Strain identifier
BacDive ID: 7438
Type strain:
Species: Microbacterium flavum
Strain Designation: YM18-098
Strain history: DSM 18909 <-- H. Kasai YM18-098.
NCBI tax ID(s): 415216 (species)
General
@ref: 7769
BacDive-ID: 7438
DSM-Number: 18909
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Microbacterium flavum YM18-098 is a mesophilic bacterium that was isolated from Ascidian .
NCBI tax id
- NCBI tax id: 415216
- Matching level: species
strain history
@ref | history |
---|---|
7769 | <- H. Kasai; YM18-098 |
67770 | DSM 18909 <-- H. Kasai YM18-098. |
doi: 10.13145/bacdive7438.20230509.8.1
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 flavum
- full scientific name: Microbacterium flavum Kageyama et al. 2008
@ref: 7769
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Microbacterium
species: Microbacterium flavum
full scientific name: Microbacterium flavum Kageyama et al. 2008
strain designation: YM18-098
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 92.29 | |
69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 7769
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7769 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.99 |
observation
- @ref: 67770
- observation: quinones: MK-11, MK-12
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | + | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | + | builds acid from | 32528 |
68371 | gentiobiose | + | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | + | builds acid from | 28087 |
68371 | starch | + | builds acid from | 28017 |
68371 | raffinose | + | builds acid from | 16634 |
68371 | melezitose | + | builds acid from | 6731 |
68371 | inulin | + | builds acid from | 15443 |
68371 | trehalose | + | builds acid from | 27082 |
68371 | sucrose | + | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | + | builds acid from | 17057 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | + | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | + | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | + | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | + | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | + | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
API 50CHac
@ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7769 | - | - | - | - | + | - | - | - | - | - | + | + | + | + | - | + | - | - | + | - | - | - | + | - | - | + | +/- | + | + | - | - | + | + | + | + | + | + | + | - | + | + | - | - | - | - | - | - | + | - | +/- |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | host species |
---|---|---|---|---|---|---|
7769 | Ascidian (D. moseleyi) | Nagasaki | Japan | JPN | Asia | |
67770 | Ascidian (Didemnum moseleyi), Nomozaki at the tips of Nagasaki Peninsula | Nagasaki Pref. | Japan | JPN | Asia | Didemnum moseleyi |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Host | #Invertebrates (Other) | #Tunicata |
Safety information
risk assessment
- @ref: 7769
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7769
- description: Microbacterium flavum gene for 16S rRNA, partial sequence
- accession: AB286029
- length: 1467
- database: ena
- NCBI tax ID: 415216
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microbacterium flavum DSM 18909 | GCA_018717645 | contig | ncbi | 415216 |
66792 | Microbacterium flavum strain DSM 18909 | 415216.5 | wgs | patric | 415216 |
GC content
@ref | GC-content | method |
---|---|---|
7769 | 70 | |
67770 | 70 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | yes | 95.657 | no |
anaerobic | no | 99.584 | no |
halophile | no | 90.141 | no |
spore-forming | no | 93.914 | no |
glucose-util | yes | 87.111 | no |
aerobic | yes | 92.302 | no |
flagellated | no | 98.087 | no |
thermophile | no | 99.707 | yes |
motile | no | 89.982 | no |
glucose-ferment | no | 91.549 | no |
External links
@ref: 7769
culture collection no.: DSM 18909, JCM 15574, MBIC 08278, NBRC 103923
straininfo link
- @ref: 76886
- straininfo: 398142
literature
Pubmed-ID | title | authors | journal | DOI | year | mesh | topic | topic2 |
---|---|---|---|---|---|---|---|---|
33682148 | Protective effect of fermented Diospyros lotus L. extracts against the high glucose-induced apoptosis of MIN6 cells. | Yin H, Yan HH, Qin CQ, Li HR, Li X, Ren DF | J Food Biochem | 10.1111/jfbc.13685 | 2021 | Apoptosis, *Diabetes Mellitus, Type 2, *Diospyros, Glucose, *Insulin-Secreting Cells, Plant Extracts/pharmacology | ||
34807813 | Microbacterium paulum sp. nov., isolated from microfiltered milk. | Bellassi P, Fontana A, Callegari ML, Cappa F, Morelli L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005119 | 2021 | Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Microbacterium/classification/isolation & purification, Milk/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry | Phylogeny | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
7769 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18909) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18909 | |
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68371 | Automatically annotated from API 50CH acid | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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 | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
76886 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398142.1 | StrainInfo: A central database for resolving microbial strain identifiers |