Strain identifier

BacDive ID: 17518

Type strain: Yes

Species: Rhodanobacter thiooxydans

Strain Designation: LCS2

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 416169 (species)

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General

@ref: 7753

BacDive-ID: 17518

DSM-Number: 18863

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Rhodanobacter thiooxydans LCS2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from biofilm.

NCBI tax id

  • NCBI tax id: 416169
  • Matching level: species

strain history

@refhistory
7753<- S.-T. Lee <- C. S. Lee; LCS2
67771<- ST Lee, KAIST

doi: 10.13145/bacdive17518.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Rhodanobacteraceae
  • genus: Rhodanobacter
  • species: Rhodanobacter thiooxydans
  • full scientific name: Rhodanobacter thiooxydans Lee et al. 2007

@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

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32181negative2.25 µm0.7 µmrod-shapedno
67771negative
125438negative94.494
125439negative99.1

pigmentation

  • @ref: 32181
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7753
  • 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

@refgrowthtypetemperature
7753positivegrowth28
32181positivegrowth05-40
32181positiveoptimum30
67771positivegrowth25

culture pH

@refabilitytypepH
32181positivegrowth05-08
32181positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
32181aerobe
67771aerobe
125439obligate aerobe99.6

spore formation

@refspore formationconfidence
32181no
125439no98.3

halophily

@refsaltgrowthtested relationconcentration
32181NaClpositivegrowth01-02 %
32181NaClpositiveoptimum1.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3218133984fucose+carbon source
3218117234glucose+carbon source
3218128087glycogen+carbon source
3218117306maltose+carbon source
32181506227N-acetylglucosamine+carbon source
3218133942ribose+carbon source
3218131011valerate+carbon source
321814853esculin+hydrolysis
3218117632nitrate+reduction

enzymes

@refvalueactivityec
32181catalase+1.11.1.6
32181gelatinase+
32181cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7753biofilmDaejonRepublic of KoreaKORAsia
67771From waste waterRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Biofilm

taxonmaps

  • @ref: 69479
  • File name: preview.99_545.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_114;96_316;97_352;98_397;99_545&stattab=map
  • Last taxonomy: Rhodanobacter
  • 16S sequence: AB286179
  • Sequence Identity:
  • Total samples: 3012
  • soil counts: 1614
  • aquatic counts: 515
  • animal counts: 424
  • plant counts: 459

Safety information

risk assessment

  • @ref: 7753
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 32181
  • description: Rhodanobacter thiooxydans gene for 16S rRNA, partial sequence
  • accession: AB286179
  • length: 1482
  • database: nuccore
  • NCBI tax ID: 1163409

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodanobacter thiooxydans LCS2GCA_000264375contigncbi1163409
66792Rhodanobacter thiooxydans LCS21163409.3wgspatric1163409
66792Rhodanobacter thiooxydans LCS22537561839draftimg1163409

GC content

  • @ref: 32181
  • GC-content: 64.6

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.1
125439BacteriaNetmotilityAbility to perform movementyes85.5
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.3
125438gram-positivegram-positivePositive reaction to Gram-stainingno94.494yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.175no
125438spore-formingspore-formingAbility to form endo- or exosporesno87.726no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.233yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes58.739no

External links

@ref: 7753

culture collection no.: DSM 18863, KCTC 12771

straininfo link

  • @ref: 86515
  • straininfo: 397222

literature

  • topic: Phylogeny
  • Pubmed-ID: 17684255
  • title: Rhodanobacter thiooxydans sp. nov., isolated from a biofilm on sulfur particles used in an autotrophic denitrification process.
  • authors: Lee CS, Kim KK, Aslam Z, Lee ST
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65086-0
  • year: 2007
  • mesh: Autotrophic Processes, Biofilms/*classification, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, Sulfur/*metabolism, Xanthomonadaceae/chemistry/*classification/*isolation & purification/physiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7753Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18863)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18863
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32181Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2842328776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João 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
86515Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397222.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1