@ref: 7753
BacDive-ID: 17518
DSM-Number: 18863
keywords: genome sequence, 16S sequence, aerobe, mesophilic, Gram-negative, rod-shaped
description: Rhodanobacter thiooxydans LCS2 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from biofilm.
| @ref | history |
|---|---|
| 7753 | <- S.-T. Lee <- C. S. Lee; LCS2 |
| 67771 | <- ST Lee, KAIST |
doi: 10.13145/bacdive17518.20251217.10
@ref: 7753
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Rhodanobacteraceae
genus: Rhodanobacter
species: Rhodanobacter thiooxydans
full scientific name: Rhodanobacter thiooxydans Lee et al. 2007
strain designation: LCS2
type strain: yes
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32181 | negative | 2.25 µm | 0.7 µm | rod-shaped | no | |
| 67771 | negative | |||||
| 125438 | negative | 94.494 | ||||
| 125439 | negative | 99.1 |
| @ref | growth | type | temperature |
|---|---|---|---|
| 7753 | positive | growth | 28 |
| 32181 | positive | growth | 05-40 |
| 32181 | positive | optimum | 30 |
| 67771 | positive | growth | 25 |
| @ref | ability | type | pH |
|---|---|---|---|
| 32181 | positive | growth | 05-08 |
| 32181 | positive | optimum | 7.5 |
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 32181 | aerobe | |
| 67771 | aerobe | |
| 125439 | obligate aerobe | 99.6 |
| @ref | spore formation | confidence |
|---|---|---|
| 32181 | no | |
| 125439 | no | 98.3 |
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32181 | NaCl | positive | growth | 01-02 % |
| 32181 | NaCl | positive | optimum | 1.5 % |
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32181 | 33984 | fucose | + | carbon source |
| 32181 | 17234 | glucose | + | carbon source |
| 32181 | 28087 | glycogen | + | carbon source |
| 32181 | 17306 | maltose | + | carbon source |
| 32181 | 506227 | N-acetylglucosamine | + | carbon source |
| 32181 | 33942 | ribose | + | carbon source |
| 32181 | 31011 | valerate | + | carbon source |
| 32181 | 4853 | esculin | + | hydrolysis |
| 32181 | 17632 | nitrate | + | reduction |
| @ref | value | activity | ec |
|---|---|---|---|
| 32181 | catalase | + | 1.11.1.6 |
| 32181 | gelatinase | + | |
| 32181 | cytochrome oxidase | + | 1.9.3.1 |
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 7753 | biofilm | Daejon | Republic of Korea | KOR | Asia |
| 67771 | From waste water | Republic of Korea | KOR | Asia |
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 99.6 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.1 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 85.5 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.3 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 94.494 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.175 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.726 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 83.233 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 95.5 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 58.739 | no |
@ref: 7753
culture collection no.: DSM 18863, KCTC 12771
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17684255 | Rhodanobacter thiooxydans sp. nov., isolated from a biofilm on sulfur particles used in an autotrophic denitrification process. | Lee CS, Kim KK, Aslam Z, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.65086-0 | 2007 | Autotrophic Processes, Biofilms/*classification, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, Sulfur/*metabolism, Xanthomonadaceae/chemistry/*classification/*isolation & purification/physiology | Genetics |
| Metabolism | 22843592 | Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities. | Kostka JE, Green SJ, Rishishwar L, Prakash O, Katz LS, Marino-Ramirez L, Jordan IK, Munk C, Ivanova N, Mikhailova N, Watson DB, Brown SD, Palumbo AV, Brooks SC. | J Bacteriol | 10.1128/jb.00871-12 | 2012 | genetics, metabolism, genetics, chemistry, Sequence Analysis, DNA, Genome, Bacterial | Transcriptome |
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 7753 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18863) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18863 | |||
| 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 | |||
| 32181 | 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 | 28423 | 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) | |||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | |||
| 126262 | A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer | 10.1093/database/baaf059 | StrainInfo—the central database for linked microbial strain identifiers |
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