Strain identifier
BacDive ID: 130332
Type strain: 
Species: Lutibacter oricola
Strain Designation: UDC377
Strain history: <- SY Ghim, Kyungpook Natl. Univ.
NCBI tax ID(s): 762486 (species)
version 8.1 (current version)
General
@ref: 21992
BacDive-ID: 130332
DSM-Number: 24956
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, rod-shaped
description: Lutibacter oricola UDC377 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from coastal sea water.
NCBI tax id
- NCBI tax id: 762486
- Matching level: species
strain history
| @ref | history |
|---|---|
| 21992 | <- S.-Y. Ghim, Kyungpook Natl. Univ., Daegu, South Korea; UDC377 |
| 67771 | <- SY Ghim, Kyungpook Natl. Univ. |
doi: 10.13145/bacdive130332.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Lutibacter
- species: Lutibacter oricola
- full scientific name: Lutibacter oricola Sung et al. 2015
@ref: 21992
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Lutibacter
species: Lutibacter oricola
full scientific name: Lutibacter oricola Sung et al. 2015
strain designation: UDC377
type strain: yes
Morphology
cell morphology
| @ref | cell shape | gram stain | confidence |
|---|---|---|---|
| 67771 | rod-shaped | ||
| 67771 | negative | ||
| 69480 | negative | 99.985 |
Culture and growth conditions
culture medium
- @ref: 21992
- 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 | range |
|---|---|---|---|---|
| 21992 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 25-28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 67771 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.986 |
observation
- @ref: 67771
- observation: quinones: MK-6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 21992 | coastal sea water | East Sea at Seo-do on the coast of Dokdo island (37° 14' 30.6'' N 131° 5' 54.6'' E) | Republic of Korea | KOR | Asia | 37.2418 | 131.098 |
| 67771 | From seawater | Dokdo | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_107196.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_333;96_24434;97_55062;98_72861;99_107196&stattab=map
- Last taxonomy: Lutibacter oricola subclade
- 16S sequence: HM031972
- Sequence Identity:
- Total samples: 49
- soil counts: 2
- aquatic counts: 45
- plant counts: 2
Safety information
risk assessment
- @ref: 21992
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21992
- description: Lutibacter oricola strain UDC377 16S ribosomal RNA gene, partial sequence
- accession: HM031972
- length: 1395
- database: ena
- NCBI tax ID: 762486
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Lutibacter oricola DSM 24956 | GCA_900106565 | contig | ncbi | 762486 |
| 66792 | Lutibacter oricola strain DSM 24956 | 762486.3 | wgs | patric | 762486 |
| 66792 | Lutibacter oricola DSM 24956 | 2693429896 | draft | img | 762486 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 21992 | 30.8 | high performance liquid chromatography (HPLC) |
| 67771 | 30.8 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 90.575 | no |
| flagellated | no | 96.521 | no |
| gram-positive | no | 97.867 | yes |
| anaerobic | no | 96.763 | no |
| aerobic | yes | 73.735 | yes |
| halophile | no | 87.351 | no |
| spore-forming | no | 95.394 | yes |
| glucose-util | yes | 80.71 | no |
| thermophile | no | 97.292 | yes |
| glucose-ferment | no | 85.668 | no |
External links
@ref: 21992
culture collection no.: DSM 24956, KCTC 23668
straininfo link
- @ref: 88865
- straininfo: 402351
literature
- topic: Phylogeny
- Pubmed-ID: 25389150
- title: Lutibacter oricola sp. nov., a marine bacterium isolated from seawater.
- authors: Sung HR, Shin KS, Ghim SY
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.067132-0
- year: 2014
- mesh: Bacterial Typing Techniques, Base Composition, Carotenoids/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
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 | |||
| 21992 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24956 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24956) | |||
| 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 | |
| 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. | 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 | |||
| 88865 | 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-ID402351.1 |