Micrococcus terreus (DSM 28110, CGMCC 1.7054, NBRC 104258)

Name: Micrococcus terreus (DSM 28110, CGMCC 1.7054, NBRC 104258)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24203

Type strain

Strain Designation V3M1

Culture col. no. DSM 28110 CGMCC 1.7054 NBRC 104258 V3M1 JCM 17489

NCBI tax ID(s) 574650

Special Collections DSMZ JCM Literature strains

Links

Micrococcus terreus V3M1 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from forest soil.

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

Name and taxonomic classification

SI-ID 404630

NBRC 104258,JCM 17489,DSM 28110

@ref 20215

Last LPSN update 2025-12-16 09:52:48

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Micrococcus

Species Micrococcus terreus

Full scientific name Micrococcus terreus Zhang et al. 2010

BacDive ID	Other strains from **Micrococcus terreus** (3)	Type strain
156063	M. terreus CCUG 60247
156122	M. terreus CCUG 60458
157207	M. terreus CCUG 70564

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape
29443	positive	0.6-0.7 µm	coccus-shaped
125438
125438	positive
125439	positive

Pigmentation

29443

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20655	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
20655	positive	growth	28	mesophilic
29443	positive	growth	20-35
29443	positive	optimum	33	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
29443	positive	optimum	7
29443	positive	growth	05-09

Physiology and metabolism

Oxygen tolerance

29443

Oxygen toleranceaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29443	NaCl	positive	growth	0-2 %
29443	NaCl	positive	optimum	1 %

Observation

@ref	Observation
29443	aggregates in chains
67770	quinones: MK-7, MK-7(H?n(2)), MK-8, MK-8(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29443	17128 ChEBI	adipate	+	carbon source
29443	16947 ChEBI	citrate	+	carbon source
29443	24265 ChEBI	gluconate	+	carbon source
29443	25115 ChEBI	malate	+	carbon source
29443	17306 ChEBI	maltose	+	carbon source
29443	18401 ChEBI	phenylacetate	+	carbon source
29443	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29443	catalase	+	1.11.1.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	starch degradation	100	10 of 10
66794	lipoate biosynthesis	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	threonine metabolism	90	9 of 10
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	pentose phosphate pathway	81.82	9 of 11
66794	gallate degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	metabolism of disaccharids	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	histidine metabolism	72.41	21 of 29
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	heme metabolism	71.43	10 of 14
66794	purine metabolism	70.21	66 of 94
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	pyrimidine metabolism	68.89	31 of 45
66794	IAA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	glutathione metabolism	64.29	9 of 14
66794	gluconeogenesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	NAD metabolism	61.11	11 of 18
66794	cysteine metabolism	61.11	11 of 18
66794	tryptophan metabolism	60.53	23 of 38
66794	O-antigen biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	oxidative phosphorylation	58.24	53 of 91
66794	propanol degradation	57.14	4 of 7
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	d-mannose degradation	55.56	5 of 9
66794	lysine metabolism	54.76	23 of 42
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	Entner Doudoroff pathway	50	5 of 10
66794	androgen and estrogen metabolism	50	8 of 16
66794	ethanol fermentation	50	1 of 2
66794	sphingosine metabolism	50	3 of 6
66794	biotin biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	vitamin B6 metabolism	45.45	5 of 11
66794	tyrosine metabolism	42.86	6 of 14
66794	methionine metabolism	42.31	11 of 26
66794	carotenoid biosynthesis	40.91	9 of 22
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	lipid A biosynthesis	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfate reduction	30.77	4 of 13
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	mevalonate metabolism	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	arachidonic acid metabolism	27.78	5 of 18
66794	degradation of hexoses	27.78	5 of 18
66794	d-xylose degradation	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	daunorubicin biosynthesis	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9
66794	polyamine pathway	21.74	5 of 23
66794	degradation of pentoses	21.43	6 of 28

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
20655	forest soil	Changbai mountains, Heilongjiang Province	China	CHN	Asia
67770	Forest soil of the Changbai mountains		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence FJ423763 (>99% sequence identity) for Micrococcus from Microbeatlas

Aquatic Samples	771
Soil Samples	1821
Animal Samples	3656
Plant Samples	672
Total Samples	6920

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20655	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2617270780 annotated assembly for Micrococcus terreus CGMCC 1.7054	contig	GCA_900116905	574650.4	2617270780	574650	73.03

Genome browser: GCA_900116905

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20655	Micrococcus terreus strain V3M1 16S ribosomal RNA gene, partial sequence	FJ423763	1514		574650
124043	Micrococcus terreus strain CGMCC 1.7054 16S ribosomal RNA gene, partial sequence.	PQ248455	601		574650

GC content

@ref	GC-content (mol%)
20655	67.2
67770	67.2
67770	68.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Micrococcus terreus CGMCC 1.7054
NCBI: GCA_900116905

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	65.40	no
125439	motility	BacteriaNetⓘ	no	82.70	no
125439	gram_stain	BacteriaNetⓘ	positive	97.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	84.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micrococcus terreus strain CGMCC 1.7054
PATRIC: 574650.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	94.60	yes
125438	anaerobic	anaerobicⓘ	no	97.21	yes
125438	spore-forming	spore-formingⓘ	no	83.86	no
125438	aerobic	aerobicⓘ	yes	85.13	yes
125438	thermophilic	thermophileⓘ	no	96.47	no
125438	flagellated	motile2+ⓘ	no	92.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Micrococcus lactis sp. nov., isolated from dairy industry waste.	Chittpurna, Singh PK, Verma D, Pinnaka AK, Mayilraj S, Korpole S	Int J Syst Evol Microbiol	10.1099/ijs.0.028043-0	2011
Phylogeny	Agrococcus terreus sp. nov. and Micrococcus terreus sp. nov., isolated from forest soil.	Zhang JY, Liu XY, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.013235-0	2009

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 )
#20655	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28110
#29443	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 #25849 (see below)
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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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Micrococcus terreus (DSM 28110, CGMCC 1.7054, NBRC 104258)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900116905

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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