Strain identifier
BacDive ID: 134005
Type strain: 
Species: Dyadobacter tibetensis
Strain Designation: Y620-1
Strain history: L. Shen Y620-1.
NCBI tax ID(s): 1211851 (species)
version 8.1 (current version)
General
@ref: 31036
BacDive-ID: 134005
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped
description: Dyadobacter tibetensis Y620-1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from glacier.
NCBI tax id
- NCBI tax id: 1211851
- Matching level: species
strain history
- @ref: 67770
- history: L. Shen Y620-1.
doi: 10.13145/bacdive134005.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Spirosomataceae
- genus: Dyadobacter
- species: Dyadobacter tibetensis
- full scientific name: Dyadobacter tibetensis Shen et al. 2013
@ref: 31036
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Cytophagaceae
genus: Dyadobacter
species: Dyadobacter tibetensis
strain designation: Y620-1
type strain: yes
Morphology
cell morphology
- @ref: 31036
- gram stain: negative
- cell length: 1.5 µm
- cell width: 0.5 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 31036
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 31036 | positive | growth | 04-35 | |
| 31036 | positive | optimum | 30 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 31036
- oxygen tolerance: aerobe
observation
| @ref | observation |
|---|---|
| 31036 | aggregates in clumps |
| 67770 | quinones: MK-7 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31036 | 22599 | arabinose | + | carbon source |
| 31036 | 17234 | glucose | + | carbon source |
| 31036 | 29864 | mannitol | + | carbon source |
| 31036 | 37684 | mannose | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31036 | acid phosphatase | + | 3.1.3.2 |
| 31036 | alkaline phosphatase | + | 3.1.3.1 |
| 31036 | alpha-galactosidase | + | 3.2.1.22 |
| 31036 | catalase | + | 1.11.1.6 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 31036 | glacier | ||||
| 67770 | Ice core section drilled 59 m-deep in Yuzhufeng Glacier | Tibetan Plateau | China | CHN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Glacier
taxonmaps
- @ref: 69479
- File name: preview.99_5073.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_496;96_2473;97_3018;98_3786;99_5073&stattab=map
- Last taxonomy: Dyadobacter tibetensis
- 16S sequence: JQ824420
- Sequence Identity:
- Total samples: 1323
- soil counts: 149
- aquatic counts: 347
- animal counts: 781
- plant counts: 46
Sequence information
16S sequences
- @ref: 31036
- description: Dyadobacter tibetensis strain Y620-1 16S ribosomal RNA gene, partial sequence
- accession: JQ824420
- length: 1353
- database: nuccore
- NCBI tax ID: 1434325
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Dyadobacter tibetensis Y620-1 | GCA_000566685 | contig | ncbi | 1434325 |
| 66792 | Dyadobacter tibetensis Y620-1 | 1434325.3 | wgs | patric | 1434325 |
| 66792 | Dyadobacter tibetensis Y620-1 | 2585427797 | draft | img | 1434325 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 31036 | 44.4 | |
| 67770 | 44.1-44.7 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 91.308 | no |
| gram-positive | no | 98.42 | yes |
| anaerobic | no | 99.31 | yes |
| halophile | no | 93.18 | no |
| spore-forming | no | 95.986 | no |
| thermophile | no | 99.174 | yes |
| glucose-util | yes | 88.852 | no |
| aerobic | yes | 92.735 | no |
| flagellated | no | 96.604 | no |
| glucose-ferment | no | 89.129 | no |
External links
@ref: 31036
culture collection no.: JCM 18589, CGMCC 1.12215
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 23606482 | Dyadobacter tibetensis sp. nov., isolated from glacial ice core. | Shen L, Liu Y, Yao T, Wang N, Xu B, Jiao N, Liu H, Zhou Y, Liu X, Wang Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.050328-0 | 2013 | Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, *Ice, Ice Cover/*microbiology, Molecular Sequence Data, Phosphatidylethanolamines, *Phylogeny, Polyenes/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Genetics | 25197470 | Draft genome sequence of Dyadobacter tibetensis type strain (Y620-1) isolated from glacial ice. | Liu Y, Hu A, Shen L, Yao T, Jiao N, Wang N, Xu B | Stand Genomic Sci | 10.4056/sigs.5649756 | 2014 | ||
| Phylogeny | 31336655 | Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment. | Shen L, Liu Y, Wang N, Adhikari NP | Microorganisms | 10.3390/microorganisms7070211 | 2019 |
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed |
|---|---|---|---|---|---|
| 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 | ||
| 31036 | 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 | 27366 | 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 | ||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |