Strain identifier

BacDive ID: 131542

Type strain: Yes

Species: Rouxiella badensis

Strain Designation: 323

Strain history: CIP <- 2016, A. Le Flèche, Inst. Pasteur, Paris, France: strain 323 <- Inst. Process Eng. Life Sci., Karlsruhe, Germany

NCBI tax ID(s): 1646377 (species)

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General

@ref: 22769

BacDive-ID: 131542

DSM-Number: 100043

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, rod-shaped

description: Rouxiella badensis 323 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from soil from the upper layer of a pristine raised bog.

NCBI tax id

  • NCBI tax id: 1646377
  • Matching level: species

strain history

@refhistory
22769<- J. Kügler, Karlsruhe Institute of Technology KIT, Germany; Serratia sp. 323 <- S. Hansen and J. Kügler, KIT
116699CIP <- 2016, A. Le Flèche, Inst. Pasteur, Paris, France: strain 323 <- Inst. Process Eng. Life Sci., Karlsruhe, Germany

doi: 10.13145/bacdive131542.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Yersiniaceae
  • genus: Rouxiella
  • species: Rouxiella badensis
  • full scientific name: Rouxiella badensis Le Flèche-Matéos et al. 2017

@ref: 22769

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Rouxiella

species: Rouxiella badensis

full scientific name: Rouxiella badensis Le Flèche-Matéos et al. 2017

strain designation: 323

type strain: yes

Morphology

cell morphology

@refgram staincell shapeconfidencemotility
43210negativerod-shaped
69480negative99.962
116699negativerod-shapedno

colony morphology

  • @ref: 43210
  • colony color: white
  • medium used: solid medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22769TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
22769LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium381.pdf
43210solid mediumyes
22769NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
116699CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
43210positivegrowth4-37
22769positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 43210
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.905

compound production

@refcompound
22769tenside
22769biosurfactant
22769glycolipid (extracellular)

observation

  • @ref: 43210
  • observation: produce surfactant

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4321017632nitrate+reduction
4321028847D-fucose+builds acid from
4321017754glycerol+builds acid from
4321017306maltose+builds acid from
432106731melezitose+builds acid from
4321016634raffinose+builds acid from
4321062345L-rhamnose+builds acid from
4321017992sucrose+builds acid from
4321032528turanose+builds acid from
4321018333D-arabitol+builds acid from
43210506227N-acetylglucosamine-builds acid from
4321062318D-lyxose-builds acid from
4321037657methyl D-glucoside-builds acid from
4321017151xylitol-builds acid from
4321027082trehalose-builds acid from
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
22769+---+--+/--+++++-+++++-
22769+---+----+-+++++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
22769soil from the upper layer of a pristine raised bogBaden Württemberg, northern Black Forest near Kaltenbronn (48.719° N, 8.459° E)GermanyDEUEurope48.7198.459
43210peat bog soilKaltenbronn, northern Black Forest, Baden-WürtembergGermanyDEUEurope
116699Environment, SoilBlack forestGermanyDEUEurope2011-07-19

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Grassland
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Wetland (Swamp)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2210.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_106;97_324;98_1724;99_2210&stattab=map
  • Last taxonomy: Yersiniaceae
  • 16S sequence: KP642161
  • Sequence Identity:
  • Total samples: 331
  • soil counts: 34
  • aquatic counts: 33
  • animal counts: 170
  • plant counts: 94

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
227691Risk group (German classification)
1166991Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
43210Rouxiella sp. 323 16S ribosomal RNA gene, partial sequenceKX7849061357nuccore1646377
22769Rouxiella badensis strain 323 16S ribosomal RNA gene, partial sequenceKP6421611281ena1646377

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rouxiella badensis DSM 100043GCA_002093665scaffoldncbi1646377
66792Rouxiella badensis strain DSM 1000431646377.3wgspatric1646377
66792Rouxiella badensis DSM 1000432832090241draftimg1646377
66792Rouxiella badensis DSM 100043GCA_026967495completencbi1646377

GC content

  • @ref: 22769
  • GC-content: 53

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno51.267no
flagellatedno92.809no
gram-positiveno97.906yes
anaerobicno99.38no
aerobicyes53.167yes
halophileno85.248no
spore-formingno96.345no
glucose-fermentyes88.353yes
thermophileno99.568no
glucose-utilyes96.517no

External links

@ref: 22769

culture collection no.: DSM 100043, CIP 111153

straininfo link

  • @ref: 89956
  • straininfo: 399278

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28100296Rouxiella badensis sp. nov. and Rouxiella silvae sp. nov. isolated from peat bog soil and emendation description of the genus Rouxiella.Le Fleche-Mateos A, Kugler JH, Hansen SH, Syldatk C, Hausmann R, Lomprez F, Vandenbogaert M, Manuguerra JC, Grimont PADInt J Syst Evol Microbiol10.1099/ijsem.0.0017942017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Gammaproteobacteria/*classification/genetics/isolation & purification, Germany, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *WetlandsTranscriptome
Phylogeny31089912Serratia microhaemolytica sp. nov., isolated from an artificial lake in Southern China.Wang J, Zheng ML, Jiao JY, Wang WJ, Li S, Xiao M, Chen C, Qu PH, Li WJAntonie Van Leeuwenhoek10.1007/s10482-019-01273-92019Anaerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/microbiology, Hydrogen-Ion Concentration, Lakes/*microbiology, Locomotion, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serratia/*classification/genetics/*isolation & purification/physiology, Sodium Chloride/metabolism, TemperatureTranscriptome

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
22769Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100043Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100043)
43210Anne Le Fleche-Mateos, Johannes H. Kügler, Silla H. Hansen, Christoph Syldatk, Rudolf Hausmann, Fabienne Lomprez, Mathias Vandenbogaert, Jean-Claude Manuguerra, Patrick A.D. GrimontRouxiella badensis sp. nov. and Rouxiella silvae sp. nov. Isolated from peat bog soil and emendation description of the genus Rouxiella10.1099/ijsem.0.001794IJSEM 67: 1255-1259 201728100296
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
68368Automatically annotated from API 20E
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
89956Reimer, 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-ID399278.1
116699Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111153Collection of Institut Pasteur (CIP 111153)