Strain identifier
BacDive ID: 13556
Type strain: 
Species: Ensifer arboris
Strain Designation: TTR38(44)
Strain history: <- K. Lindström, HAMBI <- M. Karsisto; TTR38(44)
NCBI tax ID(s): 935557 (strain), 76745 (species)
version 8.1 (current version)
General
@ref: 5014
BacDive-ID: 13556
DSM-Number: 13375
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Ensifer arboris TTR38 is a mesophilic, motile bacterium that was isolated from root nodules of Prosopis chilensis.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 935557 | strain |
| 76745 | species |
strain history
- @ref: 5014
- history: <- K. Lindström, HAMBI <- M. Karsisto; TTR38(44)
doi: 10.13145/bacdive13556.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Rhizobiaceae
- genus: Ensifer
- species: Ensifer arboris
- full scientific name: Ensifer arboris (Nick et al. 1999) Young 2003
synonyms
- @ref: 20215
- synonym: Sinorhizobium arboris
@ref: 5014
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Rhizobiaceae
genus: Ensifer
species: Ensifer arboris
full scientific name: Ensifer arboris (Nick et al. 1999) Young 2003
strain designation: TTR38(44)
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 95.681 | |
| 69480 | 99.978 | negative |
Culture and growth conditions
culture medium
- @ref: 5014
- name: RHIZOBIUM MEDIUM (DSMZ Medium 98)
- growth: yes
- link: https://mediadive.dsmz.de/medium/98
- composition: Name: RHIZOBIUM MEDIUM (DSMZ Medium 98) Composition: air-dried garden soil 80.0 g/l Agar 15.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l Na2CO3 0.2 g/l Distilled water
culture temp
- @ref: 5014
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.988 |
Isolation, sampling and environmental information
isolation
- @ref: 5014
- sample type: root nodules of Prosopis chilensis
- host species: Prosopis chilensis
- geographic location: Kosti
- country: Sudan
- origin.country: SDN
- continent: Africa
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Tree |
| #Host Body-Site | #Plant | #Root nodule |
taxonmaps
- @ref: 69479
- File name: preview.99_106.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_84;97_88;98_97;99_106&stattab=map
- Last taxonomy: Sinorhizobium
- 16S sequence: AM181744
- Sequence Identity:
- Total samples: 10577
- soil counts: 5488
- aquatic counts: 1757
- animal counts: 1189
- plant counts: 2143
Safety information
risk assessment
- @ref: 5014
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Sinorhizobium arboris strain LMG 14919 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequence | AF345281 | 983 | ena | 935557 |
| 20218 | Sinorhizobium arboris partial 16S rRNA gene, strain LMG 14919 | AM181744 | 1426 | ena | 935557 |
| 20218 | Sinorhizobium arboris gene for 16S rRNA, partial sequence, strain: NBRC 100383 | AB681158 | 1410 | ena | 935557 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sinorhizobium arboris LMG 14919 | GCA_000427465 | scaffold | ncbi | 935557 |
| 66792 | Sinorhizobium arboris LMG 14919 | 935557.3 | wgs | patric | 935557 |
| 66792 | Sinorhizobium arboris LMG 14919 | 2512047086 | draft | img | 935557 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 91.873 | no |
| flagellated | no | 72.345 | no |
| gram-positive | no | 97.972 | no |
| anaerobic | no | 97.841 | no |
| aerobic | yes | 89.403 | no |
| halophile | no | 90.507 | no |
| spore-forming | no | 94.222 | no |
| glucose-util | yes | 92.207 | no |
| thermophile | no | 99.581 | yes |
| glucose-ferment | no | 89.951 | no |
External links
@ref: 5014
culture collection no.: DSM 13375, HAMBI 1552, HAMBI 1697, LMG 14919
straininfo link
- @ref: 82745
- straininfo: 13015
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 24256411 | Stable isotope labelling reveals that NaCl stress decreases the production of Ensifer (Sinorhizobium) arboris lipochitooligosaccharide signalling molecules. | Penttinen P, Rasanen LA, Lortet G, Lindstrom K | FEMS Microbiol Lett | 10.1111/1574-6968.12303 | 2013 | Isotope Labeling, Lipopolysaccharides/*metabolism, Mass Spectrometry, Metabolomics, Salt Tolerance/*physiology, Sinorhizobium/drug effects/*physiology, Sodium Chloride/*metabolism/pharmacology, *Stress, Physiological | Biotechnology |
| Genetics | 25197433 | Genome sequence of Ensifer arboris strain LMG 14919(T); a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan. | Reeve W, Tian R, Brau L, Goodwin L, Munk C, Detter C, Tapia R, Han C, Liolios K, Huntemann M, Pati A, Woyke T, Mavrommatis K, Markowitz V, Ivanova N, Kyrpides N, Willems A | Stand Genomic Sci | 10.4056/sigs.4828625 | 2013 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5014 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13375) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13375 | |||
| 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) | |||
| 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 | |||
| 82745 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13015.1 | StrainInfo: A central database for resolving microbial strain identifiers |