA
[Ref.: #68375]	beta-glucuronidase	+	3.2.1.31	* from API ID32STA
[Ref.: #68375]	L-arginine arylamidase	-		* from API ID32STA
[Ref.: #68375]	ornithine decarboxylase	-	4.1.1.17	* from API ID32STA
[Ref.: #68375]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API ID32STA
[Ref.: #68375]	urease	+	3.5.1.5	* from API ID32STA

API® ID32STA:

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

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	Ornithine decarboxylaseODC	Esculin hydrolysisESC	Fermentation of D-glucoseGLU	Fermentation of D-fructoseFRU	Fermentation of D-mannoseMNE	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of trehaloseTRE	Fermentation of D-mannitolMAN	Fermentation of raffinoseRAF	Fermentation of D-riboseRIB	Fermentation of cellobioseCEL	Reduction of nitrateNIT	Acetoin production (Voges Proskauer test)VP	beta-Galactosidasebeta GAL	L-arginine arylamidaseArgA	Alkaline phosphatasePAL	Pyrrolidonyl arylamidasePyrA	Novobiocin resistanceNOVO	Fermentation of sucroseSAC	Fermentation of N-acetyl-glucosamineNAG	Fermentation of turanoseTUR	Fermentation of arabinoseARA	beta-Glucuronidasebeta GUR
[Ref.: #64323]	6246	+	-	-	-	+	+	+/-	+	-	-	+	-	-	-	+	-	-	-	-	-	+	+	+	-	-	+

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

[Ref.: #63798]	Sample type/isolated from	Fragments of black porus stone
[Ref.: #63798]	Sampling date	2016
[Ref.: #63798]	Geographic location (country and/or sea, region)	Ross Island,Lachman Cape
[Ref.: #63798]	Country	Antarctica
[Ref.: #63798]	Country ISO 3 Code	ATA
[Ref.: #63798]	Continent	Australia and Oceania

[Ref.: #64323]	Sample type/isolated from	fragments of black porous stone (top of the hill)
[Ref.: #64323]	Geographic location (country and/or sea, region)	James Ross Island (57° 47' 11" W, 63° 46' 58" S)
[Ref.: #64323]	Country	Antarctica
[Ref.: #64323]	Country ISO 3 Code	ATA
[Ref.: #64323]	Continent	Australia and Oceania

[Ref.: #118996]	Sample type/isolated from	Environment, Fragments of black porus stone
[Ref.: #118996]	Geographic location (country and/or sea, region)	Lachman Cap, J. Ross Island
[Ref.: #118996]	Country	Antarctica
[Ref.: #118996]	Country ISO 3 Code	ATA
[Ref.: #118996]	Continent	Antarctica
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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

[Ref.: #118996]

Biosafety level

Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Staphylococcus edaphicus CCM 8730	GCA_002614725	contig	GenBank ENA	1955013 tax ID	*
[Ref.: #66792]	Staphylococcus edaphicus strain CCM 8730 strain CCM 5085	1955013.3	wgs	PATRIC	1955013 tax ID	*
[Ref.: #66792]	Staphylococcus edaphicus CCM 8730	2802429263	draft	JGI IMG/M	1955013 tax ID	*

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: Staphylococcus edaphicus strain CCM 8730 strain CCM 5085 PATRIC: 1955013.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	99	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Staphylococcus edaphicus strain CCM 8730 strain CCM 5085 PATRIC: 1955013.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	81.283	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	99.434	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	69.837	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	60.933	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.517	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	80	no

Availability in culture collections External links

[Ref.: #64323]

Culture collection no.

DSM 104441, CCM 8730, CCUG 72269, CIP 111603

[Ref.: #110355]

SI-ID 401196

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments.	Pantucek R, Sedlacek I, Indrakova A, Vrbovska V, Maslanova I, Kovarovic V, Svec P, Kralova S, Kristofova L, Keklakova J, Petras P, Doskar J	Appl Environ Microbiol	10.1128/AEM.01746-17	2018	*

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 )

#63798 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 72269

#64323

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104441

#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) .

#68375

Automatically annotated from API ID32STA .

#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 )

#110355

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-ID401196.1 )

#118996 Collection of Institut Pasteur ; Curators of the CIP; CIP 111603
* These data were automatically processed and therefore are not curated

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Staphylococcus edaphicus strain CCM 8730 strain CCM 5085

Staphylococcus edaphicus strain CCM 8730 strain CCM 5085

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