Strain identifier
BacDive ID: 17213
Type strain: 
Species: Haloferula luteola
Strain Designation: YC6886
Strain history: <- YR Chung, Kyeongsang Univ.
NCBI tax ID(s): 595692 (species)
version 9.1 (current version)
General
@ref: 15769
BacDive-ID: 17213
DSM-Number: 21608
keywords: genome sequence, 16S sequence, Bacteria, aerobe, rod-shaped
description: Haloferula luteola YC6886 is an aerobe, rod-shaped bacterium that was isolated from roots of a halophyte, Rosetalia rugosae Thunb. ex Murray.
NCBI tax id
- NCBI tax id: 595692
- Matching level: species
strain history
| @ref | history |
|---|---|
| 15769 | <- Y. R. Chung, Gyeongsang Natl. Univ. (GNU), Jinju, Korea; YC6886 <- F. Bibi |
| 67771 | <- YR Chung, Kyeongsang Univ. |
doi: 10.13145/bacdive17213.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/verrucomicrobiota
- domain: Bacteria
- phylum: Verrucomicrobiota
- class: Verrucomicrobiia
- order: Verrucomicrobiales
- family: Verrucomicrobiaceae
- genus: Haloferula
- species: Haloferula luteola
- full scientific name: Haloferula luteola Bibi et al. 2011
@ref: 15769
domain: Bacteria
phylum: Verrucomicrobia
class: Verrucomicrobiae
order: Verrucomicrobiales
family: Verrucomicrobiaceae
genus: Haloferula
species: Haloferula luteola
full scientific name: Haloferula luteola Bibi et al. 2011
strain designation: YC6886
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | gram stain | confidence |
|---|---|---|---|---|
| 67771 | rod-shaped | no | ||
| 67771 | negative | |||
| 69480 | negative | 91.995 |
Culture and growth conditions
culture medium
- @ref: 15769
- 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 | growth | type | temperature |
|---|---|---|---|
| 15769 | positive | growth | 28 |
| 67771 | positive | growth | 25-28 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
observation
- @ref: 67771
- observation: quinones: MK-9
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 15769 | roots of a halophyte, Rosetalia rugosae Thunb. ex Murray | Rosetalia rugosae | Jinju, Namhae Island | Republic of Korea | KOR | Asia |
| 67771 | From roots of `Rosetalia rugosae` | Jinju | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Aquatic plant |
| #Host Body-Site | #Plant | #Root (Rhizome) |
taxonmaps
- @ref: 69479
- File name: preview.99_139002.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_545;96_24791;97_31038;98_39722;99_139002&stattab=map
- Last taxonomy: Haloferula luteola
- 16S sequence: FJ032193
- Sequence Identity:
- Total samples: 137
- soil counts: 4
- aquatic counts: 34
- animal counts: 99
Safety information
risk assessment
- @ref: 15769
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15769
- description: Haloferula luteola strain YC6886 16S ribosomal RNA gene, partial sequence
- accession: FJ032193
- length: 1395
- database: nuccore
- NCBI tax ID: 595692
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Haloferula luteola YC6886 | GCA_014201715 | scaffold | ncbi | 595692 |
| 66792 | Haloferula luteola DSM 21608 | 2861254865 | draft | img | 595692 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 15769 | 58.5 | high performance liquid chromatography (HPLC) |
| 67771 | 58.5 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 73 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 91.995 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 90.57 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 72.648 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.433 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.764 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 77.02 | yes |
External links
@ref: 15769
culture collection no.: DSM 21608, KCTC 22447
straininfo link
- @ref: 86212
- straininfo: 403867
literature
- topic: Phylogeny
- Pubmed-ID: 20817839
- title: Haloferula luteola sp. nov., an endophytic bacterium isolated from the root of a halophyte, Rosa rugosa, and emended description of the genus Haloferula.
- authors: Bibi F, Chung EJ, Yoon HS, Song GC, Jeon CO, Chung YR
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.022772-0
- year: 2010
- mesh: DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Gram-Negative Aerobic Bacteria/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Rosa/*microbiology
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 15769 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21608) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21608 | |
| 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 | |
| 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) | |
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
| 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 | |
| 86212 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID403867.1 | StrainInfo: A central database for resolving microbial strain identifiers |