Strain identifier

BacDive ID: 4311

Type strain: Yes

Species: Buttiauxella agrestis

Strain Designation: Gavini-F-44, F44

Strain history: CIP <- 1980, H. Leclerc, Villeneuve d'Ascq, France: strain CUETM 77-167 <- F. Gavini, INSERM, Lille, France: strain F44

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 1781

BacDive-ID: 4311

DSM-Number: 4586

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Buttiauxella agrestis Gavini-F-44 is a mesophilic, motile bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1006004strain
82977species

strain history

@refhistory
1781<- CIP <- H. Leclerc, CUETM; 77.167
67770Y. Kosako 536 <-- R. Sakazaki 536 <-- F. Gavini F44.
116163CIP <- 1980, H. Leclerc, Villeneuve d'Ascq, France: strain CUETM 77-167 <- F. Gavini, INSERM, Lille, France: strain F44

doi: 10.13145/bacdive4311.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Buttiauxella
  • species: Buttiauxella agrestis
  • full scientific name: Buttiauxella agrestis Ferragut et al. 1982

@ref: 1781

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Buttiauxella

species: Buttiauxella agrestis

full scientific name: Buttiauxella agrestis Ferragut et al. 1982 emend. Müller et al. 1996

strain designation: Gavini-F-44, F44

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes97.505
6948099.972negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1781TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
1781NUTRIENT 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
38575MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116163CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1781positivegrowth30mesophilic
38575positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.611

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

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

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
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
1781+--++------++--+-+++-

Isolation, sampling and environmental information

isolation

@refsample type
1781soil
67770Surface water
116163Environment, Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2027.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_411;98_1588;99_2027&stattab=map
  • Last taxonomy: Buttiauxella
  • 16S sequence: AJ293685
  • Sequence Identity:
  • Total samples: 7158
  • soil counts: 778
  • aquatic counts: 1274
  • animal counts: 4089
  • plant counts: 1017

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17811Risk group (German classification)
1161631Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Buttiauxella agrestis 16S rRNA gene, strain CDC 1176-81T (ATCC 33320T)AJ2936851450ena1006004
20218Buttiauxella agrestis 16S rRNA gene (strain DSM 4586)AJ2334001504ena1006004

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Buttiauxella agrestis NCTC12119GCA_900446255contigncbi82977
66792Buttiauxella agrestis ATCC 333201006004.4wgspatric1006004
66792Buttiauxella agrestis strain NCTC1211982977.5wgspatric82977
66792Buttiauxella agrestis NCTC 121192808606796draftimg82977
66792Buttiauxella agrestis CDC 1176-81, ATCC 333202588253793draftimg1006004
67770Buttiauxella agrestis ATCC 33320GCA_000735355contigncbi1006004

GC content

@refGC-contentmethod
6777047.9thermal denaturation, midpoint method (Tm)
6777049thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.513no
flagellatedno55.998no
gram-positiveno97.763no
anaerobicno97.125no
aerobicyes89.269no
halophileno89.775no
spore-formingno94.172no
thermophileno99.394no
glucose-utilyes94.922no
glucose-fermentyes92.829no

External links

@ref: 1781

culture collection no.: DSM 4586, ATCC 33320, CIP 80.31, CCUG 11756, CIP 80-31, CUETM 77.167, JCM 1090, BCRC 12221, CUETM 77-167, LMG 7861, NCTC 12119

straininfo link

  • @ref: 73803
  • straininfo: 265473

literature

topicPubmed-IDtitleauthorsjournalDOIyearmesh
Metabolism32801184Multilamellar and Multivesicular Outer Membrane Vesicles Produced by a Buttiauxella agrestis tolB Mutant.Takaki K, Tahara YO, Nakamichi N, Hasegawa Y, Shintani M, Ohkuma M, Miyata M, Futamata H, Tashiro YAppl Environ Microbiol10.1128/AEM.01131-202020Bacterial Proteins/*genetics/metabolism, Enterobacteriaceae/genetics/*physiology, Mutation, Periplasmic Proteins/*genetics/metabolism
Genetics33986092Complete Genome Sequence of Buttiauxella agrestis DSM 9389.Nakamichi N, Moriuchi R, Dohra H, Futamata H, Tashiro YMicrobiol Resour Announc10.1128/MRA.00301-212021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1781Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4586)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4586
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38575Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11125
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
73803Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265473.1StrainInfo: A central database for resolving microbial strain identifiers
116163Curators of the CIPCollection of Institut Pasteur (CIP 80.31)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2080.31