Name: Microbacterium lemovicicum ViU22
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23104

Type strain:

Species: Microbacterium lemovicicum

Strain Designation: ViU22

Culture col. no.: DSM 25044, ATCC BAA-2396, CCUG 62198, CIP 110791, NBRC 110788

Strain history: CIP <- 2014, DSMZ <- V. Chapon, CEA, Cadarache, France: strain ViU22 <- V. Chapon and L. Mondani

NCBI tax ID(s): 1072463 (species)

SI-ID 398141

DSM 25044, CCUG 62198, CIP 110791

Section

Microbacterium lemovicicum ViU22 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from natural uranium-rich soil.

Gram-positive
rod-shaped
aerobe
mesophilic
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	*Microbacteriaceae*
	Genus	*Microbacterium*
	Species	**Microbacterium lemovicicum**
	Full Scientific Name (LPSN)	Microbacterium lemovicicum Mondani et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30956]	Gram stain	positive
[Ref.: #120579]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #30956]	Cell shape	rod-shaped
[Ref.: #120579]	Cell shape	rod-shaped

[Ref.: #30956]	Motility	no
[Ref.: #120579]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.838

[Ref.: #30956]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #33652]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #33652]

Culture medium growth

[Ref.: #33652]

Culture medium composition

expand / minimize

[Ref.: #19377]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #19377]

Culture medium growth

[Ref.: #19377]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19377]

Culture medium composition

expand / minimize

[Ref.: #120579]

Culture medium

CIP Medium 72

[Ref.: #120579]

Culture medium growth

[Ref.: #120579]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #19377]	growth	28 °C
[Ref.: #30956]	growth	15-37 °C
[Ref.: #30956]	optimum	30 °C
[Ref.: #33652]	growth	30 °C
[Ref.: #62796]	growth	30 °C

[Ref.: #19377]	Temperature range	mesophilic
[Ref.: #30956]	Temperature range	mesophilic
[Ref.: #33652]	Temperature range	mesophilic
[Ref.: #62796]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #62796]

Oxygen tolerance

aerobe

[Ref.: #30956]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.962

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30956]		NaCl		growth	0-4.5	%
[Ref.: #30956]		NaCl		optimum	0.5	%

[Ref.: #19377]	Murein short key	B06
[Ref.: #19377]	Murein types	B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

[Ref.: #30956]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30956]	arabinose ChEBI	+	carbon source
[Ref.: #30956]	fructose ChEBI	+	carbon source
[Ref.: #30956]	galactose ChEBI	+	carbon source
[Ref.: #30956]	glucose ChEBI	+	carbon source
[Ref.: #30956]	glycerol ChEBI	+	carbon source
[Ref.: #30956]	maltose ChEBI	+	carbon source
[Ref.: #30956]	mannitol ChEBI	+	carbon source
[Ref.: #30956]	mannose ChEBI	+	carbon source
[Ref.: #30956]	raffinose ChEBI	+	carbon source
[Ref.: #30956]	rhamnose ChEBI	+	carbon source
[Ref.: #30956]	ribose ChEBI	+	carbon source
[Ref.: #30956]	sucrose ChEBI	+	carbon source
[Ref.: #30956]	trehalose ChEBI	+	carbon source
[Ref.: #30956]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30956]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30956]	catalase	+	1.11.1.6
[Ref.: #30956]	gelatinase	+
[Ref.: #30956]	pyrazinamidase	+	3.5.1.B15
[Ref.: #30956]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	degradation of sugar acids	84	21 of 25
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	purine metabolism	82.98	78 of 94
[Ref.: #66794]	tryptophan metabolism	81.58	31 of 38
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	degradation of hexoses	77.78	14 of 18
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	androgen and estrogen metabolism	75	12 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	phenol degradation	70	14 of 20
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	benzoyl-CoA degradation	57.14	4 of 7
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #19377]	Sample type/isolated from	natural uranium-rich soil
[Ref.: #19377]	Geographic location (country and/or sea, region)	near Limoges
[Ref.: #19377]	Country	France
[Ref.: #19377]	Country ISO 3 Code	FRA
[Ref.: #19377]	Continent	Europe

[Ref.: #62796]	Sample type/isolated from	Soil,natural uranium-rich
[Ref.: #62796]	Sampling date	2007-11-26
[Ref.: #62796]	Geographic location (country and/or sea, region)	Limoges
[Ref.: #62796]	Country	France
[Ref.: #62796]	Country ISO 3 Code	FRA
[Ref.: #62796]	Continent	Europe

[Ref.: #120579]	Sample type/isolated from	Environment, Natural uranium-rich soil
[Ref.: #120579]	Geographic location (country and/or sea, region)	Limoges
[Ref.: #120579]	Country	France
[Ref.: #120579]	Country ISO 3 Code	FRA
[Ref.: #120579]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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

[Ref.: #19377]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120579]	Biosafety level	1	Risk group (French classification)

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.: #19377]	Microbacterium lemovicicum strain ViU22 16S ribosomal RNA gene, partial sequence	JN243353	1400	ENA	1072463 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Microbacterium lemovicicum Viu22	GCA_003991875	complete	GenBank	1072463 tax ID	*
[Ref.: #66792]	Microbacterium lemovicicum Viu22	2847289766	complete	JGI IMG/M	1072463 tax ID	*

[Ref.: #19377]	GC-content	71.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30956]	GC-content	71 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Microbacterium lemovicicum Viu22 NCBI: GCA_003991875.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Microbacterium lemovicicum Viu22 NCBI: GCA_003991875.1
[Ref.: #69480]	motile	no	91.711	yes
[Ref.: #69480]	flagellated	no	98.001	yes
[Ref.: #69480]	gram-positive	yes	94.621	yes
[Ref.: #69480]	anaerobic	no	99.631	yes
[Ref.: #69480]	aerobic	yes	93.807	yes
[Ref.: #69480]	halophile	no	91.816	no
[Ref.: #69480]	spore-forming	no	94.984	yes
[Ref.: #69480]	thermophile	no	99.174	no
[Ref.: #69480]	glucose-util	yes	86.343	no
[Ref.: #69480]	glucose-ferment	no	93.281	no

Availability in culture collections External links

[Ref.: #19377]

Culture collection no.

DSM 25044, ATCC BAA-2396, CCUG 62198, CIP 110791, NBRC 110788

[Ref.: #87341]

SI-ID 398141

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microbacterium gilvum sp. nov., isolated from civet faeces.	Chen X, Li QY, Li GD, Xu FJ, Jiang Y, Han L, Jiang CL, Huang XS	Antonie Van Leeuwenhoek	10.1007/s10482-016-0718-1	2016	*
Phylogeny	Microbacterium lemovicicum sp. nov., a bacterium isolated from a natural uranium-rich soil.	Mondani L, Piette L, Christen R, Bachar D, Berthomieu C, Chapon V	Int J Syst Evol Microbiol	10.1099/ijs.0.048454-0	2012	*

References

#19377

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25044

#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 )

#30956

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 #27286 (see below)

#33652 ; Curators of the CIP;
#62796 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 62198

#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 )

#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 )

#87341

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-ID398141.1 )

#120579 Collection of Institut Pasteur ; Curators of the CIP; CIP 110791

#27286

IJSEM 2600 2013 ( DOI 10.1099/ijs.0.048454-0 , PubMed 23264499 )

* These data were automatically processed and therefore are not curated

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Microbacterium lemovicicum Viu22

Microbacterium lemovicicum Viu22

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