Staphylococcus lentus (DSM 100111, WCA-CC-3-1)

Name: Staphylococcus lentus (DSM 100111, WCA-CC-3-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131016

Type strain

Strain Designation WCA-CC-3-1

Culture col. no. DSM 100111 WCA-CC-3-1

NCBI tax ID(s) 42858

Special Collections DSMZ Mouse DZIF

Links

Staphylococcus lentus WCA-CC-3-1 is a mesophilic prokaryote that was isolated from caecal content; wildtype C57BL/6 mouse.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 397817

DSM 100111

@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 lentus

Full scientific name Staphylococcus lentus (Kloos et al. 1976) Schleifer et al. 1983

Synonyms (2)

Mammaliicoccus lentus
Staphylococcus sciuri subsp. lentus

BacDive ID	Other strains from **Staphylococcus lentus** (3)	Type strain
143637	S. lentus CCUG 20685
146910	S. lentus CCUG 32419
151251	S. lentus CCUG 43543, CIP 103585, ATCC 49574

Morphology

Colony morphology

22308

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22308	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
22308	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
22308	positive	growth	37	mesophilic

Physiology and metabolism

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	32528 ChEBI	turanose	+	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-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

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	peptidoglycan biosynthesis	100	15 of 15
66794	ethanol fermentation	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	acetoin degradation	100	3 of 3
66794	lipoate biosynthesis	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	pentose phosphate pathway	100	11 of 11
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	ribulose monophosphate pathway	100	2 of 2
66794	palmitate biosynthesis	95.45	21 of 22
66794	vitamin B1 metabolism	92.31	12 of 13
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	degradation of sugar alcohols	81.25	13 of 16
66794	glycine betaine biosynthesis	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	Entner Doudoroff pathway	80	8 of 10
66794	threonine metabolism	80	8 of 10
66794	purine metabolism	79.79	75 of 94
66794	photosynthesis	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	serine metabolism	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	butanoate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	tryptophan metabolism	71.05	27 of 38
66794	phenylalanine metabolism	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	formaldehyde oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	non-pathway related	63.16	24 of 38
66794	ketogluconate metabolism	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	leucine metabolism	61.54	8 of 13
66794	methionine metabolism	61.54	16 of 26
66794	3-chlorocatechol degradation	60	3 of 5
66794	starch degradation	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	alanine metabolism	58.62	17 of 29
66794	arginine metabolism	58.33	14 of 24
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	oxidative phosphorylation	57.14	52 of 91
66794	d-mannose degradation	55.56	5 of 9
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	lysine metabolism	54.76	23 of 42
66794	proline metabolism	54.55	6 of 11
66794	metabolism of disaccharids	54.55	6 of 11
66794	degradation of pentoses	50	14 of 28
66794	glycogen biosynthesis	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	CMP-KDO biosynthesis	50	2 of 4
66794	cysteine metabolism	50	9 of 18
66794	phenylmercury acetate degradation	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	lipid metabolism	48.39	15 of 31
66794	sulfate reduction	46.15	6 of 13
66794	tyrosine metabolism	42.86	6 of 14
66794	mevalonate metabolism	42.86	3 of 7
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	cellulose degradation	40	2 of 5
66794	propionate fermentation	40	4 of 10
66794	myo-inositol biosynthesis	40	4 of 10
66794	gallate degradation	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	vitamin B6 metabolism	36.36	4 of 11
66794	degradation of sugar acids	36	9 of 25
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	glutathione metabolism	28.57	4 of 14
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	vitamin B12 metabolism	26.47	9 of 34
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	daunorubicin biosynthesis	22.22	2 of 9
66794	polyamine pathway	21.74	5 of 23

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
22308	+	-	-	+	+	+	+	+	+	+	+	-	+	+	+	-	+/-	+/-	+	-	+	+	+	+	+/-	-
22308	+	-	-	+	+	+	+	+	+	+	+	-	+	+	+	-	+/-	+/-	+	-	+	+	+	+	+/-	-

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
22308	caecal content; wildtype C57BL/6 mouse	Freising	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364789 (>99% sequence identity) for Staphylococcus from Microbeatlas

Aquatic Samples	251
Soil Samples	269
Animal Samples	6869
Plant Samples	116
Total Samples	7505

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
22308	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	ASM2462222v1 assembly for Mammaliicoccus lentus DSM 100111	contig	GCA_024622225	42858.49	42858	67.73

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22308	Staphylococcus sp. WCA-CC-3-1 16S ribosomal RNA gene, partial sequence	KR364789	1489		1796650

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mammaliicoccus lentus DSM 100111
NCBI: GCA_024622225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	78.20	no
125439	motility	BacteriaNetⓘ	no	57.00	no
125439	gram_stain	BacteriaNetⓘ	positive	67.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	62.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mammaliicoccus lentus DSM 100111
NCBI: GCA_024622225.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.28	no
125438	anaerobic	anaerobicⓘ	no	98.45	no
125438	aerobic	aerobicⓘ	yes	70.06	no
125438	spore-forming	spore-formingⓘ	no	64.96	no
125438	thermophilic	thermophileⓘ	no	93.08	yes
125438	flagellated	motile2+ⓘ	no	76.38	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 )
#22308	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100111
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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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