Strain identifier
BacDive ID: 14279
Type strain: 
Species: Parasphingorhabdus flavimaris
Strain Designation: SW-151
Strain history: <- JH Yoon, KRIBB
NCBI tax ID(s): 266812 (species)
version 9.1 (current version)
General
@ref: 6338
BacDive-ID: 14279
DSM-Number: 16223
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative
description: Parasphingorhabdus flavimaris SW-151 is an aerobe, Gram-negative bacterium that was isolated from sea water.
NCBI tax id
- NCBI tax id: 266812
- Matching level: species
strain history
| @ref | history |
|---|---|
| 6338 | <- J.-H. Yoon; SW-151 |
| 67771 | <- JH Yoon, KRIBB |
doi: 10.13145/bacdive14279.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Parasphingorhabdus
- species: Parasphingorhabdus flavimaris
- full scientific name: Parasphingorhabdus flavimaris (Yoon and Oh 2005) Feng et al. 2020
synonyms
@ref synonym 20215 Sphingopyxis flavimaris 20215 Sphingorhabdus flavimaris
@ref: 6338
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingorhabdus
species: Sphingorhabdus flavimaris
full scientific name: Sphingorhabdus flavimaris (Yoon and Oh 2005) Jogler et al. 2013
strain designation: SW-151
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 67771 | negative | |
| 69480 | negative | 96.463 |
Culture and growth conditions
culture medium
- @ref: 6338
- name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514c
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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 |
|---|---|---|---|
| 6338 | positive | growth | 30 |
| 67771 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
observation
- @ref: 67771
- observation: quinones: Q-10
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 6338 | sea water | Yellow Sea, Baekryung Island | Republic of Korea | KOR | Asia |
| 67771 | From seawater | the west sea | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_6261.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_1750;97_2092;98_4640;99_6261&stattab=map
- Last taxonomy: Sphingomonadaceae
- 16S sequence: AY554010
- Sequence Identity:
- Total samples: 7031
- soil counts: 436
- aquatic counts: 6142
- animal counts: 308
- plant counts: 145
Safety information
risk assessment
- @ref: 6338
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6338
- description: Sphingopyxis flavimaris strain SW-151 16S ribosomal RNA gene, partial sequence
- accession: AY554010
- length: 1444
- database: nuccore
- NCBI tax ID: 266812
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Parasphingorhabdus flavimaris SW-151 | GCA_013371215 | contig | ncbi | 266812 |
| 66792 | Parasphingorhabdus flavimaris strain SW-151 | 266812.13 | wgs | patric | 266812 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 6338 | 57.8 | high performance liquid chromatography (HPLC) |
| 67771 | 58.0 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.463 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.04 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.649 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 86.478 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 96.057 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 62.699 | no |
External links
@ref: 6338
culture collection no.: DSM 16223, KCTC 12232
straininfo link
- @ref: 83434
- straininfo: 135125
literature
- topic: Phylogeny
- Pubmed-ID: 33993373
- title: Parasphingorhabdus halotolerans sp. nov. isolated from marine sediment in Jeju Island.
- authors: Kim SJ, Kim M, Lee KE, Cha IT, Park SJ
- journal: Arch Microbiol
- DOI: 10.1007/s00203-021-02366-8
- year: 2021
- mesh: Adenoma, Islet Cell, Fatty Acids/analysis, *Geologic Sediments/microbiology, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Species Specificity, *Sphingomonadaceae/classification/genetics
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 6338 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16223) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16223 | |
| 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 | |
| 83434 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID135125.1 | StrainInfo: A central database for resolving microbial strain identifiers |