Strain identifier

BacDive ID: 2092

Type strain: Yes

Species: Arcobacter nitrofigilis

Strain Designation: CI

Strain history: CIP <- 1994, LMG <- 1986, CCUG, Campylobacter nitrofragilis <- S. Neill <- 1984, McClung, Canada

NCBI tax ID(s): 572480 (strain), 28199 (species)

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

@ref: 3103

BacDive-ID: 2092

DSM-Number: 7299

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

description: Arcobacter nitrofigilis CI is a microaerophile, mesophilic, motile bacterium that was isolated from roots of Spartina alterniflora .

NCBI tax id

NCBI tax idMatching level
28199species
572480strain

strain history

@refhistory
3103<- CCUG <- C.R. McClung
67770LMG 7604 <-- CCUG 15892 <-- C. R. McClung; Beltsville Agric. Res. Center, USA; CI.
121311CIP <- 1994, LMG <- 1986, CCUG, Campylobacter nitrofragilis <- S. Neill <- 1984, McClung, Canada

doi: 10.13145/bacdive2092.20230509.8.1

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 nitrofigilis
  • full scientific name: Arcobacter nitrofigilis (McClung et al. 1983) Vandamme et al. 1991
  • synonyms

    • @ref: 20215
    • synonym: Campylobacter nitrofigilis

@ref: 3103

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Arcobacteraceae

genus: Arcobacter

species: Arcobacter nitrofigilis

full scientific name: Arcobacter nitrofigilis (McClung et al. 1983) Vandamme et al. 1991

strain designation: CI

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.172
69480100negative
121311yesnegativerod-shaped

colony morphology

@reftype of hemolysisincubation period
3103gamma1-2 days
463693 days
121311

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_7299_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3103VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115)yeshttps://mediadive.dsmz.de/medium/115Name: VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115) Composition: NaCl 15.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
3103COLUMBIA 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
38144MEDIUM 25 - for Arcobacter nitrofigilisyesDistilled water make up to (1000.000 ml);Sodium chloride (15.000 g);Magnesium chloride hexahydrate (1.000 g);Agar (15.000 g);Yeast extract (5.000 g);Horse blood(50.000 ml);Succinic acid (2.000 g);Beef extract (5.000 g);Sodium glutamate (2.000 g);Special p
121311CIP Medium 25yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=25

culture temp

@refgrowthtypetemperaturerange
3103positivegrowth25mesophilic
38144positivegrowth37mesophilic
46369positivegrowth25mesophilic
67770positivegrowth28mesophilic
121311positivegrowth22psychrophilic
121311nogrowth10psychrophilic
121311nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
3103microaerophile
46369microaerophile

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.865

halophily

@refsaltgrowthtested relationconcentration
121311NaClpositivegrowth2 %
121311NaClnogrowth4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
121311606565hippurate-hydrolysis
12131117632nitrate+reduction
12131116301nitrite-reduction
121311132112sodium thiosulfate-builds gas from
68373606565hippurate-hydrolysis
6837317634D-glucose-assimilation
6837330031succinate+assimilation

antibiotic resistance

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

metabolite production

@refChebi-IDmetaboliteproduction
6837316136hydrogen sulfideno
6836935581indoleno
12131135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
3103catalase+1.11.1.6
3103cytochrome-c oxidase+1.9.3.1
68373catalase+1.11.1.6
68373L-aspartate arylamidase-3.4.11.21
68373L-arginine arylamidase-
68373pyrrolidonyl arylamidase-3.4.19.3
68373gamma-glutamyltransferase-2.3.2.2
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121311oxidase+
121311gelatinase-
121311DNase-
121311catalase+1.11.1.6
121311lecithinase-
121311urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46369C12:06.412
    46369C14:03.314
    46369C16:031.516
    46369C18:00.618
    46369C12:0 3OH2.713.455
    46369C12:0 ALDE ?1.210.915
    46369C13:0 ISO 2OH0.413.814
    46369C14:0 3OH/C16:1 ISO I2.315.485
    46369C16:1 ω7c31.515.819
    46369C18:1 ω7c /12t/9t18.217.824
    46369C18:2 ω6,9c/C18:0 ANTE0.717.724
    46369Unidentified0.6
    46369unknown 12.4860.512.486
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
3103+-------++/-+/-+/-+/-+--++--+

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
3103-+----------+-------+
3103-++--+---+--+--++---
3103+++--+---+--+---+/----+
3103-++--+---+--+--+/-+-+/--
46369+-----------+----+--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121311---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
3103roots of Spartina alterniflora (marshland)Spartina alternifloraNova ScotiaCanadaCANNorth America
46369Roots of short Spartina alternifloraHalifax,Nova ScotiaCanadaCANNorth America
67770Roots of short Spartina. alternijloraSpartina. alternijloraHalifax, Nova ScotiaCanadaCANNorth America
121311Plant, Roots, Spartina alternifloraCanadaCANNorth America1984

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Wetland (Swamp)
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_15309.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_53;96_1229;97_1456;98_1776;99_15309&stattab=map
  • Last taxonomy: Arcobacter nitrofigilis subclade
  • 16S sequence: L14627
  • Sequence Identity:
  • Total samples: 12
  • aquatic counts: 11
  • animal counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
31031Risk group (German classification)
1213111Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3103
  • description: Arcobacter nitrofigilis 16S ribosomal RNA
  • accession: L14627
  • length: 1461
  • database: ena
  • NCBI tax ID: 28199

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arcobacter nitrofigilis DSM 7299GCA_000092245completencbi572480
66792Arcobacter nitrofigilis DSM 7299572480.3completepatric572480
66792Arcobacter nitrofigilis DSM 7299646564506completeimg572480

GC content

  • @ref: 3103
  • GC-content: 29.0
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno77no
motileyes88.29no
flagellatedyes82.424no
gram-positiveno98.279no
anaerobicno79.026no
aerobicno88.359no
halophileno72.467no
spore-formingno92.871no
thermophileno99.627yes
glucose-utilno58.571no
glucose-fermentno89.346no

External links

@ref: 3103

culture collection no.: CCUG 15892, CECT 7204, DSM 7299, ATCC 33309, CCUG 15893, LMG 7604, NCTC 12251, JCM 33357, CIP 103745

straininfo link

  • @ref: 71739
  • straininfo: 978

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3103Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7299)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7299
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
38144Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15576
46369Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15893)https://www.ccug.se/strain?id=15893
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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/
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)
71739Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID978.1StrainInfo: A central database for resolving microbial strain identifiers
121311Curators of the CIPCollection of Institut Pasteur (CIP 103745)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103745