Strain identifier

BacDive ID: 6015

Type strain: Yes

Species: Halomonas cupida

Strain history: CIP <- 2005, DSM, ATCC <- P. Baumann, Hawaii Univ., USA: strain 79, Alcaligenes cupidus

NCBI tax ID(s): 44933 (species)

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General

@ref: 1746

BacDive-ID: 6015

DSM-Number: 4740

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

description: Halomonas cupida DSM 4740 is a mesophilic, motile bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 44933
  • Matching level: species

strain history

@refhistory
1746<- ATCC <- P. Baumann
67770IAM 12552 <-- ATCC 27124 <-- P. Baumann 79.
118818CIP <- 2005, DSM, ATCC <- P. Baumann, Hawaii Univ., USA: strain 79, Alcaligenes cupidus

doi: 10.13145/bacdive6015.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Halomonas
  • species: Halomonas cupida
  • full scientific name: Halomonas cupida (Baumann et al. 1972) Dobson and Franzmann 1996
  • synonyms

    @refsynonym
    20215Alcaligenes cupidus
    20215Deleya cupida

@ref: 1746

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas cupida

full scientific name: Halomonas cupida (Baumann et al. 1972) Dobson and Franzmann 1996

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.526
6948099.881negative
118818nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1746BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 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
1746MARINE AGAR (DSMZ Medium 123)yeshttps://mediadive.dsmz.de/medium/123Name: MARINE AGAR (DSMZ Medium 123) Composition: NaCl 24.0 g/l Agar 15.0 g/l MgCl2 x 6 H2O 11.0 g/l Bacto peptone 5.0 g/l Na2SO4 4.0 g/l CaCl2 x 6 H2O 2.0 g/l Yeast extract 1.0 g/l KCl 0.7 g/l KBr 0.1 g/l SrCl2 x 6 H2O 0.04 g/l H3BO3 0.03 g/l NaSiO3 x 9 H2O 0.005 g/l NaF 0.003 g/l NH4NO3 0.002 g/l Fe(III)PO4 x 4 H2O 0.001 g/l Distilled water
34123Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118818CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
118818CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
1746positivegrowth25mesophilic
1746positivegrowth26mesophilic
34123positivegrowth30mesophilic
46437positivegrowth26mesophilic
67770positivegrowth25mesophilic
118818positivegrowth5-41
118818nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.957

halophily

  • @ref: 118818
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11881816947citrate+carbon source
1188184853esculin-hydrolysis
118818606565hippurate+hydrolysis
11881817632nitrate+reduction
11881816301nitrite-reduction
11881815792malonate+assimilation
11881817632nitrate-respiration

metabolite production

  • @ref: 118818
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
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
118818oxidase+
118818beta-galactosidase+3.2.1.23
118818alcohol dehydrogenase-1.1.1.1
118818gelatinase+/-
118818amylase-
118818DNase+
118818caseinase-3.4.21.50
118818catalase+1.11.1.6
118818tween esterase+
118818gamma-glutamyltransferase+2.3.2.2
118818lecithinase-
118818lipase-
118818lysine decarboxylase-4.1.1.18
118818ornithine decarboxylase-4.1.1.17
118818phenylalanine ammonia-lyase-4.3.1.24
118818protease-
118818tryptophan deaminase-
118818urease-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
118818-+++-++---++---++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118818+++++-+++++++--++++++++---+++--+++++++-++++++-+++++--++++--++-++-------+++-++-++++++--+-+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1746seawater
46437Seawater enrichment with allantoinoff coast of Oahu HawaiiUSAUSANorth America
118818Environment, SeawaterHawaiiUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_5920.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_430;97_491;98_562;99_5920&stattab=map
  • Last taxonomy: Halomonas cupida
  • 16S sequence: AB681733
  • Sequence Identity:
  • Total samples: 376
  • soil counts: 42
  • aquatic counts: 157
  • animal counts: 145
  • plant counts: 32

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17461Risk group (German classification)
1188181Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halomonas cupida partial 16S rRNA gene, strain DSM 4740FN2577421464ena44933
20218Halomonas cupida genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1207AB3672111207ena44933
20218Halomonas cupida genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1268AB3672121268ena44933
20218Halomonas cupida gene for 16S rRNA, partial sequence, strain: NBRC 102219AB6817331465ena44933
1746Halomonas cupida strain DSM 4740 16S ribosomal RNA gene, partial sequenceL426151471ena44933

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas cupida strain DSM 474044933.4wgspatric44933
66792Halomonas cupida strain NBRC 10221944933.8wgspatric44933
66792Halomonas cupida DSM 47402599185207draftimg44933
67770Halomonas cupida NBRC 102219GCA_007991155contigncbi44933
67770Halomonas cupida DSM 4740GCA_900142755scaffoldncbi44933

GC content

@refGC-contentmethod
6777060thermal denaturation, midpoint method (Tm)
6777060.7Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.511no
anaerobicno99.297no
halophileyes84.289no
spore-formingno97.284no
glucose-utilyes94.187no
aerobicyes96.021no
flagellatedyes66.399no
thermophileno98.821no
motileyes91.29no
glucose-fermentno72.255no

External links

@ref: 1746

culture collection no.: DSM 4740, ATCC 27124, CCUG 16075, LMG 3448, CIP 74.06, JCM 20632, CECT 5001, CIP 103199, IAM 12552, NBRC 102219, NCIMB 1978, CIP 74.6

straininfo link

  • @ref: 75501
  • straininfo: 2161

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24425813Halomonas huangheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.Miao C, Jia F, Wan Y, Zhang W, Lin M, Jin WInt J Syst Evol Microbiol10.1099/ijs.0.056556-02013Alkalies, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Halomonas/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny27380915Halomonas sediminicola sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment.Lee JC, Kim SJ, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0012782016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Halomonas/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Salinity, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1746Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4740)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4740
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
34123Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14970
46437Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 16075)https://www.ccug.se/strain?id=16075
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/
68382Automatically annotated from API zym
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
75501Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2161.1StrainInfo: A central database for resolving microbial strain identifiers
118818Curators of the CIPCollection of Institut Pasteur (CIP 103199)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103199