Strain identifier
BacDive ID: 3766
Type strain:
Species: Arcicella aurantiaca
Strain Designation: TNR-18
Strain history: <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen; TNR-18
NCBI tax ID(s): 591202 (species)
General
@ref: 16206
BacDive-ID: 3766
DSM-Number: 22214
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Arcicella aurantiaca TNR-18 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from stream water.
NCBI tax id
- NCBI tax id: 591202
- Matching level: species
strain history
- @ref: 16206
- history: <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen; TNR-18
doi: 10.13145/bacdive3766.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Spirosomataceae
- genus: Arcicella
- species: Arcicella aurantiaca
- full scientific name: Arcicella aurantiaca Sheu et al. 2010
@ref: 16206
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Spirosomaceae
genus: Arcicella
species: Arcicella aurantiaca
full scientific name: Arcicella aurantiaca Sheu et al. 2010 emend. Chen et al. 2013
strain designation: TNR-18
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29806 | negative | 01-03 µm | 0.5-0.6 µm | rod-shaped | no | |
69480 | no | 91.192 | ||||
69480 | negative | 99.999 |
pigmentation
- @ref: 29806
- production: yes
Culture and growth conditions
culture medium
- @ref: 16206
- 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 | growth | type | temperature | range |
---|---|---|---|---|
16206 | positive | growth | 28 | mesophilic |
29806 | positive | growth | 10-30 | |
29806 | positive | optimum | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29806 | positive | growth | 06-10 | alkaliphile |
29806 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29806
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
29806 | no | |
69481 | no | 100 |
69480 | no | 99.994 |
halophily
- @ref: 29806
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-0.2 %
observation
- @ref: 29806
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29806 | 16449 | alanine | + | carbon source |
29806 | 35391 | aspartate | + | carbon source |
29806 | 17057 | cellobiose | + | carbon source |
29806 | 23652 | dextrin | + | carbon source |
29806 | 28757 | fructose | + | carbon source |
29806 | 33984 | fucose | + | carbon source |
29806 | 28260 | galactose | + | carbon source |
29806 | 17234 | glucose | + | carbon source |
29806 | 29987 | glutamate | + | carbon source |
29806 | 28087 | glycogen | + | carbon source |
29806 | 17716 | lactose | + | carbon source |
29806 | 17306 | maltose | + | carbon source |
29806 | 37684 | mannose | + | carbon source |
29806 | 28053 | melibiose | + | carbon source |
29806 | 51850 | methyl pyruvate | + | carbon source |
29806 | 16634 | raffinose | + | carbon source |
29806 | 26546 | rhamnose | + | carbon source |
29806 | 17822 | serine | + | carbon source |
29806 | 30911 | sorbitol | + | carbon source |
29806 | 17992 | sucrose | + | carbon source |
29806 | 27082 | trehalose | + | carbon source |
29806 | 4853 | esculin | + | hydrolysis |
29806 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29806 | catalase | + | 1.11.1.6 |
29806 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 16206
- sample type: stream water
- geographic location: Kaohsiung Prefecture
- country: Taiwan
- origin.country: TWN
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #River (Creek)
taxonmaps
- @ref: 69479
- File name: preview.99_174211.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_200;96_14607;97_22353;98_114058;99_174211&stattab=map
- Last taxonomy: Arcicella aurantiaca subclade
- 16S sequence: FJ593908
- Sequence Identity:
- Total samples: 45
- aquatic counts: 41
- plant counts: 4
Safety information
risk assessment
- @ref: 16206
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16206
- description: Arcicella aurantiaca 16S ribosomal RNA gene, partial sequence
- accession: FJ593908
- length: 1411
- database: ena
- NCBI tax ID: 591202
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Arcicella aurantiaca DSM 22214 | GCA_003148625 | scaffold | ncbi | 591202 |
66792 | Arcicella aurantiaca strain DSM 22214 | 591202.3 | wgs | patric | 591202 |
66792 | Arcicella aurantiaca DSM 22214 | 2595698202 | draft | img | 591202 |
GC content
@ref | GC-content | method |
---|---|---|
16206 | 39.9 | high performance liquid chromatography (HPLC) |
29806 | 39.9 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 96.938 | yes |
gram-positive | no | 98.006 | yes |
anaerobic | no | 99.343 | yes |
halophile | no | 96.432 | yes |
spore-forming | no | 95.154 | yes |
glucose-util | yes | 86.404 | yes |
aerobic | yes | 90.22 | yes |
thermophile | no | 98.249 | no |
motile | no | 93.414 | yes |
glucose-ferment | no | 89.21 | no |
External links
@ref: 16206
culture collection no.: DSM 22214, BCRC 17969, LMG 25207
straininfo link
- @ref: 73278
- straininfo: 360697
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20118286 | Arcicella aurantiaca sp. nov., isolated from stream water. | Sheu SY, Yang CS, Chen MH, Arun AB, Young CC, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.021527-0 | 2010 | Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistry, Water Microbiology | Genetics |
Phylogeny | 22368167 | Arcicella rigui sp. nov., isolated from water of a wetland, and emended descriptions of the genus Arcicella, Arcicella aquatica, Arcicella rosea and Arcicella aurantiaca. | Chen WM, Yang SH, Young CC, Sheu SY | Int J Syst Evol Microbiol | 10.1099/ijs.0.037242-0 | 2012 | Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, *Water Microbiology, Wetlands | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
16206 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22214) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22214 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
29806 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26183 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
73278 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID360697.1 | StrainInfo: A central database for resolving microbial strain identifiers |