Strain identifier

BacDive ID: 2101

Type strain: Yes

Species: Arcobacter trophiarum

Strain Designation: 64, 64/2-45d5/R-39974

Variant: Isotype of BacDive ID 132895

Strain history: CIP <- 2011, LMG <- S. De Smet, Ghent Univ., Ghent, Belgium: strain 64

NCBI tax ID(s): 1032241 (strain), 708186 (species)

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General

@ref: 18040

BacDive-ID: 2101

DSM-Number: 25469

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, rod-shaped

description: Arcobacter trophiarum 64 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from feces of 14-week-old piglet at Belgian farm.

NCBI tax id

NCBI tax idMatching level
1032241strain
708186species

strain history

@refhistory
18040<- CCUG <- S. De Smet, Fac. Veterinary Medicine, Univ. Ghent, Merelbeke, Belgium
123588CIP <- 2011, LMG <- S. De Smet, Ghent Univ., Ghent, Belgium: strain 64

doi: 10.13145/bacdive2101.20230509.8.1

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 trophiarum
  • full scientific name: Arcobacter trophiarum De Smet et al. 2011

  • synonyms

    • @ref: 20215
    • synonym: Aliarcobacter trophiarum

@ref: 18040

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Arcobacteraceae

genus: Arcobacter

species: Arcobacter trophiarum

full scientific name: Arcobacter trophiarum De Smet et al. 2011

strain designation: 64, 64/2-45d5/R-39974

variant: Isotype of BacDive ID 132895

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidencemotility
29852negative1.7 µm0.4 µmrod-shaped
69480negative99.999
123588negativerod-shapedyes

colony morphology

  • @ref: 18040
  • type of hemolysis: gamma
  • incubation period: 1-2 days

pigmentation

  • @ref: 29852
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18040COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
34719MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
123588CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123588CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
18040positivegrowth30mesophilic
29852positivegrowth25-30mesophilic
29852positiveoptimum27.5mesophilic
34719positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
18040microaerophile
29852aerobe

spore formation

@refspore formationconfidence
29852no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
29852NaClpositivegrowth<4 %
29852NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12358817632nitrate-reduction
12358816301nitrite-reduction
6837316199urea-hydrolysis
6837317632nitrate+reduction
68373606565hippurate-hydrolysis
6837378019triphenyltetrazolium chloride-reduction
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
12358835581indoleno

enzymes

@refvalueactivityec
18040catalase+1.11.1.6
18040cytochrome-c oxidase+1.9.3.1
29852catalase+1.11.1.6
29852cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
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
123588oxidase+
123588catalase+1.11.1.6
123588urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123588--++-+-+---+--------

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
18040-++------+-----++---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
18040feces of 14-week-old piglet at Belgian farmWest FlandersBelgiumBELEurope
123588Animal, Pig, faecesBelgiumBELEurope2007

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
180401Risk group (German classification)
1235881Risk group (French classification)

Sequence information

16S sequences

  • @ref: 18040
  • description: Arcobacter trophiarum partial 16S rRNA gene, strain 64
  • accession: FN650333
  • length: 1309
  • database: ena
  • NCBI tax ID: 708186

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aliarcobacter trophiarum LMG 25534GCA_003355515completencbi1032241
66792Aliarcobacter trophiarum LMG 25534GCA_004116585contigncbi1032241
66792Arcobacter trophiarum LMG 255341032241.6wgspatric1032241
66792Arcobacter trophiarum LMG 255341032241.5completepatric1032241
66792Arcobacter trophiarum LMG 255342847262524completeimg1032241
66792Arcobacter trophiarum LMG 255342858249781draftimg1032241
66792Aliarcobacter trophiarum LMG 25534GCA_024584015contigncbi1032241

GC content

  • @ref: 29852
  • GC-content: 28.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.127no
flagellatedyes72.522no
gram-positiveno98.911yes
anaerobicno81.817yes
aerobicno96.364no
halophileno93.037no
spore-formingno94.879no
glucose-utilno92.558no
thermophileno90.951yes
glucose-fermentno91.058no

External links

@ref: 18040

culture collection no.: DSM 25469, LMG 25534, CCUG 59229, CIP 110286

straininfo link

  • @ref: 71748
  • straininfo: 368756

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20305065Arcobacter trophiarum sp. nov., isolated from fattening pigs.De Smet S, Vandamme P, De Zutter L, On SLW, Douidah L, Houf KInt J Syst Evol Microbiol10.1099/ijs.0.022665-02010Amplified Fragment Length Polymorphism Analysis, Animals, Arcobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/genetics, Feces/microbiology, Molecular Sequence Data, Phenotype, *Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, Species Specificity, Swine/*microbiologyGenetics
Genetics30533698Complete Genome Sequence of the Arcobacter trophiarum Type Strain LMG 25534.Miller WG, Yee EMicrobiol Resour Announc10.1128/MRA.01110-182018

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
18040Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25469)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25469
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
29852Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2622628776041
34719Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8129
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)
68373Automatically annotated from API CAM
68382Automatically annotated from API zym
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
71748Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID368756.1StrainInfo: A central database for resolving microbial strain identifiers
123588Curators of the CIPCollection of Institut Pasteur (CIP 110286)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110286