Strain identifier
BacDive ID: 13470
Type strain:
Species: Saccharopolyspora kobensis
Strain Designation: W12
Strain history: J. Zhang W12.
NCBI tax ID(s): 146035 (species)
General
@ref: 17642
BacDive-ID: 13470
DSM-Number: 45556
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped
description: Saccharopolyspora kobensis W12 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil from a field of grass.
NCBI tax id
- NCBI tax id: 146035
- Matching level: species
strain history
@ref | history |
---|---|
17642 | <- JCM <- J. Zhang; W12 |
67770 | J. Zhang W12. |
doi: 10.13145/bacdive13470.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Saccharopolyspora
- species: Saccharopolyspora kobensis
- full scientific name: Saccharopolyspora kobensis (Lacey 1989 ex Iwasake and Mori 1979) Nouioui et al. 2018
synonyms
@ref synonym 20215 Saccharopolyspora jiangxiensis 20215 Saccharopolyspora hirsuta subsp. kobensis
@ref: 17642
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Saccharopolyspora
species: Saccharopolyspora kobensis
full scientific name: Saccharopolyspora kobensis (Lacey 1989) Nouioui et al. 2018
strain designation: W12
type strain: no
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
32660 | positive | rod-shaped | no | |
69480 | positive | 100 |
Culture and growth conditions
culture medium
- @ref: 17642
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://mediadive.dsmz.de/medium/65
- composition: Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17642 | positive | growth | 28 | mesophilic |
32660 | positive | growth | 15-45 | |
32660 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32660 | positive | growth | 5.5-9.5 | alkaliphile |
32660 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 32660
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
32660 | yes | |
69481 | yes | 100 |
69480 | yes | 100 |
halophily
- @ref: 32660
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <11 %
observation
@ref | observation |
---|---|
32660 | aggregates in chains |
67770 | quinones: MK-9(H4), MK-10(H2) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32660 | 30089 | acetate | + | carbon source |
32660 | 15963 | ribitol | + | carbon source |
32660 | 22599 | arabinose | + | carbon source |
32660 | 16947 | citrate | + | carbon source |
32660 | 23652 | dextrin | + | carbon source |
32660 | 28757 | fructose | + | carbon source |
32660 | 28260 | galactose | + | carbon source |
32660 | 17234 | glucose | + | carbon source |
32660 | 17754 | glycerol | + | carbon source |
32660 | 17716 | lactose | + | carbon source |
32660 | 25115 | malate | + | carbon source |
32660 | 17306 | maltose | + | carbon source |
32660 | 29864 | mannitol | + | carbon source |
32660 | 37684 | mannose | + | carbon source |
32660 | 37657 | methyl D-glucoside | + | carbon source |
32660 | 17268 | myo-inositol | + | carbon source |
32660 | 16634 | raffinose | + | carbon source |
32660 | 26546 | rhamnose | + | carbon source |
32660 | 33942 | ribose | + | carbon source |
32660 | 30911 | sorbitol | + | carbon source |
32660 | 30031 | succinate | + | carbon source |
32660 | 17992 | sucrose | + | carbon source |
32660 | 27082 | trehalose | + | carbon source |
32660 | 18222 | xylose | + | carbon source |
32660 | 4853 | esculin | + | hydrolysis |
32660 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32660 | catalase | + | 1.11.1.6 |
32660 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
17642 | soil from a field of grass | Jiangxi Province | China | CHN | Asia |
67770 | Soil from a field of grass | Jiangxi Province | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Field |
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_35945.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_5246;97_19583;98_26504;99_35945&stattab=map
- Last taxonomy: Saccharopolyspora
- 16S sequence: EF143926
- Sequence Identity:
- Total samples: 136
- soil counts: 112
- aquatic counts: 3
- animal counts: 15
- plant counts: 6
Safety information
risk assessment
- @ref: 17642
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17642
- description: Saccharopolyspora jiangxiensis strain W12 16S ribosomal RNA gene, partial sequence
- accession: EF143926
- length: 1419
- database: ena
- NCBI tax ID: 418522
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Saccharopolyspora jiangxiensis strain CGMCC 4.3529 | 418522.7 | wgs | patric | 146035 |
66792 | Saccharopolyspora jiangxiensis CGMCC 4.3529 | 2667527438 | draft | img | 418522 |
67770 | Saccharopolyspora kobensis CGMCC 4.3529 | GCA_900112555 | scaffold | ncbi | 146035 |
GC content
@ref | GC-content | method |
---|---|---|
17642 | 70.3 | thermal denaturation, midpoint method (Tm) |
32660 | 70.3 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 90.06 | yes |
anaerobic | no | 98.935 | no |
halophile | yes | 56.13 | yes |
spore-forming | yes | 92.668 | yes |
glucose-util | yes | 87.429 | yes |
aerobic | yes | 90.561 | yes |
flagellated | no | 97.429 | yes |
thermophile | no | 96.667 | no |
motile | no | 90.887 | no |
glucose-ferment | no | 91.673 | no |
External links
@ref: 17642
culture collection no.: DSM 45556, CGMCC 4.3529, JCM 14613
straininfo link
- @ref: 82662
- straininfo: 400005
literature
- topic: Phylogeny
- Pubmed-ID: 19406796
- title: Saccharopolyspora jiangxiensis sp. nov., isolated from grass-field soil.
- authors: Zhang J, Wu D, Liu Z
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65863-0
- year: 2009
- mesh: Bacterial Typing Techniques, China, DNA, Bacterial/analysis/genetics, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, *Poaceae, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/genetics/isolation & purification/physiology, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
17642 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45556) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45556 | |||
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 | |||
32660 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28871 | 28776041 | |
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/ | ||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
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 | |||
82662 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400005.1 | StrainInfo: A central database for resolving microbial strain identifiers |