Strain identifier

BacDive ID: 22945

Type strain: Yes

Species: Arcobacter defluvii

Strain Designation: SW28-11

Strain history: LMG 25694 <-- M. J. Figueras; Univ. Rovira i Virgili, Spain; SW28-11.

NCBI tax ID(s): 873191 (species)

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General

@ref: 19121

BacDive-ID: 22945

DSM-Number: 25359

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

description: Arcobacter defluvii SW28-11 is a microaerophile, mesophilic, motile bacterium that was isolated from raw sewage, waste water plant.

NCBI tax id

  • NCBI tax id: 873191
  • Matching level: species

strain history

@refhistory
19121<- M. J. Figueras, Rovira i Virgili University, Reus, Spain; SW28-11 <- L. Collado
67770LMG 25694 <-- M. J. Figueras; Univ. Rovira i Virgili, Spain; SW28-11.

doi: 10.13145/bacdive22945.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Epsilonproteobacteria
  • order: Campylobacterales
  • family: Arcobacteraceae
  • genus: Arcobacter
  • species: Arcobacter defluvii
  • full scientific name: Arcobacter defluvii Collado et al. 2011

  • synonyms

    @refsynonym
    20215Pseudarcobacter defluvii
    20215Pseudoarcobacter defluvii

@ref: 19121

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Arcobacteraceae

genus: Arcobacter

species: Arcobacter defluvii

full scientific name: Arcobacter defluvii Collado et al. 2011

strain designation: SW28-11

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes91.504
69480100negative

colony morphology

  • @ref: 19121
  • type of hemolysis: gamma
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

  • @ref: 19121
  • name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/693
  • composition: Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

culture temp

@refgrowthtypetemperaturerange
19121positivegrowth37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 19121
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no92
69480no99.988

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
6837316199urea-hydrolysis
6837317632nitrate+reduction
68373606565hippurate-hydrolysis
6837317634D-glucose-assimilation
6837330031succinate-assimilation
6837330089acetate-assimilation
6837317272propionate-assimilation
6837325115malate-assimilation
6837316947citrate-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
6837348923erythromycinyesyes14 µg
68373474053cefazolinyesyes224 µg
68373100147nalidixic acidyesyes84 µg

metabolite production

@refChebi-IDmetaboliteproduction
6837316136hydrogen sulfideno
6836935581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
19121catalase-1.11.1.6
19121cytochrome-c oxidase+1.9.3.1
68373catalase-1.11.1.6
68373alkaline phosphatase-3.1.3.1
68373L-aspartate arylamidase-3.4.11.21
68373L-arginine arylamidase-
68373pyrrolidonyl arylamidase-3.4.19.3
68373gamma-glutamyltransferase-2.3.2.2
68373esterase+
68373urease-3.5.1.5
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
19121--------------------

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
19121-++-----------------
19121-++--+---------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19121raw sewage, waste water plantReusSpainESPEurope
67770Raw sewage from the wastewater treatment plant in the town of ReusSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Wastewater
#Engineered#Waste#Water treatment plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_1626.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_53;96_923;97_1075;98_1284;99_1626&stattab=map
  • Last taxonomy: Arcobacter
  • 16S sequence: HQ115595
  • Sequence Identity:
  • Total samples: 10767
  • soil counts: 408
  • aquatic counts: 9375
  • animal counts: 847
  • plant counts: 137

Safety information

risk assessment

  • @ref: 19121
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19121
  • description: Arcobacter defluvii strain SW28-11 16S ribosomal RNA gene, partial sequence
  • accession: HQ115595
  • length: 1402
  • database: ena
  • NCBI tax ID: 873191

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arcobacter defluvii LMG 25694GCA_013201725completencbi873191
66792Arcobacter defluvii strain CECT 7697873191.8wgspatric873191
66792Arcobacter defluvii strain LMG 25694873191.9completepatric873191
66792Arcobacter defluvii CECT 76972854854714draftimg873191
67770Arcobacter defluvii CECT 7697GCA_004115775contigncbi873191

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
flagellatedyes73.573no
gram-positiveno98.324no
anaerobicno80.773yes
aerobicno93.433yes
halophileno83.852no
spore-formingno94.574no
glucose-utilno80.743no
thermophileno99.153yes
motileyes86.44no
glucose-fermentno92.355yes

External links

@ref: 19121

culture collection no.: DSM 25359, CECT 7697, LMG 25694, JCM 33356

straininfo link

  • @ref: 87193
  • straininfo: 369524

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20889767Arcobacter defluvii sp. nov., isolated from sewage samples.Collado L, Levican A, Perez J, Figueras MJInt J Syst Evol Microbiol10.1099/ijs.0.025668-02010Arcobacter/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Chaperonin 60/genetics, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Molecular Sequence Data, Molecular Typing, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiologyGenetics
Phylogeny22401779Arcobacter bivalviorum sp. nov. and Arcobacter venerupis sp. nov., new species isolated from shellfish.Levican A, Collado L, Aguilar C, Yustes C, Dieguez AL, Romalde JL, Figueras MJSyst Appl Microbiol10.1016/j.syapm.2012.01.0022012Arcobacter/chemistry/*classification/genetics/*isolation & purification, Chaperonin 60/genetics, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Shellfish/*microbiology, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationGenetics
Phylogeny35052964The Effect of Antibiotics on Planktonic Cells and Biofilm Formation Ability of Collected Arcobacter-like Strains and Strains Isolated within the Czech Republic.Svarcova K, Pejchalova M, Silha DAntibiotics (Basel)10.3390/antibiotics110100872022

Reference

@idauthorscataloguedoi/urltitle
19121Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25359)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25359
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
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68373Automatically annotated from API CAM
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
87193Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID369524.1StrainInfo: A central database for resolving microbial strain identifiers