Staphylococcus microti (DSM 22147, CCM 4903, CCUG 55861)

Name: Staphylococcus microti (DSM 22147, CCM 4903, CCUG 55861)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14672

Type strain

Strain Designation 4005-LJ(m)

Culture col. no. DSM 22147 CCM 4903 CCUG 55861 4005-LJ(m)

NCBI tax ID(s) 569857

Special Collections DSMZ CCUG Literature strains

History <- D. Nováková, CCM; 4005-LJ(m) <- Z. Hubálek

Links

Staphylococcus microti 4005-LJ is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from liver of free-living common vole Microtus arvalis.

Gram-positive coccus-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 139493

NCTC 13832,CCM 4903,CCUG 55861,DSM 22147

@ref 20215

Last LPSN update 2026-02-09 11:21:28

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Staphylococcaceae

Genus Staphylococcus

Species Staphylococcus microti

Full scientific name Staphylococcus microti Nováková et al. 2010

BacDive ID	Other strains from **Staphylococcus microti** (1)	Type strain
154955	S. microti CCUG 55862, CCM 4904

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
29352	positive	coccus-shaped
125438	positive		90.434

Colony morphology

@ref	Type of hemolysis	Hemolysis ability
16122	beta	1

Pigmentation

29352

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16122	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
16122	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
16122	positive	growth	37	mesophilic
29352	positive	growth	15-45
60765	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
60765	aerobe
125439	microaerophile	91.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29352	NaCl	positive	growth	10 %

Observation

29352

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68375	22599 ChEBI	arabinose	-	fermentation	from API ID32STA
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
29352	28757 ChEBI	fructose	+	carbon source
29352	17234 ChEBI	glucose	+	carbon source
29352	17716 ChEBI	lactose	+	carbon source
68375	17716 ChEBI	lactose	+	fermentation	from API ID32STA
68375	17306 ChEBI	maltose	-	fermentation	from API ID32STA
29352	506227 ChEBI	N-acetylglucosamine	+	carbon source
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
29352	17992 ChEBI	sucrose	+	carbon source
68375	17992 ChEBI	sucrose	+	fermentation	from API ID32STA
29352	27082 ChEBI	trehalose	+	carbon source
68375	27082 ChEBI	trehalose	+	fermentation	from API ID32STA
68375	32528 ChEBI	turanose	-	fermentation	from API ID32STA
68375	16199 ChEBI	urea	-	hydrolysis	from API ID32STA
29352	18222 ChEBI	xylose	+	carbon source

Antibiotic resistance

@ref	ChEBI	Metabolite	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
29352	acid phosphatase	+	3.1.3.2
29352	alkaline phosphatase	+	3.1.3.1
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
29352	catalase	+	1.11.1.6
29352	cytochrome oxidase	+	1.9.3.1
68375	L-arginine arylamidase	-		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	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	acetoin degradation	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	vitamin K metabolism	100	5 of 5
66794	teichoic acid biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	ribulose monophosphate pathway	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	vitamin B1 metabolism	100	13 of 13
66794	pentose phosphate pathway	100	11 of 11
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	peptidoglycan biosynthesis	93.33	14 of 15
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	purine metabolism	81.91	77 of 94
66794	pyrimidine metabolism	80	36 of 45
66794	flavin biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	lipoate biosynthesis	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	alanine metabolism	72.41	21 of 29
66794	NAD metabolism	72.22	13 of 18
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	urea cycle	69.23	9 of 13
66794	leucine metabolism	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	proline metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	non-pathway related	60.53	23 of 38
66794	tryptophan metabolism	60.53	23 of 38
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	citric acid cycle	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	d-mannose degradation	55.56	5 of 9
66794	allantoin 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	d-xylose degradation	54.55	6 of 11
66794	metabolism of disaccharids	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	oxidative phosphorylation	50.55	46 of 91
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	CMP-KDO biosynthesis	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	vitamin B6 metabolism	45.45	5 of 11
66794	propanol degradation	42.86	3 of 7
66794	degradation of pentoses	42.86	12 of 28
66794	tyrosine metabolism	42.86	6 of 14
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	gallate degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	propionate fermentation	40	4 of 10
66794	phenol degradation	40	8 of 20
66794	lipid metabolism	38.71	12 of 31
66794	carnitine metabolism	37.5	3 of 8
66794	degradation of sugar acids	36	9 of 25
66794	glutathione metabolism	35.71	5 of 14
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	Entner Doudoroff pathway	30	3 of 10
66794	starch degradation	30	3 of 10
66794	degradation of hexoses	27.78	5 of 18
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	polyamine pathway	26.09	6 of 23
66794	glycogen biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	sulfate reduction	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	vitamin B12 metabolism	20.59	7 of 34

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
16122	-	-	-	+	+	+	-	-	+	+	+	-	-	-	+	+	-	-	+	+	+	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Rodentia (Other)
#Host Body-Site	#Organ	#Liver

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Sampling date
16122	liver of free-living common vole Microtus arvalis	Microtus arvalis	South Moravia, Breclav	Czech Republic	CZE	Europe
60765	Common vole (Microtus arvalis) liver and kidney		Drnholec	Czech Republic	CZE	Europe	2000-09-01

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
16122	yes, in single cases	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM93446v1 assembly for Staphylococcus microti DSM 22147	contig	GCA_000934465	569857.6	2627854114	569857	38.39
66792	ASM290263v1 assembly for Staphylococcus microti DSM 22147	scaffold	GCA_002902635	569857.9	2917456370	569857	27.24

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
16122	Staphylococcus microti strain CCM 4903 16S ribosomal RNA gene, partial sequence	EU888120	1477	569857
124043	Staphylococcus microti strain DSM 22147 16S ribosomal RNA gene, partial sequence.	MF678948	1283	569857
124043	Staphylococcus microti strain DSM 22147 16S ribosomal RNA gene, partial sequence 16S-23S ribosomal RNA intergenic spacer, complete sequence and 23S ribosomal RNA gene, partial sequence.	MF678892	4439	569857

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Staphylococcus microti DSM 22147
NCBI: GCA_002902635

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	58.40	no
125439	motility	BacteriaNetⓘ	no	57.30	no
125439	gram_stain	BacteriaNetⓘ	variable	72.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	91.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Staphylococcus microti DSM 22147
NCBI: GCA_002902635.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.43	yes
125438	anaerobic	anaerobicⓘ	no	95.88	yes
125438	aerobic	aerobicⓘ	yes	57.40	yes
125438	spore-forming	spore-formingⓘ	no	72.82	no
125438	thermophilic	thermophileⓘ	no	94.00	no
125438	flagellated	motile2+ⓘ	no	83.36	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Comparative Genomics of Staphylococcus rostri, an Undescribed Bacterium Isolated from Dairy Mastitis.	Klove DC, Farre M, Strube ML, Astrup LB.	Vet Sci	10.3390/vetsci10090530	2023
	Draft Genome Sequences of 64 Type Strains of 50 Species and 25 Subspecies of the Genus Staphylococcus Rosenbach 1884.	Cole K, Foster D, Russell JE, Golubchik T, Llewelyn M, Wilson DJ, Crook D, Paul J, Modernising Medical Microbiology Consortium.	Microbiol Resour Announc	10.1128/mra.00062-19	2019
Genetics	Draft Genome Sequence of Staphylococcus microti DSM 22147, Isolated from the Common Vole.	Hu X, Shang Y, Guo J, Zhang H, Liang Y, Sun J, Yue F	Genome Announc	10.1128/genomeA.00420-18	2018
Phylogeny	Staphylococcus rostri sp. nov., a haemolytic bacterium isolated from the noses of healthy pigs.	Riesen A, Perreten V	Int J Syst Evol Microbiol	10.1099/ijs.0.012443-0	2009
Phylogeny	Staphylococcus microti sp. nov., isolated from the common vole (Microtus arvalis).	Novakova D, Pantucek R, Hubalek Z, Falsen E, Busse HJ, Schumann P, Sedlacek I	Int J Syst Evol Microbiol	10.1099/ijs.0.011429-0	2009

References

#16122	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22147
#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 )
#25764	IJSEM 566 2010 ( DOI 10.1099/ijs.0.011429-0 , PubMed 19654347 )
#29352	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 #25764
#60765	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55861
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Staphylococcus microti (DSM 22147, CCM 4903, CCUG 55861)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API ID32STA

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000934465

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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