Strain identifier
BacDive ID: 24188
Type strain:
Species: Microbacterium saccharophilum
Strain Designation: K-1
Strain history: <- NBRC; NBRC 108778 <- K. Mikuni, Ensuiko Sugar Refining Co., LTD; K-1
NCBI tax ID(s): 1213358 (species)
General
@ref: 20654
BacDive-ID: 24188
DSM-Number: 28107
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Microbacterium saccharophilum K-1 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil, sucrose refining factory.
NCBI tax id
- NCBI tax id: 1213358
- Matching level: species
strain history
- @ref: 20654
- history: <- NBRC; NBRC 108778 <- K. Mikuni, Ensuiko Sugar Refining Co., LTD; K-1
doi: 10.13145/bacdive24188.20230509.8.1
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 saccharophilum
- full scientific name: Microbacterium saccharophilum Ohta et al. 2013
@ref: 20654
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Microbacterium
species: Microbacterium saccharophilum
full scientific name: Microbacterium saccharophilum Ohta et al. 2013
strain designation: K-1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30909 | positive | 0.8 µm | 0.4 µm | rod-shaped | no | |
69480 | positive | 100 |
pigmentation
- @ref: 30909
- production: yes
Culture and growth conditions
culture medium
- @ref: 20654
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20654 | positive | growth | 28 | mesophilic |
30909 | positive | growth | 09-37 | |
30909 | positive | optimum | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30909 | positive | growth | 6.0-11.0 | alkaliphile |
30909 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30909
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30909 | no | |
69481 | no | 100 |
69480 | no | 99.995 |
halophily
- @ref: 30909
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %
observation
- @ref: 30909
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30909 | 28757 | fructose | + | carbon source |
30909 | 29864 | mannitol | + | carbon source |
30909 | 18222 | xylose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30909 | catalase | + | 1.11.1.6 |
30909 | gelatinase | + |
Isolation, sampling and environmental information
isolation
- @ref: 20654
- sample type: soil, sucrose refining factory
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Industrial | #Plant (Factory) |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_1973.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_137;97_148;98_1544;99_1973&stattab=map
- Last taxonomy: Microbacterium
- 16S sequence: AB736273
- Sequence Identity:
- Total samples: 13220
- soil counts: 4083
- aquatic counts: 3329
- animal counts: 5014
- plant counts: 794
Safety information
risk assessment
- @ref: 20654
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20654
- description: Microbacterium saccharophilum gene for 16S ribosomal RNA, partial sequence
- accession: AB736273
- length: 1482
- database: ena
- NCBI tax ID: 1213358
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microbacterium saccharophilum NBRC 108778 | GCA_007992455 | contig | ncbi | 1213358 |
66792 | Microbacterium saccharophilum K-1 | GCA_008017435 | contig | ncbi | 1213358 |
66792 | Microbacterium saccharophilum strain NBRC 108778 | 1213358.6 | wgs | patric | 1213358 |
66792 | Microbacterium saccharophilum NBRC 108778 | 2903864575 | draft | img | 1213358 |
66792 | Microbacterium saccharophilum K-1 | 2903861677 | draft | img | 1213358 |
66792 | Microbacterium saccharophilum DSM 28107 | GCA_023155775 | contig | ncbi | 1213358 |
GC content
- @ref: 20654
- GC-content: 73
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 92.378 | yes |
gram-positive | yes | 93.212 | yes |
anaerobic | no | 99.279 | yes |
aerobic | yes | 91.976 | no |
halophile | no | 93.249 | yes |
spore-forming | no | 93.534 | yes |
thermophile | no | 99.217 | yes |
glucose-util | yes | 85.179 | no |
flagellated | no | 97.816 | yes |
glucose-ferment | no | 90.773 | no |
External links
@ref: 20654
culture collection no.: DSM 28107, NBRC 108778, NCIMB 14782
straininfo link
- @ref: 88141
- straininfo: 396948
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23315408 | Microbacterium saccharophilum sp. nov., isolated from a sucrose-refining factory. | Ohta Y, Ito T, Mori K, Nishi S, Shimane Y, Mikuni K, Hatada Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.047258-0 | 2013 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Lysine/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sucrose/*metabolism, Vitamin K 2/analysis | Genetics |
Phylogeny | 25239238 | Microbacterium endophyticum sp. nov. and Microbacterium halimionae sp. nov., endophytes isolated from the salt-marsh plant Halimione portulacoides and emended description of the genus Microbacterium. | Alves A, Correia A, Igual JM, Trujillo ME | Syst Appl Microbiol | 10.1016/j.syapm.2014.08.004 | 2014 | Actinobacteria/*classification/genetics/*isolation & purification, Amaranthaceae/*microbiology, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Endophytes/*classification/genetics/*isolation & purification, Fatty Acids/analysis, Molecular Sequence Data, Molecular Typing, Nucleic Acid Hybridization, Ornithine/analysis, Peptidoglycan/analysis, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysis | Enzymology |
Phylogeny | 36167780 | Microbacterium kunmingensis sp. nov., an attached bacterium of Microcystis aeruginosa. | Xiao Y, Chen M, Chen J, Mao LN, Peng YR, Gui SS, Zhang BH | J Antibiot (Tokyo) | 10.1038/s41429-022-00568-w | 2022 | RNA, Ribosomal, 16S/genetics, *Microcystis, Microbacterium, DNA, Bacterial/genetics, Bacterial Typing Techniques, Phylogeny, Sequence Analysis, DNA, *Actinomycetales, Fatty Acids/chemistry, Vitamin K 2/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
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 | ||||
20654 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28107 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28107) | ||||
30909 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27239 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | ||||
88141 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID396948.1 |