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 9.1 (current version)
General
@ref: 22773
BacDive-ID: 131546
DSM-Number: 45765
keywords: genome sequence, 16S sequence, Bacteria, spore-forming
description: Tamaricihabitans halophyticus DSM 45765 is a spore-forming 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/bacdive131546.20240916.9.1
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: 69480
- motility: no
- confidence: 91
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
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: yes
- confidence: 98
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: nuccore
- 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
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 98 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 89.387 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.162 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 77.918 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 86.886 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 94.984 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 91 | 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 |