Name: Micrococcus endophyticus DSM 17945
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7759

Type strain:

Species: Micrococcus endophyticus

Culture col. no.: DSM 17945, KCTC 19156, YIM 56238, JCM 16951

Strain history: <- S-K Tang, Yunnan Inst. Microbiol, China

NCBI tax ID(s): 455343 (species)

SI-ID 404163

DSM 17945

Special Collections

Section

When using BacDive for research please cite our paper

Micrococcus endophyticus DSM 17945 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from surface-sterilized roots of Aquilaria sinensis collected in tropical rainforest.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Micrococcaceae*
	Genus	*Micrococcus*
	Species	**Micrococcus endophyticus**
	Full Scientific Name (LPSN)	Micrococcus endophyticus Chen et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29104]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #125439]	Gram stain	positive Confidence in %98.6
[Ref.: #125438]	Gram stain	positive Confidence in %92.657

[Ref.: #29104]	Cell shape	coccus-shaped

[Ref.: #125438]	Motility	no Confidence in %93.5

[Ref.: #19758]	Colony color	Lemon yellow (1012)
[Ref.: #19758]	Incubation period	10-14 days
[Ref.: #19758]	Cultivation medium used	ISP 2

[Ref.: #19758]	Colony color	Sulfur yellow (1016)
[Ref.: #19758]	Incubation period	10-14 days
[Ref.: #19758]	Cultivation medium used	ISP 3

[Ref.: #19758]	Colony color	Green beige (1000)
[Ref.: #19758]	Incubation period	10-14 days
[Ref.: #19758]	Cultivation medium used	ISP 4

[Ref.: #19758]	Colony color	Green beige (1000)
[Ref.: #19758]	Incubation period	10-14 days
[Ref.: #19758]	Cultivation medium used	ISP 5

[Ref.: #19758]	Colony color	Traffic yellow (1023)
[Ref.: #19758]	Incubation period	10-14 days
[Ref.: #19758]	Cultivation medium used	ISP 6

[Ref.: #19758]	Colony color	Zinc yellow (1018)
[Ref.: #19758]	Incubation period	10-14 days
[Ref.: #19758]	Cultivation medium used	ISP 7

[Ref.: #29104]

Pigment production

yes

[Ref.: #19758]	Multicellular complex forming ability	no
[Ref.: #19758]	Medium Name (multicellularity)	ISP 2

[Ref.: #19758]	Multicellular complex forming ability	no
[Ref.: #19758]	Medium Name (multicellularity)	ISP 3

[Ref.: #19758]	Multicellular complex forming ability	no
[Ref.: #19758]	Medium Name (multicellularity)	ISP 4

[Ref.: #19758]	Multicellular complex forming ability	no
[Ref.: #19758]	Medium Name (multicellularity)	ISP 5

[Ref.: #19758]	Multicellular complex forming ability	no
[Ref.: #19758]	Medium Name (multicellularity)	ISP 6

[Ref.: #19758]	Multicellular complex forming ability	no
[Ref.: #19758]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7281]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #7281]

Culture medium growth

[Ref.: #7281]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7281]

Culture medium composition

expand / minimize

[Ref.: #19758]

Culture medium

ISP 2

[Ref.: #19758]

Culture medium growth

[Ref.: #19758]

Culture medium composition

expand / minimize

[Ref.: #19758]

Culture medium

ISP 3

[Ref.: #19758]

Culture medium growth

[Ref.: #19758]

Culture medium composition

expand / minimize

[Ref.: #19758]

Culture medium

ISP 4

[Ref.: #19758]

Culture medium growth

[Ref.: #19758]

Culture medium composition

expand / minimize

[Ref.: #19758]

Culture medium

ISP 5

[Ref.: #19758]

Culture medium growth

[Ref.: #19758]

Culture medium composition

expand / minimize

[Ref.: #19758]

Culture medium

ISP 6

[Ref.: #19758]

Culture medium growth

[Ref.: #19758]

Culture medium composition

expand / minimize

[Ref.: #19758]

Culture medium

ISP 7

[Ref.: #19758]

Culture medium growth

[Ref.: #19758]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7281]	growth	28 °C
[Ref.: #19758]	optimum	28 °C
[Ref.: #29104]	growth	15-37 °C
[Ref.: #29104]	optimum	28 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #29104]			optimum	7.5
[Ref.: #29104]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29104]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	facultative anaerobe Confidence in %91.3

[Ref.: #29104]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29104]		NaCl		growth	0-10	%
[Ref.: #29104]		NaCl		optimum	5	%

[Ref.: #29104]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-8(H₂), MK-7(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29104]	5-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #29104]	arabinose ChEBI	+	carbon source
[Ref.: #29104]	cellobiose ChEBI	+	carbon source
[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.: #29104]	esculin ChEBI	+	hydrolysis
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #29104]	fructose ChEBI	+	carbon source
[Ref.: #29104]	galactose ChEBI	+	carbon source
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #29104]	glucose ChEBI	+	carbon source
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29104]	maltose ChEBI	+	carbon source
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29104]	mannose ChEBI	+	carbon source
[Ref.: #29104]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #29104]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #29104]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #29104]	raffinose ChEBI	+	carbon source
[Ref.: #29104]	ribose ChEBI	+	carbon source
[Ref.: #29104]	sorbitol ChEBI	+	carbon source
[Ref.: #29104]	sucrose ChEBI	+	carbon source
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29104]	trehalose ChEBI	+	carbon source
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
	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, API Coryne
[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.: #68382]	alpha-glucosidase	+	3.2.1.20	* 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.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #29104]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #29104]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #29104]	gelatinase	+
[Ref.: #68379]	gelatinase	+		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[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
[Ref.: #68382]	valine arylamidase	+		* from API zym
	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.: #19758]	300	-	-	-	-	-	-	-	-	-	-	+	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

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.: #19758]	582	not determinedn.d.	-	+	+	+	+	+	-	-	-	-	+	-	-	-	+	-	-	-	-

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

[Ref.: #7281]	Sample type/isolated from	surface-sterilized roots of Aquilaria sinensis collected in tropical rainforest
[Ref.: #7281]	Host species	Aquilaria sinensis
[Ref.: #7281]	Geographic location (country and/or sea, region)	south-west China, Yunnan Province
[Ref.: #7281]	Country	China
[Ref.: #7281]	Country ISO 3 Code	CHN
[Ref.: #7281]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From plant
[Ref.: #67771]	Geographic location (country and/or sea, region)	Yunnan Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Surface-sterilized roots of Aquilaria sinensis from a tropical rainforest
[Ref.: #67770]	Host species	Aquilaria sinensis
[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	#Tree
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part
#Climate	#Hot	#Tropical

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU005372 (>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.: #7281]

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.: #7281]	Micrococcus endophyticus strain YIM 56238 16S ribosomal RNA gene, partial sequence	EU005372	1438	GenBank ENA	455343 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Micrococcus endophyticus DSM 17945	GCA_014205115	contig	GenBank ENA	455343 tax ID	*
[Ref.: #66792]	Micrococcus endophyticus strain DSM 17945	455343.4	wgs	PATRIC	455343 tax ID	*
[Ref.: #66792]	Micrococcus endophyticus DSM 17945	2870801768	draft	JGI IMG/M	455343 tax ID	*

[Ref.: #7281]	GC-content	72.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29104]	GC-content	72.9 mol%

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micrococcus endophyticus strain DSM 17945 PATRIC: 455343.4
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	92.657	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.248	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	82.371	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	88.02	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	94.5	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	93.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Micrococcus endophyticus DSM 17945 NCBI: GCA_014205115
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	68
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	76.3
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	98.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	facultative anaerobe	91.3

Availability in culture collections External links

[Ref.: #7281]

Culture collection no.

DSM 17945, KCTC 19156, YIM 56238, JCM 16951

[Ref.: #77202]

SI-ID 404163

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 endophyticus sp. nov., isolated from surface-sterilized Aquilaria sinensis roots.	Chen HH, Zhao GZ, Park DJ, Zhang YQ, Xu LH, Lee JC, Kim CJ, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.006296-0	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

#7281

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17945

#19758

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 )

#29104

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 #25533 (see below)

#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;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#77202

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-ID404163.1 )

#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 .

#25533

IJSEM 1070 2009 ( DOI 10.1099/ijs.0.006296-0 , PubMed 19406795 )

* These data were automatically processed and therefore are not curated

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Micrococcus endophyticus strain DSM 17945

Micrococcus endophyticus DSM 17945

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