Strain identifier
BacDive ID: 140815
Type strain:
Species: Tsuneonella rigui
Strain Designation: WW3
Strain history: <- C.N. Seong, Sunchon National Univ..
NCBI tax ID(s): 1708790 (species)
General
@ref: 43603
BacDive-ID: 140815
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming
description: Tsuneonella rigui WW3 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from freshwater of Woopo wetland.
NCBI tax id
- NCBI tax id: 1708790
- Matching level: species
strain history
@ref | history |
---|---|
67770 | C. N. Seong; Sunchon Natl. Univ., South Korea; WW3. |
67771 | <- C.N. Seong, Sunchon National Univ.. |
doi: 10.13145/bacdive140815.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Erythrobacteraceae
- genus: Tsuneonella
- species: Tsuneonella rigui
- full scientific name: Tsuneonella rigui (Kang et al. 2016) Xu et al. 2020
synonyms
- @ref: 20215
- synonym: Altererythrobacter rigui
@ref: 43603
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Erythrobacteraceae
genus: Altererythrobacter
species: Altererythrobacter rigui
strain designation: WW3
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
43603 | negative | 0.58-0.63 µm | 0.42-0.58 µm | rod-shaped | no | |
69480 | negative | 99.987 |
colony morphology
- @ref: 43603
- colony size: 1-2 mm
- colony color: Yellow
- colony shape: circular
- incubation period: 3 days
- medium used: R2A agar
Culture and growth conditions
culture medium
@ref | name | growth |
---|---|---|
43603 | Marine agar (MA) | no |
43603 | Nutrient agar (NA) | yes |
43603 | PCA | yes |
43603 | Reasoner's 2A agar (R2A) | yes |
43603 | Trypticase Soy Agar (TSA) | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43603 | positive | growth | 4-37 | |
43603 | positive | optimum | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
67771 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43603 | positive | growth | 6-9 | alkaliphile |
43603 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
43603 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.995 |
halophily
@ref | salt | growth | tested relation | concentration | halophily level |
---|---|---|---|---|---|
43603 | NaCl | positive | growth | 0-3 %(w/v) | |
43603 | NaCl | positive | optimum | 0 %(w/v) | non-halophilic |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43603 | 27689 | decanoate | - | assimilation |
43603 | 16947 | citrate | - | assimilation |
43603 | 24265 | gluconate | - | assimilation |
43603 | 17234 | glucose | - | assimilation |
43603 | 29864 | mannitol | - | assimilation |
43603 | 37684 | mannose | - | assimilation |
43603 | 506227 | N-acetylglucosamine | - | assimilation |
43603 | 18401 | phenylacetate | - | assimilation |
43603 | 28757 | fructose | - | builds acid from |
43603 | 28260 | galactose | - | builds acid from |
43603 | 17234 | glucose | - | builds acid from |
43603 | 17306 | maltose | - | builds acid from |
43603 | 29864 | mannitol | - | builds acid from |
43603 | 37684 | mannose | - | builds acid from |
43603 | 26546 | rhamnose | - | builds acid from |
43603 | 17992 | sucrose | - | builds acid from |
43603 | 27082 | trehalose | - | builds acid from |
43603 | 18222 | xylose | - | builds acid from |
43603 | 58187 | alginate | - | hydrolysis |
43603 | 85146 | carboxymethylcellulose | - | hydrolysis |
43603 | casein | - | hydrolysis | |
43603 | 17029 | chitin | - | hydrolysis |
43603 | 5291 | gelatin | - | hydrolysis |
43603 | 17368 | hypoxanthine | - | hydrolysis |
43603 | 53311 | sodium alginate | - | hydrolysis |
43603 | 28017 | starch | - | hydrolysis |
43603 | 53424 | tween 20 | - | hydrolysis |
43603 | 18186 | tyrosine | - | hydrolysis |
43603 | 16199 | urea | - | hydrolysis |
43603 | 15318 | xanthine | - | hydrolysis |
43603 | 37166 | xylan | - | hydrolysis |
43603 | 17128 | adipate | + | assimilation |
43603 | 22599 | arabinose | + | assimilation |
43603 | 25115 | malate | + | assimilation |
43603 | 32032 | potassium gluconate | + | assimilation |
43603 | 17716 | lactose | + | builds acid from |
43603 | 53426 | tween 80 | + | hydrolysis |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | is resistant | resistance conc. |
---|---|---|---|---|---|---|---|
43603 | 28971 | ampicillin | yes | yes | 10 µg (disc) | ||
43603 | 2637 | amikacin | yes | yes | 30 µg (disc) | ||
43603 | 17698 | chloramphenicol | yes | yes | 30 µg (disc) | ||
43603 | 17833 | gentamicin | yes | yes | 10 µg (disc) | ||
43603 | 6104 | kanamycin | yes | yes | 30 µg (disc) | ||
43603 | 27902 | tetracycline | yes | yes | 30 µg (disc) | ||
43603 | 28001 | vancomycin | yes | yes | 30 µg (disc) | ||
43603 | 17334 | penicillin | yes | yes | 10 Unit (disc) | ||
43603 | 48923 | erythromycin | yes | yes | 15 µg (disc) | ||
43603 | 100147 | nalidixic acid | yes | yes | 30 µg (disc) | ||
43603 | 17076 | streptomycin | yes | yes | 10 µg (disc) | ||
43603 | 8309 | polymyxin b | yes | yes | 300 Unit (disc) |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43603 | 16136 | hydrogen sulfide | no |
43603 | 35581 | indole | no |
43603 | 17632 | nitrate | yes |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43603 | catalase | + | 1.11.1.6 |
43603 | acid phosphatase | + | 3.1.3.2 |
43603 | alkaline phosphatase | + | 3.1.3.1 |
43603 | esterase (C 4) | + | |
43603 | esterase Lipase (C 8) | + | |
43603 | leucine arylamidase | + | 3.4.11.1 |
43603 | valine arylamidase | + | |
43603 | naphthol-AS-BI-phosphohydrolase | + | |
43603 | alpha-chymotrypsin | + | 3.4.21.1 |
43603 | cytochrome oxidase | - | 1.9.3.1 |
43603 | cystine arylamidase | - | 3.4.11.3 |
43603 | alpha-galactosidase | - | 3.2.1.22 |
43603 | beta-galactosidase | - | 3.2.1.23 |
43603 | alpha-glucosidase | - | 3.2.1.20 |
43603 | beta-glucosidase | - | 3.2.1.21 |
43603 | beta-glucuronidase | - | 3.2.1.31 |
43603 | lipase (C 14) | - | |
43603 | alpha-mannosidase | - | 3.2.1.24 |
43603 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
43603 | trypsin | - | 3.4.21.4 |
43603 | alpha-fucosidase | - | 3.2.1.51 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
43603 | freshwater of Woopo wetland | Woopo wetland, Changnyeong county | Republic of Korea | KOR | Asia | 35.55 | 128.416 |
67770 | Freshwater of Woopo wetland | Republic of Korea | KOR | Asia | |||
67771 | From freshwater | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Freshwater |
#Environmental | #Terrestrial | #Wetland (Swamp) |
taxonmaps
- @ref: 69479
- File name: preview.99_21384.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_543;97_13101;98_16124;99_21384&stattab=map
- Last taxonomy: Erythrobacteraceae
- 16S sequence: KP997219
- Sequence Identity:
- Total samples: 1706
- soil counts: 456
- aquatic counts: 834
- animal counts: 152
- plant counts: 264
Sequence information
16S sequences
- @ref: 43603
- description: 16S rRNA gene sequence
- accession: KP997219
- database: nuccore
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Altererythrobacter rigui strain KCTC 42620 | 1708790.3 | wgs | patric | 1708790 |
66792 | Tsuneonella rigui KCTC 42620 | 2880984762 | draft | img | 1708790 |
67770 | Tsuneonella rigui KCTC 42620 | GCA_003958625 | contig | ncbi | 1708790 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 63 | thermal denaturation, midpoint method (Tm) |
67770 | 66.7 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 87.41 | yes |
gram-positive | no | 98.141 | no |
anaerobic | no | 99.197 | no |
aerobic | yes | 89.817 | yes |
halophile | no | 93.792 | yes |
spore-forming | no | 94.374 | no |
thermophile | no | 96.336 | yes |
glucose-util | yes | 72.507 | yes |
flagellated | no | 97.092 | no |
glucose-ferment | no | 90.765 | no |
External links
@ref: 43603
culture collection no.: KCTC 42620, JCM 30975
Reference
@id | authors | title | doi/url | 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 | ||
43603 | Joo Won Kang, Mi Sun Kim, Ji Hee Lee, Keun Sik Baik, Chi Nam Seong | Altererythrobacter rigui sp. nov., isolated from wetland freshwater | 10.1099/ijsem.0.001078 | IJSEM 66: 2491-2496 2016 | 27073894 |
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 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||
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 |