Microbacterium tumbae (JCM 28836, NCIMB 15039, T7528-3-6b)

Name: Microbacterium tumbae (JCM 28836, NCIMB 15039, T7528-3-6b)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140585

Type strain

Strain Designation T7528-3-6b

Culture col. no. JCM 28836 NCIMB 15039 T7528-3-6b

NCBI tax ID(s) 1840605

Special Collections JCM Literature strains

Links

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

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

Name and taxonomic classification

SI-ID 131901

JCM 28836,NCIMB 15039

@ref 20215

Last LPSN update 2025-12-16 10:03:38

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Microbacterium

Species Microbacterium tumbae

Full scientific name Microbacterium tumbae Nishijima et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
43255	positive	1.0-1.2 µm	0.6-0.7 µm	rod-shaped

Colony morphology

43255

Colony colorcream

Culture and growth conditions

Culture medium

@ref	Name	Composition
43255	Reasoner's 2A agar (R2A)
43255	Nutrient agar (NA)
43255	SCD agar (soybean-casein digest agar)	15 g pancreatic digest of casein (BBL), 5 g papaic digest of soybean meal (BBL), 5 g sodium chloride, 15 g agar and 1 l distilled water; pH 7.3
43255	MacConkey agar

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
43255	positive	optimum	25-30	mesophilic
43255	positive	growth	10-37
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
43255	positive	optimum	7.5-8.5
43255	positive	growth	5.5-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

43255

Oxygen toleranceobligate aerobe

Spore formation

@ref	Type of spore	Spore formation
43255	spore

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43255	NaCl	positive	maximum	8 %
43255	NaCl	positive	optimum	0-1 %

Observation

67770

Observationquinones: MK-12, MK-13, MK-11

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43255	30089 ChEBI	acetate	+/-	carbon source
43255	17128 ChEBI	adipate	-	assimilation
43255	36219 ChEBI	alpha-lactose	-	builds acid from
43255	27613 ChEBI	amygdalin	+	builds acid from
43255	18305 ChEBI	arbutin	+	builds acid from
43255		casein	-	hydrolysis
43255	17057 ChEBI	cellobiose	+	builds acid from
43255	17057 ChEBI	cellobiose	-	carbon source
43255	16947 ChEBI	citrate	-	carbon source
43255	17108 ChEBI	D-arabinose	-	builds acid from
43255	18333 ChEBI	D-arabitol	-	builds acid from
43255	15824 ChEBI	D-fructose	+	builds acid from
43255	28847 ChEBI	D-fucose	-	builds acid from
43255	12936 ChEBI	D-galactose	+	builds acid from
43255	17634 ChEBI	D-glucose	+	assimilation
43255	17634 ChEBI	D-glucose	+	builds acid from
43255	62318 ChEBI	D-lyxose	+	builds acid from
43255	16899 ChEBI	D-mannitol	+	assimilation
43255	16899 ChEBI	D-mannitol	+	builds acid from
43255	16024 ChEBI	D-mannose	+	assimilation
43255	16024 ChEBI	D-mannose	+	builds acid from
43255	16988 ChEBI	D-ribose	+	builds acid from
43255	17924 ChEBI	D-sorbitol	-	builds acid from
43255	16443 ChEBI	D-tagatose	-	builds acid from
43255	65327 ChEBI	D-xylose	+	builds acid from
43255	27689 ChEBI	decanoate	-	assimilation
43255	16991 ChEBI	dna	+	hydrolysis
43255	17113 ChEBI	erythritol	-	builds acid from
43255	4853 ChEBI	esculin	+	hydrolysis
43255		esculin ferric citrate	+	builds acid from
43255	29806 ChEBI	fumarate	-	carbon source
43255	16813 ChEBI	galactitol	-	builds acid from
43255	5291 ChEBI	gelatin	-	hydrolysis
43255	28066 ChEBI	gentiobiose	+/-	builds acid from
43255	17234 ChEBI	glucose	-	fermentation
43255	17754 ChEBI	glycerol	-	builds acid from
43255	28087 ChEBI	glycogen	-	builds acid from
43255	15443 ChEBI	inulin	-	builds acid from
43255	16977 ChEBI	L-alanine	-	carbon source
43255	30849 ChEBI	L-arabinose	+	assimilation
43255	30849 ChEBI	L-arabinose	+	builds acid from
43255	18403 ChEBI	L-arabitol	-	builds acid from
43255	16467 ChEBI	L-arginine	-	carbon source
43255	29991 ChEBI	L-aspartate	+/-	carbon source
43255	18287 ChEBI	L-fucose	+/-	builds acid from
43255	62345 ChEBI	L-rhamnose	-	builds acid from
43255	17266 ChEBI	L-sorbose	-	builds acid from
43255	65328 ChEBI	L-xylose	-	builds acid from
43255	61995 ChEBI	lecithin	-	hydrolysis
43255	25115 ChEBI	malate	+	assimilation
43255	25115 ChEBI	malate	+/-	carbon source
43255	17306 ChEBI	maltose	+	assimilation
43255	17306 ChEBI	maltose	+	builds acid from
43255	6731 ChEBI	melezitose	-	builds acid from
43255	28053 ChEBI	melibiose	-	builds acid from
43255	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
43255	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
43255	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
43255	17268 ChEBI	myo-inositol	-	builds acid from
43255	506227 ChEBI	N-acetylglucosamine	-	assimilation
43255	506227 ChEBI	N-acetylglucosamine	-	builds acid from
43255	17632 ChEBI	nitrate	-	reduction
43255	18401 ChEBI	phenylacetate	-	assimilation
43255		potassium 2-dehydro-D-gluconate	-	builds acid from
43255		potassium 5-dehydro-D-gluconate	-	builds acid from
43255	32032 ChEBI	potassium gluconate	-	assimilation
43255	32032 ChEBI	potassium gluconate	-	builds acid from
43255	17272 ChEBI	propionate	-	carbon source
43255	15361 ChEBI	pyruvate	+/-	carbon source
43255	16634 ChEBI	raffinose	-	builds acid from
43255	15963 ChEBI	ribitol	-	builds acid from
43255	17814 ChEBI	salicin	+	builds acid from
43255	53258 ChEBI	sodium citrate	-	assimilation
43255	28017 ChEBI	starch	-	hydrolysis
43255	28017 ChEBI	starch	-	builds acid from
43255	30031 ChEBI	succinate	+	carbon source
43255	17992 ChEBI	sucrose	+	builds acid from
43255	27082 ChEBI	trehalose	+	builds acid from
43255	32528 ChEBI	turanose	+	builds acid from
43255	53424 ChEBI	tween 20	-	hydrolysis
43255	53426 ChEBI	tween 80	+/-	hydrolysis
43255	18186 ChEBI	tyrosine	-	hydrolysis
43255	17151 ChEBI	xylitol	+/-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite
43255	15688 ChEBI	acetoin
43255	16136 ChEBI	hydrogen sulfide
43255	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
43255	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
43255	acid phosphatase	+	3.1.3.2
43255	alkaline phosphatase	+	3.1.3.1
43255	alpha-chymotrypsin	-	3.4.21.1
43255	alpha-fucosidase	+	3.2.1.51
43255	alpha-galactosidase	+	3.2.1.22
43255	alpha-glucosidase	+	3.2.1.20
43255	alpha-mannosidase	+	3.2.1.24
43255	arginine dihydrolase	-	3.5.3.6
43255	beta-galactosidase	+	3.2.1.23
43255	beta-glucosidase	+	3.2.1.21
43255	beta-glucuronidase	-	3.2.1.31
43255	catalase	+	1.11.1.6
43255	cystine arylamidase	-	3.4.11.3
43255	cytochrome oxidase	-	1.9.3.1
43255	esterase (C 4)	+
43255	esterase Lipase (C 8)	+
43255	leucine arylamidase	+	3.4.11.1
43255	lipase (C 14)	-
43255	lysine decarboxylase	-	4.1.1.18
43255	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43255	naphthol-AS-BI-phosphohydrolase	-
43255	ornithine decarboxylase	-	4.1.1.17
43255	trypsin	+	3.4.21.4
43255	tryptophan deaminase	-	4.1.99.1
43255	urease	-	3.5.1.5
43255	valine arylamidase	-

Fatty acid profile

Metadata FA analysis

@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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
43255	samples collected from stone chambers of the Takamatsuzuka and Kitora tumuli	2007-05-28	Asuka village, Nara Prefecture, Japan	Japan	JPN	Asia
67770	Between east wall 1 and ceiling stone 2 (during relocation of the stone chamber) of the Takamatsuzuka Tumulus		Asuka Village, Nara Pref.	Japan	JPN	Asia

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
43255	Microbacterium tumbae gene for 16S ribosomal RNA, partial cds, strain: T7528-3-6b	LC148840	1448		1840605

GC content

@ref	GC-content (mol%)	Method
43255	70.1
67770	70.1	high performance liquid chromatography (HPLC)

Genome-based predictions

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;
#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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Microbacterium tumbae (JCM 28836, NCIMB 15039, T7528-3-6b)

Name and taxonomic classification