Strain identifier
BacDive ID: 133798
Type strain: 
Species: Kistimonas scapharcae
Strain Designation: A36
Strain history: J.-W. Bae A36.
NCBI tax ID(s): 1036133 (species)
version 8.1 (current version)
General
@ref: 30546
BacDive-ID: 133798
keywords: 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped
description: Kistimonas scapharcae A36 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from Ark clam.
NCBI tax id
- NCBI tax id: 1036133
- Matching level: species
strain history
- @ref: 67770
- history: J.-W. Bae A36.
doi: 10.13145/bacdive133798.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Oceanospirillales
- family: Endozoicomonadaceae
- genus: Kistimonas
- species: Kistimonas scapharcae
- full scientific name: Kistimonas scapharcae Lee et al. 2012
@ref: 30546
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Endozoicomonadaceae
genus: Kistimonas
species: Kistimonas scapharcae
strain designation: A36
type strain: yes
Morphology
cell morphology
- @ref: 30546
- gram stain: negative
- cell length: 2.25 µm
- cell width: 0.3 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 30546
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 30546 | positive | growth | 10-45 | |
| 30546 | positive | optimum | 33.5 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30546 | positive | growth | 06-10 | alkaliphile |
| 30546 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 30546
- oxygen tolerance: facultative anaerobe
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30546 | NaCl | positive | growth | 0-5 % |
| 30546 | NaCl | positive | optimum | 1 % |
observation
- @ref: 67770
- observation: quinones: Q-9
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30546 | 16449 | alanine | + | carbon source |
| 30546 | 22653 | asparagine | + | carbon source |
| 30546 | 35391 | aspartate | + | carbon source |
| 30546 | 29987 | glutamate | + | carbon source |
| 30546 | 18257 | ornithine | + | carbon source |
| 30546 | 17822 | serine | + | carbon source |
| 30546 | 30031 | succinate | + | carbon source |
| 30546 | 53423 | tween 40 | + | carbon source |
| 30546 | 53426 | tween 80 | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30546 | acid phosphatase | + | 3.1.3.2 |
| 30546 | alkaline phosphatase | + | 3.1.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type |
|---|---|
| 30546 | Ark clam |
| 67770 | Dead ark clam on the south coast of Korea |
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Mollusca
taxonmaps
- @ref: 69479
- File name: preview.99_40317.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_202;96_18815;97_23296;98_29426;99_40317&stattab=map
- Last taxonomy: Kistimonas scapharcae
- 16S sequence: JF811908
- Sequence Identity:
- Total samples: 1353
- soil counts: 96
- aquatic counts: 1106
- animal counts: 130
- plant counts: 21
Sequence information
16S sequences
- @ref: 30546
- description: Kistimonas scapharcae strain A36 16S ribosomal RNA gene, partial sequence
- accession: JF811908
- length: 1473
- database: nuccore
- NCBI tax ID: 1036133
GC content
| @ref | GC-content | method |
|---|---|---|
| 30546 | 47.3 | |
| 67770 | 47.3 | thermal denaturation, midpoint method (Tm) |
External links
@ref: 30546
culture collection no.: KACC 16204, JCM 17805
literature
- topic: Phylogeny
- Pubmed-ID: 22247211
- title: Kistimonas scapharcae sp. nov., isolated from a dead ark clam (Scapharca broughtonii), and emended description of the genus Kistimonas.
- authors: Lee J, Shin NR, Lee HW, Roh SW, Kim MS, Kim YO, Bae JW
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.038422-0
- year: 2012
- mesh: Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Scapharca/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysis
- 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 | ||
| 30546 | 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 | 26877 | 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/ |