Strain identifier
BacDive ID: 13637
Type strain: 
Species: Rhizobium tibeticum
Strain history: <- W. X. Chen, China Agric. Univ., College Biol. Sci., Beijing <- B. C. Hou; CCBAU 85039
NCBI tax ID(s): 501024 (species)
version 8.1 (current version)
General
@ref: 15554
BacDive-ID: 13637
DSM-Number: 21102
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Rhizobium tibeticum DSM 21102 is a mesophilic, Gram-negative bacterium that was isolated from root nodules of Trigonella archiducis-nicolai Vassilcz.
NCBI tax id
- NCBI tax id: 501024
- Matching level: species
strain history
- @ref: 15554
- history: <- W. X. Chen, China Agric. Univ., College Biol. Sci., Beijing <- B. C. Hou; CCBAU 85039
doi: 10.13145/bacdive13637.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Rhizobiaceae
- genus: Rhizobium
- species: Rhizobium tibeticum
- full scientific name: Rhizobium tibeticum Hou et al. 2009
@ref: 15554
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Rhizobiaceae
genus: Rhizobium
species: Rhizobium tibeticum
full scientific name: Rhizobium tibeticum Hou et al. 2009
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.987
Culture and growth conditions
culture medium
- @ref: 15554
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
- @ref: 15554
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 15554
- sample type: root nodules of Trigonella archiducis-nicolai (Širj.) Vassilcz
- host species: Trigonella archiducis-nicolai
- geographic location: Tibet
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Shrub (Scrub) |
| #Host Body-Site | #Plant | #Root nodule |
taxonmaps
- @ref: 69479
- File name: preview.99_1324.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_62;97_441;98_503;99_1324&stattab=map
- Last taxonomy: Rhizobium
- 16S sequence: EU256404
- Sequence Identity:
- Total samples: 347
- soil counts: 58
- aquatic counts: 29
- animal counts: 20
- plant counts: 240
Safety information
risk assessment
- @ref: 15554
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 15554 | Rhizobium tibeticum strain CCBAU 85039 16S ribosomal RNA gene, partial sequence | EU256404 | 1364 | ena | 501024 |
| 15554 | Rhizobium etli strain CCBAU 85039 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | EU288744 | 1713 | ena | 29449 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhizobium tibeticum CCBAU85039 | GCA_900108425 | contig | ncbi | 501024 |
| 66792 | Rhizobium tibeticum CGMCC 1.7071 | GCA_900110205 | scaffold | ncbi | 501024 |
| 66792 | Rhizobium tibeticum strain CCBAU85039 | 501024.6 | wgs | patric | 501024 |
| 66792 | Rhizobium tibeticum strain CGMCC 1.7071 | 501024.7 | wgs | patric | 501024 |
| 66792 | Rhizobium tibeticum CGMCC 1.7071 | 2671180023 | draft | img | 501024 |
GC content
- @ref: 15554
- GC-content: 59.7
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| glucose-ferment | no | 90.866 | no |
| motile | yes | 89.552 | no |
| flagellated | no | 82.686 | no |
| gram-positive | no | 96.964 | no |
| anaerobic | no | 98.03 | no |
| aerobic | yes | 92.772 | no |
| halophile | no | 89.028 | no |
| spore-forming | no | 95.08 | no |
| thermophile | no | 99.467 | no |
| glucose-util | yes | 89.181 | no |
External links
@ref: 15554
culture collection no.: DSM 21102, CCBAU 85039, CGMCC 1.7071, LMG 24453
straininfo link
- @ref: 82820
- straininfo: 364849
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19643889 | Rhizobium tibeticum sp. nov., a symbiotic bacterium isolated from Trigonella archiducis-nicolai (Sirj.) Vassilcz. | Hou BC, Wang ET, Li Y Jr, Jia RZ, Chen WF, Gao Y, Dong RJ, Chen WX | Int J Syst Evol Microbiol | 10.1099/ijs.0.009647-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification/physiology, Root Nodules, Plant/microbiology/physiology, *Symbiosis, Tibet, Trigonella/*microbiology/physiology | Genetics |
| Phylogeny | 25701848 | Rhizobium metallidurans sp. nov., a symbiotic heavy metal resistant bacterium isolated from the Anthyllis vulneraria Zn-hyperaccumulator. | Grison CM, Jackson S, Merlot S, Dobson A, Grison C | Int J Syst Evol Microbiol | 10.1099/ijs.0.000130 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fabaceae/*microbiology, Fatty Acids/chemistry, France, Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Symbiosis, *Zinc | Genetics |
| Genetics | 28126941 | Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T. | Torres Tejerizo G, Wibberg D, Winkler A, Ormeno-Orrillo E, Martinez-Romero E, Niehaus K, Puhler A, Kalinowski J, Lagares A, Schluter A, Pistorio M | Genome Announc | 10.1128/genomeA.01513-16 | 2017 |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 15554 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21102) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21102 | |
| 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 | |
| 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 | |
| 82820 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID364849.1 | StrainInfo: A central database for resolving microbial strain identifiers |