Strain identifier

BacDive ID: 140585

Type strain: Yes

Species: Microbacterium tumbae

Strain Designation: T7528-3-6b

Culture col. no.: JCM 28836, NCIMB 15039

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General

@ref: 43255

BacDive-ID: 140585

keywords: mesophilic, obligate aerobe, Bacteria, 16S sequence, gram-positive, rod-shaped

description: 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.

doi: 10.13145/bacdive140585.20201210.5

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinobacteria
  • domain: Bacteria
  • phylum: Actinobacteria
  • class: Actinobacteria
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium tumbae
  • full scientific name: Microbacterium tumbae Nishijima et al. 2017

@ref: 43255

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium tumbae

strain designation: T7528-3-6b

type strain: yes

Morphology

cell morphology

  • @ref: 43255
  • gram stain: positive
  • cell length: 1.0-1.2 µm
  • cell width: 0.6-0.7 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43255
  • colony color: cream

Culture and growth conditions

culture medium

@refnamegrowthcomposition
43255Reasoner's 2A agar (R2A)yes
43255Nutrient agar (NA)yes
43255SCD agar (soybean-casein digest agar)yes15 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
43255MacConkey agarno

culture temp

@refgrowthtypetemperaturerange
43255positiveoptimum25-30mesophilic
43255positivegrowth10-37

culture pH

@refabilitytypepH
43255positivegrowth5.5-9.0
43255positiveoptimum7.5-8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43255
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 43255
  • type of spore: spore
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43255NaClpositivemaximum8 %
43255NaClpositiveoptimum0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4325517632nitrate-reduction
4325517234glucose-fermentation
4325516991dna+hydrolysis
4325553426tween 80+/-hydrolysis
4325528017starch-hydrolysis
43255casein-hydrolysis
4325561995lecithin-hydrolysis
4325518186tyrosine-hydrolysis
4325553424tween 20-hydrolysis
432555291gelatin-hydrolysis
432554853esculin+hydrolysis
4325517634D-glucose+assimilation
4325530849L-arabinose+assimilation
4325516024D-mannose+assimilation
4325516899D-mannitol+assimilation
4325517306maltose+assimilation
4325525115malate+assimilation
43255506227N-acetylglucosamine-assimilation
4325532032potassium gluconate-assimilation
4325527689decanoate-assimilation
4325517128adipate-assimilation
4325553258sodium citrate-assimilation
4325518401phenylacetate-assimilation
4325530849L-arabinose+builds acid from
4325516988D-ribose+builds acid from
4325565327D-xylose+builds acid from
4325512936D-galactose+builds acid from
4325517634D-glucose+builds acid from
4325515824D-fructose+builds acid from
4325516024D-mannose+builds acid from
4325516899D-mannitol+builds acid from
4325527613amygdalin+builds acid from
4325518305arbutin+builds acid from
43255esculin ferric citrate+builds acid from
4325517814salicin+builds acid from
4325517057cellobiose+builds acid from
4325517306maltose+builds acid from
4325517992sucrose+builds acid from
4325527082trehalose+builds acid from
4325517151xylitol+/-builds acid from
4325528066gentiobiose+/-builds acid from
4325532528turanose+builds acid from
4325562318D-lyxose+builds acid from
4325518287L-fucose+/-builds acid from
4325517754glycerol-builds acid from
4325517113erythritol-builds acid from
4325517108D-arabinose-builds acid from
4325565328L-xylose-builds acid from
4325515963ribitol-builds acid from
4325574863methyl beta-D-xylopyranoside-builds acid from
4325517266L-sorbose-builds acid from
4325562345L-rhamnose-builds acid from
4325516813galactitol-builds acid from
4325517268myo-inositol-builds acid from
4325517924D-sorbitol-builds acid from
4325543943methyl alpha-D-mannoside-builds acid from
43255320061methyl alpha-D-glucopyranoside-builds acid from
43255506227N-acetylglucosamine-builds acid from
4325536219alpha-lactose-builds acid from
4325528053melibiose-builds acid from
4325515443inulin-builds acid from
432556731melezitose-builds acid from
4325516634raffinose-builds acid from
4325528017starch-builds acid from
4325528087glycogen-builds acid from
4325516443D-tagatose-builds acid from
4325528847D-fucose-builds acid from
4325518333D-arabitol-builds acid from
4325518403L-arabitol-builds acid from
4325532032potassium gluconate-builds acid from
43255potassium 2-dehydro-D-gluconate-builds acid from
43255potassium 5-dehydro-D-gluconate-builds acid from
4325530031succinate+carbon source
4325517057cellobiose-carbon source
4325517272propionate-carbon source
4325529806fumarate-carbon source
4325516947citrate-carbon source
4325516467L-arginine-carbon source
4325516977L-alanine-carbon source
4325530089acetate+/-carbon source
4325529991L-aspartate+/-carbon source
4325525115malate+/-carbon source
4325515361pyruvate+/-carbon source

metabolite production

@refChebi-IDmetaboliteproduction
4325535581indoleno
4325516136hydrogen sulfideno
4325515688acetoinno

metabolite tests

  • @ref: 43255
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

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

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43255C14:0 iso0.9
    43255C15:0 iso10.1
    43255C15:0 anteiso46.5
    43255C16:0 iso18.3
    43255C16:01
    43255C17:0 iso2.1
    43255C17:0 anteiso21.1
  • type of FA analysis: whole cell analysis
  • incubation medium: SCD agar
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • software version: Sherlock 6.0
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

  • @ref: 43255
  • sample type: samples collected from stone chambers of the Takamatsuzuka and Kitora tumuli
  • sampling date: 2007-05-28
  • geographic location: Asuka village, Nara Prefecture, Japan
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Geologic

Sequence information

16S sequences

  • @ref: 43255
  • description: 16S rRNA gene sequences
  • accession: LC148840
  • length: 1448
  • database: ena
  • NCBI tax ID: 1840605

GC content

  • @ref: 43255
  • GC-content: 70.1

External links

@ref: 43255

culture collection no.: JCM 28836, NCIMB 15039

Reference

@idauthorstitledoi/urljournal
20215D.Gleim, M.Kracht, N.Weiss et. al.Prokaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes sincehttp://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.html
43255Miyuki Nishijima, Nozomi Tazato, Yutaka Handa, Nao Umekawa, Rika Kigawa, Chie Sano and Junta SugiyamaMicrobacterium tumbae sp. nov., an actinobacterium isolated from the stone chamber of ancient tumulus10.1099/ijsem.0.001863IJSEM 67: 1777-1783 2017