Strain identifier
BacDive ID: 134053
Type strain: 
Species: Nibrella saemangeumensis
Strain Designation: GCR0103
Strain history: K. Y. Jahng GCR0103.
NCBI tax ID(s): 1084526 (species)
version 9 (current version)
General
@ref: 31145
BacDive-ID: 134053
keywords: 16S sequence, Bacteria, Gram-negative, rod-shaped
description: Nibrella saemangeumensis GCR0103 is a Gram-negative, rod-shaped bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 1084526
- Matching level: species
strain history
- @ref: 67770
- history: K. Y. Jahng GCR0103.
doi: 10.13145/bacdive134053.20240510.9
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Spirosomataceae
- genus: Nibrella
- species: Nibrella saemangeumensis
- full scientific name: Nibrella saemangeumensis Kang et al. 2013
@ref: 31145
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Cytophagaceae
genus: Nibrella
species: Nibrella saemangeumensis
strain designation: GCR0103
type strain: yes
Morphology
cell morphology
- @ref: 31145
- gram stain: negative
- cell length: 7.3 µm
- cell width: 1.15 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 31145
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 31145 | positive | growth | 15-37 |
| 31145 | positive | optimum | 25 |
| 67770 | positive | growth | 25 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31145 | positive | growth | 6.5-10.0 | alkaliphile |
| 31145 | positive | optimum | 7.5 |
Physiology and metabolism
halophily
- @ref: 31145
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-0.4 %
observation
- @ref: 31145
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31145 | 21217 | L-alaninamide | + | carbon source |
| 31145 | 16449 | alanine | + | carbon source |
| 31145 | 22599 | arabinose | + | carbon source |
| 31145 | 24265 | gluconate | + | carbon source |
| 31145 | 29987 | glutamate | + | carbon source |
| 31145 | 28087 | glycogen | + | carbon source |
| 31145 | 24996 | lactate | + | carbon source |
| 31145 | 25017 | leucine | + | carbon source |
| 31145 | 28053 | melibiose | + | carbon source |
| 31145 | 37657 | methyl D-glucoside | + | carbon source |
| 31145 | 506227 | N-acetylglucosamine | + | carbon source |
| 31145 | 51850 | methyl pyruvate | + | carbon source |
| 31145 | 30031 | succinate | + | carbon source |
| 31145 | 27082 | trehalose | + | carbon source |
| 31145 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31145 | acid phosphatase | + | 3.1.3.2 |
| 31145 | alkaline phosphatase | + | 3.1.3.1 |
| 31145 | alpha-galactosidase | + | 3.2.1.22 |
| 31145 | catalase | + | 1.11.1.6 |
| 31145 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 31145 | seawater | |||
| 67770 | Seawater of the Saemangeum Embankment in Jeollabuk-do | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_58833.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15841;96_26008;97_32633;98_41860;99_58833&stattab=map
- Last taxonomy: Nibrella saemangeumensis subclade
- 16S sequence: JN607159
- Sequence Identity:
- Total samples: 1545
- soil counts: 790
- aquatic counts: 308
- animal counts: 326
- plant counts: 121
Sequence information
16S sequences
- @ref: 31145
- description: Nibrella saemangeumensis strain GCR0103 16S ribosomal RNA gene, partial sequence
- accession: JN607159
- length: 1343
- database: nuccore
- NCBI tax ID: 1084526
GC content
- @ref: 31145
- GC-content: 56
External links
@ref: 31145
culture collection no.: KACC 16453, JCM 17927
literature
- topic: Phylogeny
- Pubmed-ID: 23907222
- title: Nibrella saemangeumensis gen. nov., sp. nov. and Nibrella viscosa sp. nov., novel members of the family Cytophagaceae, isolated from seawater.
- authors: Kang JY, Chun J, Choi A, Cho JC, Jahng KY
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.053439-0
- year: 2013
- mesh: Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Spermidine/chemistry, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
Reference
| @id | authors | title | doi/url | ID_cross_reference | 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 | ||
| 31145 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27473 | 28776041 |
| 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/ |