Strain identifier

BacDive ID: 2097

Type strain: Yes

Species: Arcobacter halophilus

Strain Designation: LA31B

Strain history: CIP <- 2004, S.P. Donachie, Honolulu, USA: strain LA31B

NCBI tax ID(s): 197482 (species)

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General

@ref: 7326

BacDive-ID: 2097

DSM-Number: 18005

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

description: Arcobacter halophilus LA31B is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from hypersaline lagoon.

NCBI tax id

  • NCBI tax id: 197482
  • Matching level: species

strain history

@refhistory
7326<- CIP <- S. P. Donachie, Univ. of Hawaii; LA31B
339662004, S.P. Donachie, Honolulu, USA: strain LA31B
119813CIP <- 2004, S.P. Donachie, Honolulu, USA: strain LA31B

doi: 10.13145/bacdive2097.20230509.8.1

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 halophilus
  • full scientific name: Arcobacter halophilus Donachie et al. 2005

  • synonyms

    @refsynonym
    20215Malaciobacter halophilus
    20215Malacobacter halophilus

@ref: 7326

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Campylobacterales

family: Arcobacteraceae

genus: Arcobacter

species: Arcobacter halophilus

full scientific name: Arcobacter halophilus Donachie et al. 2005

strain designation: LA31B

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23170negative1.5-2.5 µm0.4-0.5 µmrod-shapedyespolar
69480yes92.977
69480negative100

colony morphology

@refincubation periodtype of hemolysiscolony sizecolony colorcolony shapemedium used
73261-2 days
231703 daysgamma1-2 mmoff-whitecircular5 % blood agar containing 3.5 % NaCl

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7326BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: None 50.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l NaCl 1.0 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
231705 % blood agar containing 3.5 % NaClyes
33966MEDIUM 589 - for Arcobacter holophilusyesDistilled water make up to (950.000 ml);Sodium chloride (30.000 g);Agar(15.000 g);Nutrient agar 1,5% (20.000 g);Sheep blood (50.000 ml)
119813CIP Medium 589yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=589

culture temp

@refgrowthtypetemperaturerange
7326positivegrowth28mesophilic
23170positivegrowth18-22psychrophilic
33966positivegrowth22psychrophilic
60019positivegrowth22psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 60019
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no95
69480no99.983

halophily

  • @ref: 23170
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: <2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23170606565hippurate-hydrolysis
2317017632nitrate+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 resistantis sensitivesensitivity conc.
231703393carbenicillinyesno
231703542cephalothinyesno
6837348923erythromycinyesyes14 µg
68373474053cefazolinyesyes224 µg
68373100147nalidixic acidyesyes84 µg

metabolite production

  • @ref: 68373
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
7326catalase-1.11.1.6
23170alkaline phosphatase-3.1.3.1
23170catalase-1.11.1.6
23170cytochrome oxidase+1.9.3.1
23170DNase-
23170urease-3.5.1.5
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

API CAM

@refURENITESTHIPGGTTTCPYRAArgAAspAPALH2SGLUSUTNALCFZACEPROPMLTCITEROCAT
7326-+------------------+
7326-+-------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
7326hypersaline lagoonHawaiiUSAUSANorth America
23170hypersaline lagoon on Laysan Atoll
60019Water from hypersaline lagoonHawaiian Islands,Laysan AtollUSAUSANorth America2000-10-01
119813Laysan hypersaline lagoonNorthwestern Hawaiian Islands, HawaiiUnited States of AmericaUSANorth America2000

isolation source categories

Cat1Cat2
#Environmental#Aquatic
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_13499.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_53;96_6919;97_8297;98_10195;99_13499&stattab=map
  • Last taxonomy: Malaciobacter halophilus subclade
  • 16S sequence: AF513455
  • Sequence Identity:
  • Total samples: 52
  • soil counts: 3
  • aquatic counts: 47
  • animal counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
73261Risk group (German classification)
1198131Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7326
  • description: Arcobacter halophilus strain LA31B 16S ribosomal RNA gene, partial sequence
  • accession: AF513455
  • length: 1402
  • database: ena
  • NCBI tax ID: 197482

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Malaciobacter halophilus CCUG 53805GCA_003346755completencbi197482
66792Malaciobacter halophilus DSM 18005GCA_002837275scaffoldncbi197482
66792Arcobacter halophilus strain CCUG 53805197482.10completepatric197482
66792Arcobacter halophilus strain DSM 18005197482.6wgspatric197482
66792Arcobacter halophilus CCUG 538052847264534completeimg197482
66792Arcobacter halophilus DSM 180052873824862draftimg197482

GC content

  • @ref: 23170
  • GC-content: 35.0
  • method: Thermal denaturation, fluorometry

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileyes88.506no
flagellatedyes86.839yes
gram-positiveno98.998yes
anaerobicno63.774yes
aerobicno94.065yes
halophileno62.307no
spore-formingno93.81no
glucose-utilno81.406yes
thermophileno98.297yes
glucose-fermentno90.292no

External links

@ref: 7326

culture collection no.: CCUG 53805, DSM 18005, ATCC BAA 1022, CIP 108450

straininfo link

  • @ref: 71744
  • straininfo: 138970

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879267Arcobacter halophilus sp. nov., the first obligate halophile in the genus Arcobacter.Donachie SP, Bowman JP, On SLW, Alam MInt J Syst Evol Microbiol10.1099/ijs.0.63581-02005Arcobacter/*classification/cytology/*isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, Bacterial, Genes, rRNA, Growth Inhibitors/pharmacology, Hawaii, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/*pharmacology, *Water MicrobiologyEnzymology
Phylogeny19654359Arcobacter marinus sp. nov.Kim HM, Hwang CY, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.007740-02009Arcobacter/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Genetics30533711Complete Genome Sequence of the Arcobacter halophilus Type Strain CCUG 53805.Miller WG, Yee E, Bono JLMicrobiol Resour Announc10.1128/MRA.01077-182018

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7326Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18005)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18005
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
23170Stuart P. Donachie, John P. Bowman, Stephen L. W. On, Maqsudul Alam10.1099/ijs.0.63581-0Arcobacter halophilus sp. nov., the first obligate halophile in the genus ArcobacterIJSEM 55: 1271-1277 200515879267
33966Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6074
60019Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53805)https://www.ccug.se/strain?id=53805
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
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
71744Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138970.1StrainInfo: A central database for resolving microbial strain identifiers
119813Curators of the CIPCollection of Institut Pasteur (CIP 108450)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108450