Name: Micrococcus yunnanensis DSM 21948
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7760

Type strain:

Species: Micrococcus yunnanensis

Culture col. no.: DSM 21948, CCTCC AA 208060, JCM 16547, YIM 65004, CCUG 59864

Strain history: DSM 21948 <-- G.-Z. Zhao YIM 65004.

NCBI tax ID(s): 566027 (species)

SI-ID 364159

DSM 21948, LMG 25808, JCM 16547

Special Collections

Section

Micrococcus yunnanensis DSM 21948 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from surface-sterilized roots of Polyspora axillaris.

coccus-shaped
Gram-positive
aerobe
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Micrococcaceae*
	Genus	*Micrococcus*
	Species	**Micrococcus yunnanensis**
	Full Scientific Name (LPSN)	Micrococcus yunnanensis Zhao et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29287]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %91.788

[Ref.: #29287]	Cell length	0.9 µm

[Ref.: #29287]	Cell width	0.9 µm

[Ref.: #29287]	Cell shape	coccus-shaped

[Ref.: #29287]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94

[Ref.: #18345]	Colony color	Zinc yellow (1018)
[Ref.: #18345]	Incubation period	10-14 days
[Ref.: #18345]	Cultivation medium used	ISP 2

[Ref.: #18345]	Colony color	Sulfur yellow (1016)
[Ref.: #18345]	Incubation period	10-14 days
[Ref.: #18345]	Cultivation medium used	ISP 3

[Ref.: #18345]	Colony color	Ivory (1014)
[Ref.: #18345]	Incubation period	10-14 days
[Ref.: #18345]	Cultivation medium used	ISP 4

[Ref.: #18345]	Colony color	Sulfur yellow (1016)
[Ref.: #18345]	Incubation period	10-14 days
[Ref.: #18345]	Cultivation medium used	ISP 5

[Ref.: #18345]	Colony color	Lemon yellow (1012)
[Ref.: #18345]	Incubation period	10-14 days
[Ref.: #18345]	Cultivation medium used	ISP 6

[Ref.: #18345]	Colony color	Zinc yellow (1018)
[Ref.: #18345]	Incubation period	10-14 days
[Ref.: #18345]	Cultivation medium used	ISP 7

[Ref.: #29287]

Pigment production

[Ref.: #18345]	Multicellular complex forming ability	no
[Ref.: #18345]	Medium Name (multicellularity)	ISP 2

[Ref.: #18345]	Multicellular complex forming ability	no
[Ref.: #18345]	Medium Name (multicellularity)	ISP 3

[Ref.: #18345]	Multicellular complex forming ability	no
[Ref.: #18345]	Medium Name (multicellularity)	ISP 4

[Ref.: #18345]	Multicellular complex forming ability	no
[Ref.: #18345]	Medium Name (multicellularity)	ISP 5

[Ref.: #18345]	Multicellular complex forming ability	no
[Ref.: #18345]	Medium Name (multicellularity)	ISP 6

[Ref.: #18345]	Multicellular complex forming ability	no
[Ref.: #18345]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16064]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #16064]

Culture medium growth

[Ref.: #16064]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16064]

Culture medium composition

expand / minimize

[Ref.: #18345]

Culture medium

ISP 2

[Ref.: #18345]

Culture medium growth

[Ref.: #18345]

Culture medium composition

expand / minimize

[Ref.: #18345]

Culture medium

ISP 3

[Ref.: #18345]

Culture medium growth

[Ref.: #18345]

Culture medium composition

expand / minimize

[Ref.: #18345]

Culture medium

ISP 4

[Ref.: #18345]

Culture medium growth

[Ref.: #18345]

Culture medium composition

expand / minimize

[Ref.: #18345]

Culture medium

ISP 5

[Ref.: #18345]

Culture medium growth

[Ref.: #18345]

Culture medium composition

expand / minimize

[Ref.: #18345]

Culture medium

ISP 6

[Ref.: #18345]

Culture medium growth

[Ref.: #18345]

Culture medium composition

expand / minimize

[Ref.: #18345]

Culture medium

ISP 7

[Ref.: #18345]

Culture medium growth

[Ref.: #18345]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16064]	growth	28 °C
[Ref.: #18345]	optimum	28 °C
[Ref.: #29287]	growth	04-45 °C
[Ref.: #29287]	optimum	28 °C
[Ref.: #62139]	growth	37 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #29287]			optimum	7.0-8.0
[Ref.: #29287]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29287]	Oxygen tolerance	aerobe
[Ref.: #62139]	Oxygen tolerance	aerobe

[Ref.: #29287]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29287]		NaCl		growth	0-15	%

[Ref.: #67770]

Observation

quinones: MK-8(H₂), MK-7(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #18345]	arabinose ChEBI	-
[Ref.: #18345]	cellulose ChEBI	-
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #18345]	fructose ChEBI	-
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #18345]	glucose ChEBI	+
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #18345]	mannitol ChEBI	-
[Ref.: #29287]	melibiose ChEBI	+	carbon source
[Ref.: #18345]	myo-inositol ChEBI	-
[Ref.: #18345]	raffinose ChEBI	-
[Ref.: #18345]	rhamnose ChEBI	-
[Ref.: #18345]	sucrose ChEBI	+
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29287]	trehalose ChEBI	+	carbon source
[Ref.: #29287]	tween 80 ChEBI	+	carbon source
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #18345]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68379]	alpha-glucosidase	+	3.2.1.20	* from API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68379]	beta-galactosidase	-	3.2.1.23	* from API Coryne, API zym
[Ref.: #68379]	beta-glucosidase	-	3.2.1.21	* from API Coryne, API zym
[Ref.: #68379]	beta-glucuronidase	-	3.2.1.31	* from API Coryne, API zym
[Ref.: #29287]	catalase	+	1.11.1.6
[Ref.: #68379]	catalase	+	1.11.1.6	* from API Coryne
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	+		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68379]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API Coryne, API zym
[Ref.: #68379]	pyrrolidonyl arylamidase	+	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

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

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #18345]	35	+/-	-	+	-	-	-	+	-	-	-	+	not determinedn.d.	-	-	-	-	+/-	-	-	-	not determinedn.d.
[Ref.: #62139]	1789	-	+	+	+	-	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	+

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #18345]	55	not determinedn.d.	+	+	+	+	+	+	+	-	-	-	+	-	-	-	+	-	-	-	-
[Ref.: #62139]	2148	-	+	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #16064]	Sample type/isolated from	surface-sterilized roots of Polyspora axillaris
[Ref.: #16064]	Host species	Polyspora axillaris
[Ref.: #16064]	Geographic location (country and/or sea, region)	Yunnan Province
[Ref.: #16064]	Country	China
[Ref.: #16064]	Country ISO 3 Code	CHN
[Ref.: #16064]	Continent	Asia

[Ref.: #62139]	Sample type/isolated from	Surface-sterilized Polyspora axillaris roots
[Ref.: #62139]	Geographic location (country and/or sea, region)	Yunnan Province
[Ref.: #62139]	Country	China
[Ref.: #62139]	Country ISO 3 Code	CHN
[Ref.: #62139]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Roots of Polyspora axillaris
[Ref.: #67770]	Host species	Polyspora axillaris
[Ref.: #67770]	Geographic location (country and/or sea, region)	Yunnan Province, south-west China
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Shrub (Scrub)
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ214355 (>99% sequence identity) for Micrococcus from Microbeatlas

Aquatic Samples	9695
Soil Samples	6060
Animal Samples	37863
Plant Samples	3126
Total Samples	56744

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

[Ref.: #16064]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #16064]	Micrococcus yunnanensis strain YIM 65004 16S ribosomal RNA gene, partial sequence	FJ214355	1426	GenBank ENA	566027 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Micrococcus yunnanensis DSM 21948	GCA_014138885	contig	GenBank ENA	566027 tax ID	*
[Ref.: #66792]	Micrococcus yunnanensis strain DSM 21948	566027.8	wgs	PATRIC	566027 tax ID	*
[Ref.: #66792]	Micrococcus yunnanensis DSM 21948	2870804320	draft	JGI IMG/M	566027 tax ID	*

[Ref.: #16064]	GC-content	71.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29287]	GC-content	71.7 mol%

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: Micrococcus yunnanensis strain DSM 21948 PATRIC: 566027.5
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Micrococcus yunnanensis strain DSM 21948 PATRIC: 566027.8
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	91.788	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.351	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	83.974	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	84.826	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	94	yes

Availability in culture collections External links

[Ref.: #16064]

Culture collection no.

DSM 21948, CCTCC AA 208060, JCM 16547, YIM 65004, CCUG 59864

[Ref.: #77203]

SI-ID 364159

Literature:

Topic	Title	Authors	Journal	DOI	Year
Biotechnology	Optimization of Nutrients and Culture Conditions for Alkaline Protease Production Using Two Endophytic Micrococci: Micrococcus aloeverae and Micrococcus yunnanensis.	Prakash O, Nimonkar Y, Chavadar MS, Bharti N, Pawar S, Sharma A, Shouche YS	Indian J Microbiol	10.1007/s12088-017-0638-4	2017	*
Phylogeny	Description of Micrococcus aloeverae sp. nov., an endophytic actinobacterium isolated from Aloe vera.	Prakash O, Nimonkar Y, Munot H, Sharma A, Vemuluri VR, Chavadar MS, Shouche YS	Int J Syst Evol Microbiol	10.1099/ijs.0.063339-0	2014	*
Phylogeny	Micrococcus yunnanensis sp. nov., a novel actinobacterium isolated from surface-sterilized Polyspora axillaris roots.	Zhao GZ, Li J, Qin S, Zhang YQ, Zhu WY, Jiang CL, Xu LH, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.010256-0	2009	*
Phylogeny	Micrococcus porci sp. nov., Isolated from Feces of Black Pig (Sus scrofa).	Lee AY, Chen CH, Liou JS, Lin YC, Hamada M, Wang YT, Peng LL, Chang SC, Chen CC, Lin CF, Huang L, Huang CH	Life (Basel)	10.3390/life12111749	2022	*

References

#16064

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21948

#18345

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 )

#29287

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 #25703 (see below)

#62139 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 59864

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#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 .

#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 )

#77203

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-ID364159.1 )

#25703

IJSEM 2383 2009 ( DOI 10.1099/ijs.0.010256-0 , PubMed 19620366 )

* These data were automatically processed and therefore are not curated

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Micrococcus yunnanensis strain DSM 21948

Micrococcus yunnanensis strain DSM 21948

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