Strain identifier
BacDive ID: 133644
Type strain: 
Species: Fodinibius salinus
Strain history: <- X.-L. Cui, YIM <- J.-H. Liu and Y.-X. Wang, YIM
NCBI tax ID(s): 860790 (species)
version 9.1 (current version)
General
@ref: 16044
BacDive-ID: 133644
DSM-Number: 21935
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped
description: Fodinibius salinus DSM 21935 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from hypersaline environment.
NCBI tax id
- NCBI tax id: 860790
- Matching level: species
strain history
- @ref: 16044
- history: <- X.-L. Cui, YIM <- J.-H. Liu and Y.-X. Wang, YIM
doi: 10.13145/bacdive133644.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/balneolota
- domain: Bacteria
- phylum: Balneolota
- class: Balneolia
- order: Balneolales
- family: Balneolaceae
- genus: Fodinibius
- species: Fodinibius salinus
- full scientific name: Fodinibius salinus Wang et al. 2012
@ref: 16044
domain: Bacteria
phylum: Balneolaeota
class: Balneolia
order: Balneolales
family: Balneolaceae
genus: Fodinibius
species: Fodinibius salinus
full scientific name: Fodinibius salinus Wang et al. 2012
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29903 | negative | 1.0-3.0 µm | 0.3 µm | rod-shaped | no | |
| 69480 | negative | 93.042 |
pigmentation
- @ref: 29903
- production: yes
Culture and growth conditions
culture medium
- @ref: 16044
- name: MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514b
- composition: Name: MEDIUM 514 plus additional salt (DSMZ Medium 514b) Composition: NaCl 19.45 g/l Agar 17.5 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 |
|---|---|---|---|
| 16044 | positive | growth | 28 |
| 29903 | positive | growth | 25-45 |
| 29903 | positive | optimum | 37 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29903 | positive | growth | 6.0-9.0 | alkaliphile |
| 29903 | positive | optimum | 7.5-8.0 |
Physiology and metabolism
oxygen tolerance
- @ref: 29903
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29903 | no | |
| 69480 | no | 92.125 |
| 69481 | no | 100 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29903 | NaCl | positive | growth | 4-23 % |
| 29903 | NaCl | positive | optimum | 10-15 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29903 | 16947 | citrate | + | carbon source |
| 29903 | 53423 | tween 40 | + | carbon source |
| 29903 | 53426 | tween 80 | + | carbon source |
| 29903 | 4853 | esculin | + | hydrolysis |
| 29903 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29903 | catalase | + | 1.11.1.6 |
| 29903 | gelatinase | + | |
| 29903 | cytochrome oxidase | + | 1.9.3.1 |
| 29903 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 29903 | hypersaline environment | ||||||
| 16044 | sediment from a salt mine | Yunnan,Fenggang salt mine (23°28' N 100° 43' E) | China | CHN | Asia | 23.4667 | 100.717 |
isolation source categories
- Cat1: #Condition
- Cat2: #Saline
taxonmaps
- @ref: 69479
- File name: preview.99_129680.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2060;96_50549;97_65079;98_86842;99_129680&stattab=map
- Last taxonomy: Fodinibius salinus subclade
- 16S sequence: HM153810
- Sequence Identity:
- Total samples: 129
- soil counts: 19
- aquatic counts: 110
Safety information
risk assessment
- @ref: 16044
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16044
- description: Fodinibius salinus strain YIM D17 16S ribosomal RNA gene, partial sequence
- accession: HM153810
- length: 1466
- database: nuccore
- NCBI tax ID: 860790
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Fodinibius salinus DSM 21935 | GCA_008124865 | contig | ncbi | 860790 |
| 66792 | Fodinibius salinus strain DSM 21935 | 860790.3 | wgs | patric | 860790 |
| 66792 | Fodinibius salinus DSM 21935 | 2728369742 | draft | img | 860790 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16044 | 43.0 | high performance liquid chromatography (HPLC) |
| 29903 | 43 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 93.042 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.43 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 79.084 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 92.125 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 84.821 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 81.006 | no |
External links
@ref: 16044
culture collection no.: DSM 21935, ACCC 10716, YIM D17
straininfo link
- @ref: 91541
- straininfo: 403871
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21441370 | Fodinibius salinus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a salt mine. | Wang YX, Liu JH, Xiao W, Zhang XX, Li YQ, Lai YH, Ji KY, Wen ML, Cui XL | Int J Syst Evol Microbiol | 10.1099/ijs.0.025502-0 | 2011 | Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Lipids/analysis, *Mining, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species Specificity | Genetics |
| Phylogeny | 32123983 | Aliifodinibius salipaludis sp. nov., Isolated from Saline-Alkaline Soil. | Zhao X, Miao S, Sun Y, Gong Q, Zhao J, Wang J, Zhang G | Curr Microbiol | 10.1007/s00284-019-01863-w | 2020 | *Bacteria/chemistry/classification/genetics, China, Genome, Bacterial/genetics, Hydrogen-Ion Concentration, Soil Microbiology | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16044 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21935) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21935 | |||
| 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 | |||
| 29903 | 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 | 26275 | 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) | |||
| 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 | |||
| 91541 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID403871.1 | StrainInfo: A central database for resolving microbial strain identifiers |