Strain identifier
BacDive ID: 162356
Type strain: 
Species: Halococcus sediminicola
Strain history: S. W. Roh; Korea Basic Sci. Inst., South Korea; CBA1101.
NCBI tax ID(s): 1264579 (species)
version 9.1 (current version)
General
@ref: 67770
BacDive-ID: 162356
keywords: genome sequence, 16S sequence, Archaea, Gram-negative
description: Halococcus sediminicola JCM 18965 is a Gram-negative archaeon that was isolated from Marine sediment from the bay of Gangjin.
NCBI tax id
- NCBI tax id: 1264579
- Matching level: species
strain history
- @ref: 67770
- history: S. W. Roh; Korea Basic Sci. Inst., South Korea; CBA1101.
doi: 10.13145/bacdive162356.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Halobacteriales
- family: Halococcaceae
- genus: Halococcus
- species: Halococcus sediminicola
- full scientific name: Halococcus sediminicola Yim et al. 2014
@ref: 67770
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Halococcaceae
genus: Halococcus
species: Halococcus sediminicola
full scientific name: Halococcus sediminicola Yim et al. 2014
type strain: yes
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 37
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Marine sediment from the bay of Gangjin
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
taxonmaps
- @ref: 69479
- File name: preview.99_189302.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17821;96_69656;97_90465;98_122958;99_189302&stattab=map
- Last taxonomy: Halococcus sediminicola
- 16S sequence: JX989265
- Sequence Identity:
- Total samples: 1
- aquatic counts: 1
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 67770 | Halococcus sediminicola strain CBA1101 from South Korea 16S ribosomal RNA gene, partial sequence | JX989265 | 1406 | nuccore | 1264579 |
| 124043 | Halococcus sediminicola gene for 16S ribosomal RNA, partial sequence, strain: JCM 18965. | AB935407 | 1474 | nuccore | 1264579 |
Genome sequences
- @ref: 67770
- description: Halococcus sediminicola CBA1101
- accession: GCA_000755245
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1264579
GC content
- @ref: 67770
- GC-content: 66
- 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 | 71.576 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 85.744 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 83.043 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 82.124 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 86.532 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 87.5 | no |
External links
@ref: 67770
culture collection no.: JCM 18965, CECT 8275
straininfo link
- @ref: 113493
- straininfo: 394018
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24132728 | Halococcus sediminicola sp. nov., an extremely halophilic archaeon isolated from a marine sediment. | Yim KJ, Cha IT, Whon TW, Lee HW, Song HS, Kim KN, Nam YD, Lee SJ, Bae JW, Rhee SK, Choi JS, Seo MJ, Roh SW, Kim D | Antonie Van Leeuwenhoek | 10.1007/s10482-013-0054-7 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Geologic Sediments/*microbiology, Halococcus/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/metabolism | Metabolism |
| Genetics | 25468064 | Draft genome sequence of the extremely halophilic archaeon Halococcus sediminicola CBA1101(T) isolated from a marine sediment sample. | Yim KJ, Kim BY, Lee HW, Song HS, Nam YD, Choi JS, Choi HJ, Seo MJ, Yoon C, Kim KN, Kim D, Rhee JK, Roh SW | Mar Genomics | 10.1016/j.margen.2014.10.003 | 2014 | Phylogeny |
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 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 |
| 113493 | 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-ID394018.1 |
| 124043 | Dr. Isabel Schober, Dr. Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy |