Strain identifier
BacDive ID: 140585
Type strain:
Species: Microbacterium tumbae
Strain Designation: T7528-3-6b
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)
General
@ref: 43255
BacDive-ID: 140585
keywords: 16S sequence, Bacteria, obligate aerobe, mesophilic, 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.
NCBI tax id
- NCBI tax id: 1840605
- Matching level: species
strain history
- @ref: 67770
- history: K. Okada and J. Sugiyama; Tokyo Natl. Res. Inst. for Cult. Prop. and TechnoSuruga Lab. Co., Ltd., Japan; T7528-3-6b.
doi: 10.13145/bacdive140585.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- 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
@ref | name | growth | composition |
---|---|---|---|
43255 | Reasoner's 2A agar (R2A) | yes | |
43255 | Nutrient agar (NA) | yes | |
43255 | SCD agar (soybean-casein digest agar) | yes | 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 | no |
culture temp
@ref | growth | type | temperature | 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 | growth | 5.5-9.0 | alkaliphile |
43255 | positive | optimum | 7.5-8.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 43255
- oxygen tolerance: obligate aerobe
spore formation
- @ref: 43255
- type of spore: spore
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43255 | NaCl | positive | maximum | 8 % |
43255 | NaCl | positive | optimum | 0-1 % |
observation
- @ref: 67770
- observation: quinones: MK-12, MK-13, MK-11
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43255 | 17632 | nitrate | - | reduction |
43255 | 17234 | glucose | - | fermentation |
43255 | 16991 | dna | + | hydrolysis |
43255 | 53426 | tween 80 | +/- | hydrolysis |
43255 | 28017 | starch | - | hydrolysis |
43255 | casein | - | hydrolysis | |
43255 | 61995 | lecithin | - | hydrolysis |
43255 | 18186 | tyrosine | - | hydrolysis |
43255 | 53424 | tween 20 | - | hydrolysis |
43255 | 5291 | gelatin | - | hydrolysis |
43255 | 4853 | esculin | + | hydrolysis |
43255 | 17634 | D-glucose | + | assimilation |
43255 | 30849 | L-arabinose | + | assimilation |
43255 | 16024 | D-mannose | + | assimilation |
43255 | 16899 | D-mannitol | + | assimilation |
43255 | 17306 | maltose | + | assimilation |
43255 | 25115 | malate | + | assimilation |
43255 | 506227 | N-acetylglucosamine | - | assimilation |
43255 | 32032 | potassium gluconate | - | assimilation |
43255 | 27689 | decanoate | - | assimilation |
43255 | 17128 | adipate | - | assimilation |
43255 | 53258 | sodium citrate | - | assimilation |
43255 | 18401 | phenylacetate | - | assimilation |
43255 | 30849 | L-arabinose | + | builds acid from |
43255 | 16988 | D-ribose | + | builds acid from |
43255 | 65327 | D-xylose | + | builds acid from |
43255 | 12936 | D-galactose | + | builds acid from |
43255 | 17634 | D-glucose | + | builds acid from |
43255 | 15824 | D-fructose | + | builds acid from |
43255 | 16024 | D-mannose | + | builds acid from |
43255 | 16899 | D-mannitol | + | builds acid from |
43255 | 27613 | amygdalin | + | builds acid from |
43255 | 18305 | arbutin | + | builds acid from |
43255 | esculin ferric citrate | + | builds acid from | |
43255 | 17814 | salicin | + | builds acid from |
43255 | 17057 | cellobiose | + | builds acid from |
43255 | 17306 | maltose | + | builds acid from |
43255 | 17992 | sucrose | + | builds acid from |
43255 | 27082 | trehalose | + | builds acid from |
43255 | 17151 | xylitol | +/- | builds acid from |
43255 | 28066 | gentiobiose | +/- | builds acid from |
43255 | 32528 | turanose | + | builds acid from |
43255 | 62318 | D-lyxose | + | builds acid from |
43255 | 18287 | L-fucose | +/- | builds acid from |
43255 | 17754 | glycerol | - | builds acid from |
43255 | 17113 | erythritol | - | builds acid from |
43255 | 17108 | D-arabinose | - | builds acid from |
43255 | 65328 | L-xylose | - | builds acid from |
43255 | 15963 | ribitol | - | builds acid from |
43255 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
43255 | 17266 | L-sorbose | - | builds acid from |
43255 | 62345 | L-rhamnose | - | builds acid from |
43255 | 16813 | galactitol | - | builds acid from |
43255 | 17268 | myo-inositol | - | builds acid from |
43255 | 17924 | D-sorbitol | - | builds acid from |
43255 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
43255 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
43255 | 506227 | N-acetylglucosamine | - | builds acid from |
43255 | 36219 | alpha-lactose | - | builds acid from |
43255 | 28053 | melibiose | - | builds acid from |
43255 | 15443 | inulin | - | builds acid from |
43255 | 6731 | melezitose | - | builds acid from |
43255 | 16634 | raffinose | - | builds acid from |
43255 | 28017 | starch | - | builds acid from |
43255 | 28087 | glycogen | - | builds acid from |
43255 | 16443 | D-tagatose | - | builds acid from |
43255 | 28847 | D-fucose | - | builds acid from |
43255 | 18333 | D-arabitol | - | builds acid from |
43255 | 18403 | L-arabitol | - | builds acid from |
43255 | 32032 | potassium gluconate | - | builds acid from |
43255 | potassium 2-dehydro-D-gluconate | - | builds acid from | |
43255 | potassium 5-dehydro-D-gluconate | - | builds acid from | |
43255 | 30031 | succinate | + | carbon source |
43255 | 17057 | cellobiose | - | carbon source |
43255 | 17272 | propionate | - | carbon source |
43255 | 29806 | fumarate | - | carbon source |
43255 | 16947 | citrate | - | carbon source |
43255 | 16467 | L-arginine | - | carbon source |
43255 | 16977 | L-alanine | - | carbon source |
43255 | 30089 | acetate | +/- | carbon source |
43255 | 29991 | L-aspartate | +/- | carbon source |
43255 | 25115 | malate | +/- | carbon source |
43255 | 15361 | pyruvate | +/- | carbon source |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43255 | 35581 | indole | no |
43255 | 16136 | hydrogen sulfide | no |
43255 | 15688 | acetoin | no |
metabolite tests
- @ref: 43255
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
43255 | catalase | + | 1.11.1.6 |
43255 | cytochrome oxidase | - | 1.9.3.1 |
43255 | beta-galactosidase | + | 3.2.1.23 |
43255 | urease | - | 3.5.1.5 |
43255 | arginine dihydrolase | - | 3.5.3.6 |
43255 | lysine decarboxylase | - | 4.1.1.18 |
43255 | ornithine decarboxylase | - | 4.1.1.17 |
43255 | tryptophan deaminase | - | 4.1.99.1 |
43255 | alkaline phosphatase | + | 3.1.3.1 |
43255 | esterase (C 4) | + | |
43255 | esterase Lipase (C 8) | + | |
43255 | leucine arylamidase | + | 3.4.11.1 |
43255 | trypsin | + | 3.4.21.4 |
43255 | acid phosphatase | + | 3.1.3.2 |
43255 | alpha-galactosidase | + | 3.2.1.22 |
43255 | alpha-glucosidase | + | 3.2.1.20 |
43255 | beta-glucosidase | + | 3.2.1.21 |
43255 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
43255 | alpha-mannosidase | + | 3.2.1.24 |
43255 | alpha-fucosidase | + | 3.2.1.51 |
43255 | lipase (C 14) | - | |
43255 | cystine arylamidase | - | 3.4.11.3 |
43255 | alpha-chymotrypsin | - | 3.4.21.1 |
43255 | valine arylamidase | - | |
43255 | naphthol-AS-BI-phosphohydrolase | - | |
43255 | beta-glucuronidase | - | 3.2.1.31 |
fatty acid profile
fatty acids
@ref fatty acid percentage 43255 C14:0 iso 0.9 43255 C15:0 iso 10.1 43255 C15:0 anteiso 46.5 43255 C16:0 iso 18.3 43255 C16:0 1 43255 C17:0 iso 2.1 43255 C17:0 anteiso 21.1 - 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 | sample type | sampling date | geographic location | country | origin.country | 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 |
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 | GC-content | method |
---|---|---|
43255 | 70.1 | |
67770 | 70.1 | high performance liquid chromatography (HPLC) |
External links
@ref: 43255
culture collection no.: JCM 28836, NCIMB 15039
literature
- topic: Phylogeny
- Pubmed-ID: 28604332
- title: Microbacterium tumbae sp. nov., an actinobacterium isolated from the stone chamber of ancient tumulus.
- authors: Nishijima M, Tazato N, Handa Y, Umekawa N, Kigawa R, Sano C, Sugiyama J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001863
- year: 2017
- mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Japan, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry
- topic2: Transcriptome
Reference
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
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 | 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 | 10.1099/ijsem.0.001863 | IJSEM 67: 1777-1783 2017 | 28604332 |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ |