Strain identifier
BacDive ID: 24033
Type strain: 
Species: Salegentibacter echinorum
Strain Designation: HD4
Strain history: <- Z.-J. Du, Shandong University at Weihai; HD4
NCBI tax ID(s): 1073325 (species)
version 8.1 (current version)
General
@ref: 20801
BacDive-ID: 24033
DSM-Number: 24579
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Salegentibacter echinorum HD4 is a mesophilic bacterium that was isolated from sea urchin Hemicentrotus pulcherrimus.
NCBI tax id
- NCBI tax id: 1073325
- Matching level: species
strain history
- @ref: 20801
- history: <- Z.-J. Du, Shandong University at Weihai; HD4
doi: 10.13145/bacdive24033.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Salegentibacter
- species: Salegentibacter echinorum
- full scientific name: Salegentibacter echinorum Xia et al. 2014
@ref: 20801
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Salegentibacter
species: Salegentibacter echinorum
full scientific name: Salegentibacter echinorum Xia et al. 2014
strain designation: HD4
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 91.197 | |
| 69480 | 99.985 | negative |
Culture and growth conditions
culture medium
- @ref: 20801
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
- @ref: 20801
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.99 |
Isolation, sampling and environmental information
isolation
- @ref: 20801
- sample type: sea urchin Hemicentrotus pulcherrimus
- host species: Hemicentrotus pulcherrimus
- geographic location: Yellow Sea (122°01'57.0''E 37°52'40.2''N)
- country: China
- origin.country: CHN
- continent: Asia
- latitude: 37.8778
- longitude: 122.033
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Echinodermata
taxonmaps
- @ref: 69479
- File name: preview.99_6691.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_3168;97_3884;98_4935;99_6691&stattab=map
- Last taxonomy: Salegentibacter echinorum subclade
- 16S sequence: JN040280
- Sequence Identity:
- Total samples: 703
- soil counts: 32
- aquatic counts: 462
- animal counts: 204
- plant counts: 5
Safety information
risk assessment
- @ref: 20801
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20801
- description: Salegentibacter echinorum collected-by Tingting Miao 16S ribosomal RNA gene, partial sequence
- accession: JN040280
- length: 1495
- database: ena
- NCBI tax ID: 1073325
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Salegentibacter echinorum DSM 24579 | GCA_900129445 | scaffold | ncbi | 1073325 |
| 66792 | Salegentibacter echinorum strain DSM 24579 | 1073325.3 | wgs | patric | 1073325 |
| 66792 | Salegentibacter echinorum DSM 24579 | 2695420921 | draft | img | 1073325 |
GC content
- @ref: 20801
- GC-content: 37
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 90.282 | no |
| flagellated | no | 94.193 | no |
| gram-positive | no | 98.019 | no |
| anaerobic | no | 99.203 | no |
| aerobic | yes | 87.671 | no |
| halophile | yes | 73.703 | no |
| spore-forming | no | 94.673 | no |
| thermophile | no | 99.786 | yes |
| glucose-util | yes | 86.785 | no |
| glucose-ferment | no | 87.371 | no |
External links
@ref: 20801
culture collection no.: DSM 24579, CICC 10466, NRRL B-59666
straininfo link
- @ref: 88006
- straininfo: 403577
literature
- topic: Phylogeny
- Pubmed-ID: 23754662
- title: Salegentibacter echinorum sp. nov., isolated from the sea urchin Hemicentrotus pulcherrimus.
- authors: Xia HF, Li XL, Liu QQ, Miao TT, Du ZJ, Chen GJ
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-013-9950-0
- year: 2013
- mesh: Animals, Bacteria, Aerobic/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification, Hemicentrotus/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature
- 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 | |||
| 20801 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24579 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24579) | |||
| 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 | |||
| 88006 | 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-ID403577.1 |