Strain identifier
BacDive ID: 160702
Type strain: 
Species: Roseovarius litorisediminis
Strain Designation: D1-W8
Strain history: <- J.-S. Lee, KCTC; KCTC 32327 <- J.-H. Yoon, Sungkyunkwan Univ.; D1-W8
NCBI tax ID(s): 1312363 (species)
version 9.1 (current version)
General
@ref: 67612
BacDive-ID: 160702
DSM-Number: 110551
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Roseovarius litorisediminis D1-W8 is a Gram-negative bacterium that was isolated from Tidal flat sediment.
NCBI tax id
- NCBI tax id: 1312363
- Matching level: species
strain history
- @ref: 67612
- history: <- J.-S. Lee, KCTC; KCTC 32327 <- J.-H. Yoon, Sungkyunkwan Univ.; D1-W8
doi: 10.13145/bacdive160702.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Roseovarius
- species: Roseovarius litorisediminis
- full scientific name: Roseovarius litorisediminis (Park et al. 2013) Hördt et al. 2020
synonyms
- @ref: 20215
- synonym: Pelagicola litorisediminis
@ref: 67612
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Roseovarius
species: Roseovarius litorisediminis
full scientific name: Roseovarius litorisediminis (Park et al. 2013) Hördt et al. 2020
strain designation: D1-W8
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.319
Culture and growth conditions
culture medium
- @ref: 67612
- 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: 67612
- growth: positive
- type: growth
- temperature: 25
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 91.732
Isolation, sampling and environmental information
isolation
- @ref: 67612
- sample type: Tidal flat sediment
- geographic location: Boseong
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
Safety information
risk assessment
- @ref: 67612
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 67612
- description: Pelagicola litorisediminis strain D1-W8 16S ribosomal RNA gene, partial sequence
- accession: KC708867
- length: 1390
- database: nuccore
- NCBI tax ID: 1312363
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Roseovarius litorisediminis CECT 8287 | GCA_900172295 | contig | ncbi | 1312363 |
| 66792 | Pelagicola litorisediminis strain CECT 8287 | 1312363.4 | wgs | patric | 1312363 |
| 66792 | Pelagicola litorisediminis CECT 8287 | 2791354896 | draft | img | 1312363 |
GC content
- @ref: 67612
- GC-content: 57.9
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99.319 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.278 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 91.732 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 88.17 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.792 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 68.699 | no |
External links
@ref: 67612
culture collection no.: DSM 110551, KCTC 32327, CECT 8287
straininfo link
- @ref: 112929
- straininfo: 390810
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 23736906 | Pelagicola litorisediminis sp. nov., a novel alphaproteobacterium isolated from tidal flat sediment. | Park S, Jung YT, Yoon JH | Antonie Van Leeuwenhoek | 10.1007/s10482-013-9930-4 | 2013 | Anti-Bacterial Agents/pharmacology, Base Composition, Base Sequence, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Lipids/analysis, Microbial Sensitivity Tests, Molecular Sequence Data, Phenotype, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/classification/drug effects/genetics/growth & development/*isolation & purification/metabolism/ultrastructure, Sequence Alignment, Sequence Homology, Nucleic Acid, Species Specificity, Temperature, *Water Microbiology | Genetics |
| Phylogeny | 27246498 | Nitropelagius marinus gen. nov., sp. nov., Isolated From Seawater, Je-bu island, South Korea [corrected]. | Jeong SH, Lee SS | Curr Microbiol | 10.1007/s00284-016-1069-x | 2016 | Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Islands, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/classification/genetics/*isolation & purification/metabolism, Seawater/*microbiology | Metabolism |
| Phylogeny | 31647402 | Pelagicola marinus sp. nov. isolated from deep-sea water. | Choi YS, Oh JS, Roh DH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003764 | 2019 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 31702535 | Roseovarius spongiae sp. nov., a bacterium isolated from marine sponge. | Zhuang L, Luo L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003750 | 2020 | Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 36268866 | Roseovarius carneus sp. nov., a novel bacterium isolated from a coastal phytoplankton bloom in Xiamen. | Sun X, Lin D, Han Y, Sun J, Ye J, Chen B, Tang K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005577 | 2022 | RNA, Ribosomal, 16S/genetics, *Phosphatidylethanolamines, Catalase/genetics, Phylogeny, Ubiquinone/chemistry, Phytoplankton, Sodium Chloride, Base Composition, DNA, Bacterial/genetics, Bacterial Typing Techniques, Fatty Acids/chemistry, Sequence Analysis, DNA, *Rhodobacteraceae, Phospholipids/chemistry, Glycolipids, Phosphatidylglycerols, Nucleotides | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 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 | |
| 67612 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-110551 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 110551) | |
| 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 | |
| 112929 | 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-ID390810.1 |