Strain identifier
BacDive ID: 4311
Type strain:
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
NCBI tax ID(s): 1006004 (strain), 82977 (species)
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 id | Matching level |
---|---|
1006004 | strain |
82977 | species |
strain history
@ref | history |
---|---|
1781 | <- CIP <- H. Leclerc, CUETM; 77.167 |
67770 | Y. Kosako 536 <-- R. Sakazaki 536 <-- F. Gavini F44. |
116163 | CIP <- 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
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 97.505 | |
69480 | 99.972 | negative |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1781 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
1781 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
38575 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
116163 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1781 | positive | growth | 30 | mesophilic |
38575 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.611 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 30849 | L-arabinose | + | fermentation |
68368 | 27613 | amygdalin | + | fermentation |
68368 | 28053 | melibiose | + | fermentation |
68368 | 17992 | sucrose | - | fermentation |
68368 | 62345 | L-rhamnose | + | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | - | fermentation |
68368 | 16899 | D-mannitol | + | fermentation |
68368 | 17634 | D-glucose | + | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | + | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | cytochrome oxidase | - | 1.9.3.1 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | + | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1781 | + | - | - | + | + | - | - | - | - | - | - | + | + | - | - | + | - | + | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
1781 | soil |
67770 | Surface water |
116163 | Environment, 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
@ref | biosafety level | biosafety level comment |
---|---|---|
1781 | 1 | Risk group (German classification) |
116163 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Buttiauxella agrestis 16S rRNA gene, strain CDC 1176-81T (ATCC 33320T) | AJ293685 | 1450 | ena | 1006004 |
20218 | Buttiauxella agrestis 16S rRNA gene (strain DSM 4586) | AJ233400 | 1504 | ena | 1006004 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Buttiauxella agrestis NCTC12119 | GCA_900446255 | contig | ncbi | 82977 |
66792 | Buttiauxella agrestis ATCC 33320 | 1006004.4 | wgs | patric | 1006004 |
66792 | Buttiauxella agrestis strain NCTC12119 | 82977.5 | wgs | patric | 82977 |
66792 | Buttiauxella agrestis NCTC 12119 | 2808606796 | draft | img | 82977 |
66792 | Buttiauxella agrestis CDC 1176-81, ATCC 33320 | 2588253793 | draft | img | 1006004 |
67770 | Buttiauxella agrestis ATCC 33320 | GCA_000735355 | contig | ncbi | 1006004 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 47.9 | thermal denaturation, midpoint method (Tm) |
67770 | 49 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 90.513 | no |
flagellated | no | 55.998 | no |
gram-positive | no | 97.763 | no |
anaerobic | no | 97.125 | no |
aerobic | yes | 89.269 | no |
halophile | no | 89.775 | no |
spore-forming | no | 94.172 | no |
thermophile | no | 99.394 | no |
glucose-util | yes | 94.922 | no |
glucose-ferment | yes | 92.829 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh |
---|---|---|---|---|---|---|---|
Metabolism | 32801184 | Multilamellar 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 Y | Appl Environ Microbiol | 10.1128/AEM.01131-20 | 2020 | Bacterial Proteins/*genetics/metabolism, Enterobacteriaceae/genetics/*physiology, Mutation, Periplasmic Proteins/*genetics/metabolism |
Genetics | 33986092 | Complete Genome Sequence of Buttiauxella agrestis DSM 9389. | Nakamichi N, Moriuchi R, Dohra H, Futamata H, Tashiro Y | Microbiol Resour Announc | 10.1128/MRA.00301-21 | 2021 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1781 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4586) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4586 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
38575 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/11125 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
73803 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265473.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116163 | Curators of the CIP | Collection of Institut Pasteur (CIP 80.31) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2080.31 |