Strain identifier

BacDive ID: 132963

Type strain: Yes

Species: Rhabdobacter roseus

Strain Designation: R49

Strain history: J. Kim; Kyonggi Univ., South Korea; R49.

NCBI tax ID(s): 1655419 (species)

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General

@ref: 24751

BacDive-ID: 132963

DSM-Number: 105074

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

description: Rhabdobacter roseus R49 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from soil.

NCBI tax id

  • NCBI tax id: 1655419
  • Matching level: species

strain history

@refhistory
24751<- KACC <- J. Kim, Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, South Korea; R49
67770J. Kim; Kyonggi Univ., South Korea; R49.

doi: 10.13145/bacdive132963.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Rhabdobacter
  • species: Rhabdobacter roseus
  • full scientific name: Rhabdobacter roseus Dahal and Kim 2016

@ref: 24751

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Rhabdobacter

species: Rhabdobacter roseus

full scientific name: Rhabdobacter roseus Dahal and Kim 2016

strain designation: R49

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65205negative2.36-2.76 µm0.82-0.93 µmrod-shapedno
69480no92.022
69480negative99.999

colony morphology

  • @ref: 65205
  • colony size: 1-3 mm
  • colony color: pink
  • colony shape: circular
  • incubation period: 5 days
  • medium used: R2A agar

pigmentation

@refproductionname
65205noflexirubin-type pigments
65205yescarotenoid

multimedia

  • @ref: 24751
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_105074.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24751R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
65205Nutrient agar (NA)yes
65205trypticase soy agaryes
65205sorbitol MacConkey agarno
65205Mueller-Hinton agaryes
65205brain heart infusion agaryes
65205veal infusion agaryes
65205potato dextrose agarno
65205peptone wateryes
65205MRS agarno
65205Reasoner's 2A agar (R2A)yes

culture temp

@refgrowthtypetemperaturerange
24751positivegrowth28mesophilic
65205positivegrowth10-37
65205positiveoptimum25-30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
65205positiveoptimum6.5-8.0
65205positivegrowth5-10alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 65205
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
65205no
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
65205NaClpositiveoptimum0 %
65205NaClpositivegrowth0-5 %

observation

  • @ref: 65205
  • observation: Hydrogen sulphide is not produced as a result of culture in SIM medium.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65205168082-dehydro-D-gluconate-carbon source
652053557154-nitrophenyl beta-D-galactopyranoside+assimilation
65205581435-dehydro-D-gluconate+carbon source
6520517128adipate-assimilation
6520527613amygdalin+assimilation
6520527613amygdalin+carbon source
6520522599arabinose+/-assimilation
6520518305arbutin+carbon source
6520527689decanoate-assimilation
6520517057cellobiose+carbon source
6520516947citrate-assimilation
6520515963ribitol-carbon source
6520518333D-arabitol-carbon source
6520515824D-fructose-carbon source
6520528847D-fucose-carbon source
6520512936D-galactose-carbon source
6520517634D-glucose+carbon source
6520517634D-glucose+/-assimilation
6520562318D-lyxose+carbon source
6520516899D-mannitol-assimilation
6520516899D-mannitol-carbon source
6520516024D-mannose+assimilation
6520516024D-mannose+carbon source
6520516988D-ribose-carbon source
6520517924D-sorbitol-carbon source
6520516443D-tagatose-carbon source
6520565327D-xylose+carbon source
6520516813galactitol-carbon source
6520517113erythritol-carbon source
65205esculin ferric citrate+assimilation
65205esculin ferric citrate+carbon source
652055291gelatin-assimilation
6520528066gentiobiose+carbon source
6520524265gluconate-carbon source
6520517234glucose-fermentation
6520517754glycerol-carbon source
6520528087glycogen-carbon source
6520517268myo-inositol-carbon source
6520515443inulin-carbon source
6520518403L-arabitol-carbon source
6520516467L-arginine-assimilation
6520518287L-fucose+carbon source
6520517266L-sorbose-carbon source
6520516828L-tryptophan-assimilation
6520565328L-xylose-carbon source
6520517716lactose+carbon source
6520525115malate-assimilation
6520517306maltose+assimilation
6520517306maltose+carbon source
6520529864mannitol-assimilation
652056731melezitose-carbon source
6520528053melibiose+/-assimilation
65205320061methyl alpha-D-glucopyranoside+carbon source
6520543943methyl alpha-D-mannoside+carbon source
6520574863methyl beta-D-xylopyranoside-carbon source
6520517268myo-inositol-assimilation
65205506227N-acetylglucosamine+assimilation
65205506227N-acetylglucosamine+carbon source
6520517632nitrate-reduction
6520518401phenylacetate-assimilation
6520532032potassium gluconate-assimilation
6520516634raffinose+carbon source
6520526546rhamnose+/-assimilation
6520517814salicin+carbon source
6520553258sodium citrate-assimilation
6520530911sorbitol-assimilation
6520528017starch-carbon source
6520528017starch-hydrolysis
6520517992sucrose+/-assimilation
6520527082trehalose+carbon source
6520532528turanose-carbon source
6520553423tween 40-hydrolysis
6520553425tween 60-hydrolysis
6520553426tween 80-hydrolysis
6520516199urea-assimilation
6520516199urea-hydrolysis
6520517151xylitol-carbon source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6520517833gentamicinyesyes10 µg (disc)
6520517076streptomycinyesyes10 µg (disc)
6520527902tetracyclineyesyes30 µg (disc)
6520528368novobiocinyesyes30 µg (disc)
652056104kanamycinyesyes30 µg (disc)
652057507neomycinyesyes30 µg (disc)
6520528077rifampicinyesyes30 µg (disc)
65205100147nalidixic acidyesyes30 µg (disc)
6520545924trimethoprimyesyes30 µg (disc)
652059332sulfamethoxazoleyesyes30 µg (disc)
6520517698chloramphenicolyesyes100 µg (disc)
6520528971ampicillinyesyes10 µg (disc)
6520517334penicillinyesyes10 µg (disc)
6520527641cycloheximideyesyes30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
6520515688acetoinno
6520516136hydrogen sulfideno
6520535581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
6520517234glucose-
6520515688acetoin-

enzymes

@refvalueactivityec
65205cytochrome oxidase+1.9.3.1
65205catalase+1.11.1.6
65205DNase-
65205alkaline phosphatase+3.1.3.1
65205esterase (C 4)+
65205esterase Lipase (C 8)+
65205leucine arylamidase+3.4.11.1
65205valine arylamidase+
65205cystine arylamidase+3.4.11.3
65205trypsin+3.4.21.4
65205alpha-chymotrypsin+3.4.21.1
65205acid phosphatase+3.1.3.2
65205naphthol-AS-BI-phosphohydrolase+
65205alpha-galactosidase+3.2.1.22
65205beta-galactosidase+3.2.1.23
65205alpha-glucosidase+3.2.1.20
65205N-acetyl-beta-glucosaminidase+3.2.1.52
65205alpha-mannosidase+3.2.1.24
65205lipase (C 14)-
65205beta-glucuronidase-3.2.1.31
65205alpha-fucosidase-3.2.1.51
65205arginine dihydrolase-3.5.3.6
65205lysine decarboxylase-4.1.1.18

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65205C14:01
    65205C16:06.6
    65205C13:11.6
    65205C16:1ω5c17.5
    65205C15:0 iso 3OH1
    65205C16:0 iso 3OH1.2
    65205C16:0 3OH1.3
    65205C17:0 iso 3OH3.7
    65205C16:1ω7c and/or C16:1ω6c40.7
    65205C15:0 iso21.4
  • type of FA analysis: whole cell analysis
  • incubation medium: R2a agar
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24751soilHwaseongRepublic of KoreaKORAsia
65205soilHwaseong, Gyeonggi-DoRepublic of KoreaKORAsia
67770Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_50857.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_496;96_22918;97_28656;98_36531;99_50857&stattab=map
  • Last taxonomy: Rhabdobacter roseus subclade
  • 16S sequence: KP324792
  • Sequence Identity:
  • Total samples: 543
  • soil counts: 125
  • aquatic counts: 269
  • animal counts: 129
  • plant counts: 20

Safety information

risk assessment

  • @ref: 24751
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24751
  • description: Rhabdobacter roseus strain R49 16S ribosomal RNA gene, partial sequence
  • accession: KP324792
  • length: 1434
  • database: ena
  • NCBI tax ID: 1655419

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhabdobacter roseus DSM 105074GCA_014202275scaffoldncbi1655419
66792Rhabdobacter roseus strain DSM 1050741655419.3wgspatric1655419
66792Rhabdobacter roseus DSM 1050742861391593draftimg1655419

GC content

  • @ref: 65205
  • GC-content: 53.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.274no
gram-positiveno97.988yes
anaerobicno99.267no
aerobicyes89.704yes
halophileno93.911yes
spore-formingno95.291yes
glucose-utilyes86.805no
thermophileno99.154yes
motileno93.237yes
glucose-fermentno87.12yes

External links

@ref: 24751

culture collection no.: DSM 105074, JCM 30685, KACC 18395, KEMB 9005-318

straininfo link

  • @ref: 91240
  • straininfo: 396855

literature

  • topic: Phylogeny
  • Pubmed-ID: 26508300
  • title: Rhabdobacter roseus gen. nov., sp. nov., isolated from soil.
  • authors: Dahal RH, Kim J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000714
  • year: 2015
  • mesh: Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24751Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105074Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105074)
65205Ram Hari Dahal, Jaisoo KimRhabdobacter roseus gen. nov., sp. nov., isolated from soil10.1099/ijsem.0.000714IJSEM 66: 308-314 201626508300
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91240Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID396855.1