Name: Microbacterium tumbae T7528-3-6b
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140585

Type strain:

Species: Microbacterium tumbae

Strain Designation: T7528-3-6b

Culture col. no.: JCM 28836, NCIMB 15039

Strain history: K. Okada and J. Sugiyama; Tokyo Natl. Res. Inst. for Cult. Prop. and TechnoSuruga Lab. Co., Ltd., Japan; T7528-3-6b.

NCBI tax ID(s): 1840605 (species)

Section

Microbacterium tumbae T7528-3-6b is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from samples collected from stone chambers of the Takamatsuzuka and Kitora tumuli.

Gram-positive
rod-shaped
mesophilic
obligate aerobe
16S sequence
Bacteria

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 tumbae**
	Full Scientific Name (LPSN)	Microbacterium tumbae Nishijima et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43255]	Gram stain	positive

[Ref.: #43255]	Cell length	1.0-1.2 µm

[Ref.: #43255]	Cell width	0.6-0.7 µm

[Ref.: #43255]	Cell shape	rod-shaped

[Ref.: #43255]	Motility	no

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Colony color

cream

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

SCD agar (soybean-casein digest agar)

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

MacConkey agar

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Culture medium growth

		Temperature
[Ref.: #43255]	optimum	25-30 °C
[Ref.: #43255]	growth	10-37 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #43255]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43255]			optimum	7.5-8.5
[Ref.: #43255]			growth	5.5-9.0

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

obligate aerobe

[Ref.: #43255]	Type of spore	spore
[Ref.: #43255]	Ability of spore formation	no

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43255]		NaCl		maximum	8	%
[Ref.: #43255]		NaCl		optimum	0-1	%

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Observation

quinones: MK-12, MK-13, MK-11

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43255]	acetate ChEBI	+/-	carbon source
[Ref.: #43255]	adipate ChEBI	-	assimilation
[Ref.: #43255]	alpha-lactose ChEBI	-	builds acid from
[Ref.: #43255]	amygdalin ChEBI	+	builds acid from
[Ref.: #43255]	arbutin ChEBI	+	builds acid from
[Ref.: #43255]	casein	-	hydrolysis
[Ref.: #43255]	cellobiose ChEBI	+	builds acid from
[Ref.: #43255]	cellobiose ChEBI	-	carbon source
[Ref.: #43255]	citrate ChEBI	-	carbon source
[Ref.: #43255]	D-arabinose ChEBI	-	builds acid from
[Ref.: #43255]	D-arabitol ChEBI	-	builds acid from
[Ref.: #43255]	D-fructose ChEBI	+	builds acid from
[Ref.: #43255]	D-fucose ChEBI	-	builds acid from
[Ref.: #43255]	D-galactose ChEBI	+	builds acid from
[Ref.: #43255]	D-glucose ChEBI	+	assimilation
[Ref.: #43255]	D-glucose ChEBI	+	builds acid from
[Ref.: #43255]	D-lyxose ChEBI	+	builds acid from
[Ref.: #43255]	D-mannitol ChEBI	+	assimilation
[Ref.: #43255]	D-mannitol ChEBI	+	builds acid from
[Ref.: #43255]	D-mannose ChEBI	+	assimilation
[Ref.: #43255]	D-mannose ChEBI	+	builds acid from
[Ref.: #43255]	D-ribose ChEBI	+	builds acid from
[Ref.: #43255]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #43255]	D-tagatose ChEBI	-	builds acid from
[Ref.: #43255]	D-xylose ChEBI	+	builds acid from
[Ref.: #43255]	decanoate ChEBI	-	assimilation
[Ref.: #43255]	dna ChEBI	+	hydrolysis
[Ref.: #43255]	erythritol ChEBI	-	builds acid from
[Ref.: #43255]	esculin ChEBI	+	hydrolysis
[Ref.: #43255]	esculin ferric citrate	+	builds acid from
[Ref.: #43255]	fumarate ChEBI	-	carbon source
[Ref.: #43255]	galactitol ChEBI	-	builds acid from
[Ref.: #43255]	gelatin ChEBI	-	hydrolysis
[Ref.: #43255]	gentiobiose ChEBI	+/-	builds acid from
[Ref.: #43255]	glucose ChEBI	-	fermentation
[Ref.: #43255]	glycerol ChEBI	-	builds acid from
[Ref.: #43255]	glycogen ChEBI	-	builds acid from
[Ref.: #43255]	inulin ChEBI	-	builds acid from
[Ref.: #43255]	L-alanine ChEBI	-	carbon source
[Ref.: #43255]	L-arabinose ChEBI	+	assimilation
[Ref.: #43255]	L-arabinose ChEBI	+	builds acid from
[Ref.: #43255]	L-arabitol ChEBI	-	builds acid from
[Ref.: #43255]	L-arginine ChEBI	-	carbon source
[Ref.: #43255]	L-aspartate ChEBI	+/-	carbon source
[Ref.: #43255]	L-fucose ChEBI	+/-	builds acid from
[Ref.: #43255]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #43255]	L-sorbose ChEBI	-	builds acid from
[Ref.: #43255]	L-xylose ChEBI	-	builds acid from
[Ref.: #43255]	lecithin ChEBI	-	hydrolysis
[Ref.: #43255]	malate ChEBI	+	assimilation
[Ref.: #43255]	malate ChEBI	+/-	carbon source
[Ref.: #43255]	maltose ChEBI	+	assimilation
[Ref.: #43255]	maltose ChEBI	+	builds acid from
[Ref.: #43255]	melezitose ChEBI	-	builds acid from
[Ref.: #43255]	melibiose ChEBI	-	builds acid from
[Ref.: #43255]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #43255]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #43255]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #43255]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43255]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43255]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #43255]	nitrate ChEBI	-	reduction
[Ref.: #43255]	phenylacetate ChEBI	-	assimilation
[Ref.: #43255]	potassium 2-dehydro-D-gluconate	-	builds acid from
[Ref.: #43255]	potassium 5-dehydro-D-gluconate	-	builds acid from
[Ref.: #43255]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43255]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #43255]	propionate ChEBI	-	carbon source
[Ref.: #43255]	pyruvate ChEBI	+/-	carbon source
[Ref.: #43255]	raffinose ChEBI	-	builds acid from
[Ref.: #43255]	ribitol ChEBI	-	builds acid from
[Ref.: #43255]	salicin ChEBI	+	builds acid from
[Ref.: #43255]	sodium citrate ChEBI	-	assimilation
[Ref.: #43255]	starch ChEBI	-	hydrolysis
[Ref.: #43255]	starch ChEBI	-	builds acid from
[Ref.: #43255]	succinate ChEBI	+	carbon source
[Ref.: #43255]	sucrose ChEBI	+	builds acid from
[Ref.: #43255]	trehalose ChEBI	+	builds acid from
[Ref.: #43255]	turanose ChEBI	+	builds acid from
[Ref.: #43255]	tween 20 ChEBI	-	hydrolysis
[Ref.: #43255]	tween 80 ChEBI	+/-	hydrolysis
[Ref.: #43255]	tyrosine ChEBI	-	hydrolysis
[Ref.: #43255]	xylitol ChEBI	+/-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43255]	acetoin ChEBI	no
[Ref.: #43255]	hydrogen sulfide ChEBI	no
[Ref.: #43255]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #43255]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #43255]	acid phosphatase	+	3.1.3.2
[Ref.: #43255]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43255]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43255]	alpha-fucosidase	+	3.2.1.51
[Ref.: #43255]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43255]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43255]	alpha-mannosidase	+	3.2.1.24
[Ref.: #43255]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43255]	beta-galactosidase	+	3.2.1.23
[Ref.: #43255]	beta-glucosidase	+	3.2.1.21
[Ref.: #43255]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43255]	catalase	+	1.11.1.6
[Ref.: #43255]	cystine arylamidase	-	3.4.11.3
[Ref.: #43255]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43255]	esterase (C 4)	+
[Ref.: #43255]	esterase Lipase (C 8)	+
[Ref.: #43255]	leucine arylamidase	+	3.4.11.1
[Ref.: #43255]	lipase (C 14)	-
[Ref.: #43255]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43255]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43255]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #43255]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43255]	trypsin	+	3.4.21.4
[Ref.: #43255]	tryptophan deaminase	-	4.1.99.1
[Ref.: #43255]	urease	-	3.5.1.5
[Ref.: #43255]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43255]

Fatty acid	Percentage
C15:0 anteiso	46.5
C17:0 anteiso	21.1
C16:0 iso	18.3
C15:0 iso	10.1
C17:0 iso	2.1
C16:0	1
C14:0 iso	0.9

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

[Ref.: #43255]	Sample type/isolated from	samples collected from stone chambers of the Takamatsuzuka and Kitora tumuli
[Ref.: #43255]	Sampling date	2007-05-28
[Ref.: #43255]	Geographic location (country and/or sea, region)	Asuka village, Nara Prefecture, Japan
[Ref.: #43255]	Country	Japan
[Ref.: #43255]	Country ISO 3 Code	JPN
[Ref.: #43255]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Between east wall 1 and ceiling stone 2 (during relocation of the stone chamber) of the Takamatsuzuka Tumulus
[Ref.: #67770]	Geographic location (country and/or sea, region)	Asuka Village, Nara Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Geologic

What are isolation sources categories?

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.: #43255]	16S rRNA gene sequences	LC148840	1448	ENA	1840605 tax ID

[Ref.: #43255]	GC-content	70.1 mol%
[Ref.: #67770]	GC-content	70.1 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #43255]

Culture collection no.

JCM 28836, NCIMB 15039

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microbacterium tumbae sp. nov., an actinobacterium isolated from the stone chamber of ancient tumulus.	Nishijima M, Tazato N, Handa Y, Umekawa N, Kigawa R, Sano C, Sugiyama J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001863	2017	*

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 )

#43255

Miyuki Nishijima, Nozomi Tazato, Yutaka Handa, Nao Umekawa, Rika Kigawa, Chie Sano and Junta Sugiyama: Microbacterium tumbae sp. nov., an actinobacterium isolated from the stone chamber of ancient tumulus. IJSEM 67: 1777 - 1783 2017 ( DOI 10.1099/ijsem.0.001863 , PubMed 28604332 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
* These data were automatically processed and therefore are not curated

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