Strain identifier
BacDive ID: 24738
Type strain: 
Species: Sediminibacterium goheungense
Strain history: <- CECT 8100 <- K. Joh, Dept. Biosci. and Biotechnology, Hankuk Univ. of Foreign Studies, Yongin, Republic of Korea; HME7863 <- K. Joh and Y. C. Joung
NCBI tax ID(s): 1086393 (species)
version 9.1 (current version)
General
@ref: 21190
BacDive-ID: 24738
DSM-Number: 28323
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Sediminibacterium goheungense DSM 28323 is a Gram-negative bacterium that was isolated from freshwater reservoir water.
NCBI tax id
- NCBI tax id: 1086393
- Matching level: species
strain history
- @ref: 21190
- history: <- CECT 8100 <- K. Joh, Dept. Biosci. and Biotechnology, Hankuk Univ. of Foreign Studies, Yongin, Republic of Korea; HME7863 <- K. Joh and Y. C. Joung
doi: 10.13145/bacdive24738.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Chitinophagia
- order: Chitinophagales
- family: Chitinophagaceae
- genus: Sediminibacterium
- species: Sediminibacterium goheungense
- full scientific name: Sediminibacterium goheungense Kang et al. 2014
@ref: 21190
domain: Bacteria
phylum: Bacteroidetes
class: Chitinophagia
order: Sphingobacteriales
family: Chitinophagaceae
genus: Sediminibacterium
species: Sediminibacterium goheungense
full scientific name: Sediminibacterium goheungense Kang et al. 2014
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 90.297
colony morphology
- @ref: 21190
- incubation period: 1-2 days
Culture and growth conditions
culture medium
- @ref: 21190
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
- @ref: 21190
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 92.136 |
| 69481 | no | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 21190
- sample type: freshwater reservoir water
- geographic location: Goheung (34° 35' 31'' N 127° 19' 11'' E)
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
- latitude: 34.5919
- longitude: 127.32
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Built environment | #Water reservoir (Aquarium/pool) |
| #Environmental | #Aquatic | #Freshwater |
taxonmaps
- @ref: 69479
- File name: preview.99_11859.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_185;96_5998;97_7215;98_8906;99_11859&stattab=map
- Last taxonomy: Sediminibacterium goheungense subclade
- 16S sequence: JN674641
- Sequence Identity:
- Total samples: 54892
- soil counts: 17026
- aquatic counts: 27764
- animal counts: 6002
- plant counts: 4100
Safety information
risk assessment
- @ref: 21190
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21190
- description: Sediminibacterium goheungense strain HME7863 from South Korea 16S ribosomal RNA gene, partial sequence
- accession: JN674641
- length: 1390
- database: nuccore
- NCBI tax ID: 1086393
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sediminibacterium goheungense DSM 28323 | GCA_004361915 | contig | ncbi | 1086393 |
| 66792 | Sediminibacterium goheungense strain DSM 28323 | 1086393.3 | wgs | patric | 1086393 |
| 66792 | Sediminibacterium goheungense DSM 28323 | 2695421017 | draft | img | 1086393 |
GC content
- @ref: 21190
- GC-content: 40.5
- method: fluorimetric
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 | 90.297 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.631 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 92.136 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 88.804 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 94.501 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 89.25 | no |
External links
@ref: 21190
culture collection no.: DSM 28323, CECT 8100, KCTC 23945, HME 7863
straininfo link
- @ref: 88566
- straininfo: 393353
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24425738 | Sediminibacterium goheungense sp. nov., isolated from a freshwater reservoir. | Kang H, Kim H, Lee BI, Joung Y, Joh K | Int J Syst Evol Microbiol | 10.1099/ijs.0.055137-0 | 2014 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 27412118 | Filimonas aurantiibacter sp. nov., an orange-pigmented bacterium isolated from lake water and emended description of the genus Filimonas. | Albert RA, Waas NE, Pavlons SC, Pearson JL, Roecker J, Tewalt N, Cleeve N, Rossello-Mora R, Busse HJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001305 | 2016 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Michigan, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 33104819 | Sediminibacterium soli sp. nov., isolated from soil. | Wu S, Zhong L, Liao S, Li T, Zhou Z, Wang G | Arch Microbiol | 10.1007/s00203-020-02089-2 | 2020 | Bacteroidetes/*classification/genetics, Base Composition, Fatty Acids/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity | Transcriptome |
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 | |||
| 21190 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28323 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28323) | |||
| 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 | |||
| 88566 | 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-ID393353.1 |