Strain identifier

BacDive ID: 133023

Type strain: Yes

Species: Rufibacter ruber

Strain Designation: CAI-18b

Strain history: <- T. Felföldi, Eötvös Loránd Univ. Budapest, Hungary; CAI-18b <- I. Máthé, Sapientia University, Romania

NCBI tax ID(s): 1549639 (species)

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General

@ref: 24811

BacDive-ID: 133023

DSM-Number: 29854

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

description: Rufibacter ruber CAI-18b is an aerobe, heterotroph, Gram-negative bacterium that forms circular colonies and was isolated from bioreactor treating landfill leachate.

NCBI tax id

  • NCBI tax id: 1549639
  • Matching level: species

strain history

  • @ref: 24811
  • history: <- T. Felföldi, Eötvös Loránd Univ. Budapest, Hungary; CAI-18b <- I. Máthé, Sapientia University, Romania

doi: 10.13145/bacdive133023.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Hymenobacteraceae
  • genus: Rufibacter
  • species: Rufibacter ruber
  • full scientific name: Rufibacter ruber Kýrová et al. 2016

  • synonyms

    • @ref: 20215
    • synonym: Rufibacter quisquiliarum

@ref: 24811

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Rufibacter

species: Rufibacter quisquiliarum

full scientific name: Rufibacter quisquiliarum Felföldi et al. 2016

strain designation: CAI-18b

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25111negative0.7-1.6 µm0.3-0.5 µmrod-shapedyes
69480negative99.995

colony morphology

  • @ref: 25111
  • colony size: 2 mm
  • colony color: pinkish-red
  • colony shape: circular
  • medium used: R2A agar medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25111Reasoner's 2A agar (R2A)yes
24811R2A 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

culture temp

@refgrowthtypetemperaturerange
25111positivegrowth4-45
25111positiveoptimum20-37
24811positivegrowth21psychrophilic

culture pH

@refabilitytypepHPH range
25111positivegrowth7.0-11.0alkaliphile
25111positiveoptimum8.0-10.0

Physiology and metabolism

oxygen tolerance

  • @ref: 25111
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 25111
  • type: heterotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.966

halophily

  • @ref: 25111
  • salt: NaCl
  • tested relation: optimum
  • concentration: 0-2.0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25111168082-dehydro-D-gluconate-assimilation
25111174265-dehydro-D-gluconate-assimilation
2511127613amygdalin-assimilation
2511118305arbutin-assimilation
2511116947citrate-assimilation
2511115963ribitol-assimilation
2511118333D-arabitol-assimilation
2511115824D-fructose-assimilation
2511128847D-fucose-assimilation
2511162318D-lyxose-assimilation
2511116899D-mannitol-assimilation
251116731melezitose-assimilation
2511116988D-ribose-assimilation
2511117924D-sorbitol-assimilation
2511116443D-tagatose-assimilation
2511165327D-xylose-assimilation
2511127689decanoate-assimilation
2511117113erythritol-assimilation
2511116813galactitol-assimilation
2511124265gluconate-assimilation
2511117234glucose-fermentation
2511117754glycerol-assimilation
2511117268myo-inositol-assimilation
2511130849L-arabinose-assimilation
2511118403L-arabitol-assimilation
2511118287L-fucose-assimilation
2511162345L-rhamnose-assimilation
2511117266L-sorbose-assimilation
2511165328L-xylose-assimilation
25111320061methyl alpha-D-glucopyranoside-assimilation
2511143943methyl alpha-D-mannoside-assimilation
2511174863methyl beta-D-xylopyranoside-assimilation
2511117632nitrate-reduction
2511118401phenylacetate-assimilation
2511117814salicin-assimilation
2511127897tryptophan-energy source
2511132528turanose-assimilation
2511117151xylitol-assimilation
2511117057cellobiose+assimilation
2511112936D-galactose+assimilation
2511117634D-glucose+assimilation
2511116024D-mannose+assimilation
251114853esculin+assimilation
251115291gelatin+hydrolysis
2511128066gentiobiose+assimilation
2511128087glycogen+assimilation
2511117716lactose+assimilation
2511117306maltose+assimilation
2511128053melibiose+assimilation
25111506227N-acetylglucosamine+assimilation
2511128017starch+assimilation
2511127082trehalose+assimilation

metabolite production

  • @ref: 25111
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 25111
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25111acid phosphatase+3.1.3.2
25111alkaline phosphatase+3.1.3.1
25111alpha-chymotrypsin-3.4.21.1
25111alpha-fucosidase-3.2.1.51
25111alpha-galactosidase+3.2.1.22
25111alpha-glucosidase+3.2.1.20
25111alpha-mannosidase-3.2.1.24
25111arginine dihydrolase-3.5.3.6
25111beta-galactosidase-3.2.1.23
25111beta-glucosidase-3.2.1.21
25111beta-glucuronidase-3.2.1.31
25111caseinase+3.4.21.50
25111catalase+1.11.1.6
25111cystine arylamidase+3.4.11.3
25111cytochrome oxidase+1.9.3.1
25111esterase (C 4)+
25111esterase lipase (C 8)+
25111gelatinase+
25111leucine arylamidase+3.4.11.1
25111lipase (C 14)-
25111N-acetyl-beta-glucosaminidase+3.2.1.52
25111naphthol-AS-BI-phosphohydrolase+
25111trypsin+3.4.21.4
25111tryptophan deaminase-4.1.99.1
25111urease-3.5.1.5
25111valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture temperatureisolation procedure
24811bioreactor treating landfill leachateTransylvania, Harghita County, Odorheiu SecuiescRomaniaROUEurope
25111diluted R2A-based medium20-22standard dilution plate method

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Waste#Landfill
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_7045.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_60;96_2442;97_2976;98_5176;99_7045&stattab=map
  • Last taxonomy: Rufibacter
  • 16S sequence: KM083132
  • Sequence Identity:
  • Total samples: 2322
  • soil counts: 450
  • aquatic counts: 721
  • animal counts: 1055
  • plant counts: 96

Safety information

risk assessment

  • @ref: 24811
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24811
  • description: Rufibacter quisquiliarum strain CAI-18b 16S ribosomal RNA gene, partial sequence
  • accession: KM083132
  • length: 1434
  • database: ena
  • NCBI tax ID: 1549639

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rufibacter quisquiliarum DSM 29854GCA_014138425contigncbi1549639
66792Rufibacter quisquiliarum strain DSM 298541549639.3wgspatric1549639
66792Rufibacter quisquiliarum DSM 298542827981459draftimg1549639

GC content

  • @ref: 24811
  • GC-content: 50.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.209yes
gram-positiveno98.066yes
anaerobicno99.493yes
aerobicyes90.294yes
halophileno94.503no
spore-formingno93.6no
thermophileno96.996no
glucose-utilyes89.907yes
flagellatedno96.64no
glucose-fermentno91.047yes

External links

@ref: 24811

culture collection no.: DSM 29854, NCAIM B.02614

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27612451Rufibacter quisquiliarum sp. nov., a new member of the phylum Bacteroidetes isolated from a bioreactor treating landfill leachate.Felfoldi T, Mentes A, Schumann P, Keki Z, Mathe I, Marialigeti K, Toth EMInt J Syst Evol Microbiol10.1099/ijsem.0.0014882016Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Romania, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water Pollutants, ChemicalTranscriptome
Phylogeny33135105Rhodocytophaga rosea sp. nov. and Nibribacter ruber sp. nov., two radiation-resistant bacteria isolated from soil.Park Y, Maeng S, Han JH, Lee SE, Zhang J, Kim MK, Cha IT, Lee KE, Lee BH, Kim MKAntonie Van Leeuwenhoek10.1007/s10482-020-01488-12020Bacterial Typing Techniques, Bacteroidetes/genetics, Base Composition, *Cytophagaceae/genetics, DNA, Bacterial/genetics, Fatty Acids, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil, Soil Microbiology

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
24811Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29854Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29854)
25111T. M. Felföldi, A.,Schumann, P.,Kéki, Z.,Máthé, I.,Márialigeti, K.,Tóth, E. M.Rufibacter quisquiliarum sp. nov., a new member of the phylum Bacteroidetes isolated from a bioreactor treating landfill leachate10.1099/ijsem.0.001488IJSEM 66: 5150-5154 201627612451
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
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