Strain identifier
BacDive ID: 14409
Type strain: 
Species: Sinobaca qinghaiensis
Strain history: <- W.-J. Li, YIM
NCBI tax ID(s): 342944 (species)
version 8.1 (current version)
General
@ref: 6687
BacDive-ID: 14409
DSM-Number: 17008
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, coccus-shaped
description: Sinobaca qinghaiensis DSM 17008 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from saline soil.
NCBI tax id
- NCBI tax id: 342944
- Matching level: species
strain history
- @ref: 6687
- history: <- W.-J. Li, YIM
doi: 10.13145/bacdive14409.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Sinobaca
- species: Sinobaca qinghaiensis
- full scientific name: Sinobaca qinghaiensis (Li et al. 2006) Li et al. 2008
synonyms
- @ref: 20215
- synonym: Sinococcus qinghaiensis
@ref: 6687
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Sinobaca
species: Sinobaca qinghaiensis
full scientific name: Sinobaca qinghaiensis (Li et al. 2006) Li et al. 2008
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|
| 31716 | positive | 0.8-1 µm | coccus-shaped | yes | |
| 69480 | yes | 93.367 | |||
| 69480 | positive | 100 |
pigmentation
- @ref: 31716
- production: yes
Culture and growth conditions
culture medium
- @ref: 6687
- 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 |
|---|---|---|---|---|
| 6687 | positive | growth | 28 | mesophilic |
| 31716 | positive | growth | 28-30 | mesophilic |
| 31716 | positive | optimum | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31716 | positive | growth | 7.5-9 | alkaliphile |
| 31716 | positive | optimum | 8-9.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 31716
- oxygen tolerance: aerobe
spore formation
- @ref: 31716
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31716 | NaCl | positive | growth | 01-25 % |
| 31716 | NaCl | positive | optimum | 10 % |
observation
- @ref: 31716
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31716 | 17057 | cellobiose | + | carbon source |
| 31716 | 28757 | fructose | + | carbon source |
| 31716 | 28260 | galactose | + | carbon source |
| 31716 | 17234 | glucose | + | carbon source |
| 31716 | 17306 | maltose | + | carbon source |
| 31716 | 29864 | mannitol | + | carbon source |
| 31716 | 37684 | mannose | + | carbon source |
| 31716 | 17992 | sucrose | + | carbon source |
| 31716 | 27082 | trehalose | + | carbon source |
enzymes
- @ref: 31716
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 6687
- sample type: saline soil
- geographic location: Qinghai Province
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Condition | #Saline |
Safety information
risk assessment
- @ref: 6687
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6687
- description: Sinobaca qinghaiensis strain YIM 70212 16S ribosomal RNA gene, partial sequence
- accession: DQ168584
- length: 1531
- database: ena
- NCBI tax ID: 342944
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sinobaca qinghaiensis DSM 17008 | GCA_003610495 | scaffold | ncbi | 342944 |
| 66792 | Sinobaca qinghaiensis strain DSM 17008 | 342944.3 | wgs | patric | 342944 |
| 66792 | Sinobaca qinghaiensis DSM 17008 | 2636416020 | draft | img | 342944 |
GC content
- @ref: 6687
- GC-content: 47
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 84 | no |
| motile | yes | 86.737 | yes |
| flagellated | yes | 70.477 | no |
| gram-positive | yes | 90.733 | yes |
| anaerobic | no | 99.095 | yes |
| aerobic | yes | 93.996 | yes |
| halophile | yes | 94.615 | yes |
| spore-forming | no | 63.202 | yes |
| glucose-util | yes | 89.388 | no |
| thermophile | no | 97.038 | no |
| glucose-ferment | no | 88.931 | no |
External links
@ref: 6687
culture collection no.: DSM 17008, KCTC 3943, YIM 70212
straininfo link
- @ref: 83553
- straininfo: 232151
literature
- topic: Phylogeny
- Pubmed-ID: 16738089
- title: Sinococcus qinghaiensis gen. nov., sp. nov., a novel member of the order Bacillales from a saline soil in China.
- authors: Li WJ, Zhang YQ, Schumann P, Tian XP, Zhang YQ, Xu LH, Jiang CL
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64111-0
- year: 2006
- mesh: Bacillus/*classification, China, Gram-Positive Bacteria/classification/*isolation & purification, Molecular Sequence Data, Phylogeny, Rhizobiaceae/*classification/isolation & purification, Soil/*analysis, *Soil Microbiology
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 6687 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17008) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17008 | ||||
| 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 | ||||
| 31716 | 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 | 27992 | 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) | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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) | ||||
| 83553 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID232151.1 | StrainInfo: A central database for resolving microbial strain identifiers |