Strain identifier
BacDive ID: 131546
Type strain: 
Species: Tamaricihabitans halophyticus
Strain history: <- S. Qin, Jiangasu Normal University, China; KLBMP 1356
NCBI tax ID(s): 1262583 (species)
version 8.1 (current version)
General
@ref: 22773
BacDive-ID: 131546
DSM-Number: 45765
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Tamaricihabitans halophyticus DSM 45765 is a spore-forming, mesophilic bacterium that was isolated from surface sterilized root of the halophyte Tamarix chinensis Lour, healthy plant tissue.
NCBI tax id
- NCBI tax id: 1262583
- Matching level: species
strain history
- @ref: 22773
- history: <- S. Qin, Jiangasu Normal University, China; KLBMP 1356
doi: 10.13145/bacdive131546.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Tamaricihabitans
- species: Tamaricihabitans halophyticus
- full scientific name: Tamaricihabitans halophyticus Qin et al. 2015
@ref: 22773
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Tamaricihabitans
species: Tamaricihabitans halophyticus
full scientific name: Tamaricihabitans halophyticus Qin et al. 2015
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 94.497 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 22773
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
- @ref: 22773
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 98 |
| 69480 | yes | 99.448 |
Isolation, sampling and environmental information
isolation
- @ref: 22773
- sample type: surface sterilized root of the halophyte Tamarix chinensis Lour, healthy plant tissue
- host species: Tamarix chinensis
- geographic location: Jiangsu province, coastal area
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Tree |
| #Host Body-Site | #Plant | #Root (Rhizome) |
| #Host Body-Site | #Plant | #Sterilized plant part |
taxonmaps
- @ref: 69479
- File name: preview.99_121714.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_47878;97_61542;98_81922;99_121714&stattab=map
- Last taxonomy: Tamaricihabitans halophyticus subclade
- 16S sequence: JX982738
- Sequence Identity:
- Total samples: 937
- soil counts: 458
- aquatic counts: 170
- animal counts: 241
- plant counts: 68
Safety information
risk assessment
- @ref: 22773
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22773
- description: Tamaricihabitans halophyticus 16S ribosomal RNA gene, partial sequence
- accession: JX982738
- length: 1445
- database: ena
- NCBI tax ID: 1262583
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Tamaricihabitans halophyticus DSM 45765 | GCA_004340875 | contig | ncbi | 1262583 |
| 66792 | Tamaricihabitans halophyticus strain DSM 45765 | 1262583.3 | wgs | patric | 1262583 |
| 66792 | Tamaricihabitans halophyticus DSM 45765 | 2795385477 | draft | img | 1262583 |
GC content
- @ref: 22773
- GC-content: 67.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 98 | no |
| motile | no | 92.278 | no |
| gram-positive | yes | 85.392 | no |
| anaerobic | no | 98.819 | no |
| aerobic | yes | 92.702 | no |
| halophile | yes | 62.267 | no |
| spore-forming | yes | 64.872 | no |
| glucose-util | yes | 88.999 | no |
| flagellated | no | 98.071 | no |
| thermophile | no | 96.468 | yes |
| glucose-ferment | no | 91.279 | no |
External links
@ref: 22773
culture collection no.: DSM 45765, NBRC 109361, KLBMP 1356
straininfo link
- @ref: 89960
- straininfo: 400618
literature
- topic: Phylogeny
- Pubmed-ID: 26410726
- title: Tamaricihabitans halophyticus gen. nov., sp. nov., an endophytic actinomycete of the family Pseudonocardiaceae.
- authors: Qin S, Bai JL, Wang Y, Feng WW, Yuan B, Sun Y, Cao CL, Ju XY, Huang Y, Jiang JH
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.000628
- year: 2015
- mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, Mycolic Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tamaricaceae/*microbiology, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Enzymology
Reference
| @id | authors | title | doi/url | catalogue | journal | 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 | |||
| 22773 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45765 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45765) | |||
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 89960 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID400618.1 |