Staphylococcus xylosus (DSM 28566, 33-ERD13C)

Name: Staphylococcus xylosus (DSM 28566, 33-ERD13C)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131024

Type strain

Strain Designation 33-ERD13C

Culture col. no. DSM 28566 33-ERD13C

NCBI tax ID(s) 1288

Special Collections DSMZ Mouse DZIF

Links

Staphylococcus xylosus 33-ERD13C is a mesophilic prokaryote that was isolated from caecal content; TNF^deltaARE/+ C57BL/6 mouse.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404950

DSM 28566

@ref 20215

Last LPSN update 2025-12-16 10:01:08

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Staphylococcaceae

Genus Staphylococcus

Species Staphylococcus xylosus

Full scientific name Staphylococcus xylosus Schleifer and Kloos 1975 (Approved Lists 1980)

BacDive ID	Other strains from **Staphylococcus xylosus** (9)	Type strain
14599	S. xylosus KL 162, KL62, CCUG 7324, NCTC 11043, DSM ... (type strain)
14598	S. xylosus LRA 1641 575, LRA 164 15 75, DSM 6179, ATCC ...
14600	S. xylosus SL 8, DSM 20267
135389	S. xylosus AmMS 151, CIP 104065, ATCC 49148, CCUG 51322
141644	S. xylosus CCUG 4314, NCTC 10517
146726	S. xylosus CCUG 32025
148399	S. xylosus CCUG 35374
153954	S. xylosus CCUG 51763
169306	S. xylosus G2B1, DSM 26538

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	96

Colony morphology

22316

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22316	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22316	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	91.3

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68375	29016 ChEBI	arginine	-	hydrolysis	from API ID32STA
68375	17057 ChEBI	cellobiose	-	fermentation	from API ID32STA
68375	15824 ChEBI	D-fructose	+	fermentation	from API ID32STA
68375	17634 ChEBI	D-glucose	+	fermentation	from API ID32STA
68375	16899 ChEBI	D-mannitol	+	fermentation	from API ID32STA
68375	16024 ChEBI	D-mannose	+	fermentation	from API ID32STA
68375	16988 ChEBI	D-ribose	-	fermentation	from API ID32STA
68375	4853 ChEBI	esculin	-	hydrolysis	from API ID32STA
68375	17716 ChEBI	lactose	+	fermentation	from API ID32STA
68375	17306 ChEBI	maltose	+	fermentation	from API ID32STA
68375	59640 ChEBI	N-acetylglucosamine	+	fermentation	from API ID32STA
68375	17632 ChEBI	nitrate	+	reduction	from API ID32STA
68375	18257 ChEBI	ornithine	-	degradation	from API ID32STA
68375	16634 ChEBI	raffinose	-	fermentation	from API ID32STA
68375	17992 ChEBI	sucrose	+	fermentation	from API ID32STA
68375	27082 ChEBI	trehalose	+	fermentation	from API ID32STA
68375	16199 ChEBI	urea	+	hydrolysis	from API ID32STA

Antibiotic resistance

@ref	ChEBI	Metabolite	Is antibiotic	Is resistant	Resistance conc.
68375	28368	novobiocin			1.8 µg	from API ID32STA

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68375	15688 ChEBI	acetoin		from API ID32STA

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
68375	15688 ChEBI	acetoin	+	from API ID32STA

Enzymes

@ref	Value	Activity	Ec
68375	alkaline phosphatase	+	3.1.3.1	from API ID32STA
68375	arginine dihydrolase	-	3.5.3.6	from API ID32STA
68375	beta-galactosidase	+	3.2.1.23	from API ID32STA
68375	beta-glucosidase	-	3.2.1.21	from API ID32STA
68375	beta-glucuronidase	+	3.2.1.31	from API ID32STA
68375	ornithine decarboxylase	-	4.1.1.17	from API ID32STA
68375	pyrrolidonyl arylamidase	+	3.4.19.3	from API ID32STA
68375	urease	+	3.5.1.5	from API ID32STA

API ID32STA

@ref	URE	ADH (Arg)	ODC	ESC	GLU	FRU	MNE	MAL	LAC	TRE	MAN	RAF	RIB	CEL	Reduction of nitrateNIT	Acetoin production (Voges Proskauer test)VP	beta GAL	L-arginine arylamidaseArgA	PAL	Pyrrolidonyl arylamidasePyrA	NOVO	SAC	NAG	TUR	ARA	beta GUR
22316	+	-	-	-	+	+	+	+	+	+	+	-	-	-	+	+	+	+/-	+	+	+	+	+	-	+	+
22316	+	-	-	-	+	+	+	+	+	+	+	-	-	-	+	+	+	-	+	+	+	+	+	+/-	+	+
22316	+	-	-	-	+	+	+	+	+	+	+	-	-	-	+	+	+	-	+	+	+	+	+	-	+/-	+
22316	+	-	-	-	+	+	+	+	+	+	+	-	-	-	+	+	+	-	+	+	+	+	+	+/-	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	#Large intestine
#Host Body Product	#Gastrointestinal tract	#Caecal content

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22316	caecal content; TNF^deltaARE/+ C57BL/6 mouse	Freising	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364788 (>99% sequence identity) for Staphylococcus from Microbeatlas

Aquatic Samples	1554
Soil Samples	930
Animal Samples	23674
Plant Samples	763
Total Samples	26921

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
22316	yes, in single cases	yes, in single cases	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM2462188v1 assembly for Staphylococcus xylosus DSM 28566	contig	GCA_024621885	1288.338	1288	76.51

Genome browser: GCA_024621885

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22316	Staphylococcus sp. ERD13C 16S ribosomal RNA gene, partial sequence	KR364788	1445		1796649

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Staphylococcus xylosus DSM 28566
NCBI: GCA_024621885

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	54.60	no
125439	motility	BacteriaNetⓘ	no	52.20	no
125439	gram_stain	BacteriaNetⓘ	positive	96.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	91.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Staphylococcus xylosus DSM 28566
NCBI: GCA_024621885.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	83.60	no
125438	anaerobic	anaerobicⓘ	no	99.44	no
125438	aerobic	aerobicⓘ	yes	63.47	no
125438	spore-forming	spore-formingⓘ	no	70.48	no
125438	thermophilic	thermophileⓘ	no	93.60	no
125438	flagellated	motile2+ⓘ	no	80.80	no

Literature

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 )
#22316	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28566
#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 .
#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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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