Strain identifier
BacDive ID: 17436
Type strain: 
Species: Xanthobacter tagetidis
Strain Designation: TagT2C
Strain history: <- A.P. Wood, TagT2C
NCBI tax ID(s): 60216 (species)
version 8.1 (current version)
General
@ref: 4203
BacDive-ID: 17436
DSM-Number: 11105
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Xanthobacter tagetidis TagT2C is a mesophilic, Gram-negative bacterium that was isolated from root balls of tagetes plants.
NCBI tax id
- NCBI tax id: 60216
- Matching level: species
strain history
- @ref: 4203
- history: <- A.P. Wood, TagT2C
doi: 10.13145/bacdive17436.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Xanthobacteraceae
- genus: Xanthobacter
- species: Xanthobacter tagetidis
- full scientific name: Xanthobacter tagetidis Padden et al. 1997
@ref: 4203
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Xanthobacteraceae
genus: Xanthobacter
species: Xanthobacter tagetidis
full scientific name: Xanthobacter tagetidis Padden et al. 1997
strain designation: TagT2C
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.985
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 4203 | HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) | yes | https://mediadive.dsmz.de/medium/428 | Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water |
| 4203 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | 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: 4203
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.986 |
Isolation, sampling and environmental information
isolation
- @ref: 4203
- sample type: root balls of tagetes plants
- country: United Kingdom
- origin.country: GBR
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
taxonmaps
- @ref: 69479
- File name: preview.99_29531.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_355;96_1529;97_1825;98_22014;99_29531&stattab=map
- Last taxonomy: Xanthobacter tagetidis subclade
- 16S sequence: X99469
- Sequence Identity:
- Total samples: 105
- soil counts: 5
- aquatic counts: 54
- animal counts: 39
- plant counts: 7
Safety information
risk assessment
- @ref: 4203
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Xanthobacter tagetidis partial 16S RNA gene
- accession: X99469
- length: 1412
- database: ena
- NCBI tax ID: 60216
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Xanthobacter tagetidis DSM 11105 | GCA_014206845 | scaffold | ncbi | 60216 |
| 66792 | Xanthobacter tagetidis strain DSM 11105 | 60216.6 | wgs | patric | 60216 |
| 66792 | Xanthobacter tagetidis DSM 11105 | 2828305725 | draft | img | 60216 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 86.655 | no |
| gram-positive | no | 98.944 | no |
| anaerobic | no | 95.063 | no |
| aerobic | yes | 80.805 | no |
| halophile | no | 83.841 | no |
| spore-forming | no | 96.738 | no |
| glucose-util | yes | 79.957 | no |
| thermophile | no | 94.623 | yes |
| motile | no | 75.484 | no |
| glucose-ferment | no | 91.604 | no |
External links
@ref: 4203
culture collection no.: DSM 11105
straininfo link
- @ref: 86432
- straininfo: 43874
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 9103627 | Xanthobacter tagetidis sp. nov., an organism associated with Tagetes species and able to grow on substituted thiophenes. | Padden AN, Rainey FA, Kelly DP, Wood AP | Int J Syst Bacteriol | 10.1099/00207713-47-2-394 | 1997 | Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Gram-Negative Aerobic Bacteria/genetics/*metabolism/ultrastructure, Microscopy, Electron, Molecular Sequence Data, Phylogeny, Plants/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Thiophenes/*metabolism | Metabolism |
| Genetics | 31296671 | Draft Genome Sequence of Xanthobacter tagetidis ATCC 700314(T). | Fatima SA, Goen AE, MacLea KS | Microbiol Resour Announc | 10.1128/MRA.00242-19 | 2019 | ||
| Phylogeny | 31592754 | Aquabacter cavernae sp. nov., a bacterium isolated from cave soil. | Duo JL, Cha QY, Zhou XK, Zhang TK, Qin SC, Yang PX, Zhu ML, Mo MH, Duan YQ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003585 | 2019 | Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4203 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11105) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11105 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 86432 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID43874.1 | StrainInfo: A central database for resolving microbial strain identifiers |