Strain identifier

BacDive ID: 17325

Type strain: Yes

Species: Beneckea nereis

Strain history: CIP <- 1988, NCIB <- 1972, P. Baumann: strain 80, Beneckea nereida

NCBI tax ID(s): 1219068 (strain), 693 (species)

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General

@ref: 8193

BacDive-ID: 17325

DSM-Number: 19584

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

description: Beneckea nereis DSM 19584 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater enriched with propanol.

NCBI tax id

NCBI tax idMatching level
1219068strain
693species

strain history

@refhistory
8193<- CCUG <- CECT <- NCMB <- P. Baumann; 80
67770IAM 14407 <-- ATCC 25917 <-- P. Baumann 80 ("Beneckea nereida").
121274CIP <- 1988, NCIB <- 1972, P. Baumann: strain 80, Beneckea nereida

doi: 10.13145/bacdive17325.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Beneckea
  • species: Beneckea nereis
  • full scientific name: Beneckea nereis corrig. (ex Baumann et al. 1971) Harwood et al. 1980

  • synonyms

    @refsynonym
    20215Beneckea nereida
    20215Vibrio nereis

@ref: 8193

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio nereis

full scientific name: Vibrio nereis (Harwood et al. 1980) Baumann et al. 1981

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
125438yes90.836
12543899.5negative
12543998.9negative
121274yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8193BACTO 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
40558Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121274CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
8193positivegrowth28
40558positivegrowth25
49289positivegrowth30
67770positivegrowth25
121274positivegrowth15-41
121274nogrowth5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
49289aerobe
121274facultative anaerobe
125439obligate aerobe98.8

spore formation

@refspore formationconfidence
125438no93.393
125439no99.4

halophily

@refsaltgrowthtested relationconcentration
121274NaClpositivegrowth2-10 %
121274NaClnogrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12127416947citrate-carbon source
1212744853esculin-hydrolysis
12127417234glucose+fermentation
12127417716lactose-fermentation
12127417632nitrate+reduction
12127416301nitrite-reduction
121274132112sodium thiosulfate-builds gas from
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
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

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleyes
12127435581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole+
12127415688acetoin-
12127417234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121274oxidase+
121274beta-galactosidase-3.2.1.23
121274alcohol dehydrogenase-1.1.1.1
121274gelatinase+/-
121274amylase-
121274caseinase-3.4.21.50
121274catalase+1.11.1.6
121274tween esterase-
121274lecithinase-
121274lipase-
121274lysine decarboxylase-4.1.1.18
121274ornithine decarboxylase-4.1.1.17
121274phenylalanine ammonia-lyase-4.3.1.24
121274tryptophan deaminase-
121274urease-3.5.1.5
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382esterase lipase (C 8)+
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121274-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
8193++++----+---++++-++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121274-----------+-----------+-------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121274---+---++----------++---------------------------+++++---------+--+---------++----+----+--++-++-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8193seawater enriched with propanolHawaii, off coast of OahuUSAUSANorth America
49289Seawater enriched with propanolHawaii,off coast of OahuUSAUSANorth America
67770Seawater enriched with propanolOahu, HIUSAUSANorth America
121274Environment, Seawater enriched with propanolOahu, HawaiiUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Environmental#Aquatic#Marine

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
81931Risk group (German classification)
1212742Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio nereis 16S rRNAD11212216nuccore693
20218Vibrio nereis 16S rRNAD11261199nuccore693
20218Vibrio nereis 16S rRNAD11310191nuccore693
20218Vibrio nereis strain ATCC 25917 16S ribosomal RNA gene, partial sequenceHQ8904631471nuccore693
8193V.nereis (ATCC 25917T) gene for 16S ribosomal RNAX747161436nuccore693
124043Vibrio nereis DNA, 16S-23S rRNA intergenic spacer and 23S rRNA, partial sequence, strain: IAM 14407.AB255725298nuccore693
124043Vibrio nereis gene for 16S rRNA, partial sequence, strain: NBRC 15637.AB6809231478nuccore693

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio nereis NBRC 156371219068.3wgspatric1219068
66792Vibrio nereis strain DSM 19584693.5wgspatric693
66792Vibrio nereis DSM 195842740892531draftimg693
66792Vibrio nereis NBRC 156372675903410draftimg1219068
67770Vibrio nereis NBRC 15637GCA_001591105contigncbi1219068
67770Vibrio nereis DSM 19584GCA_001274805contigncbi693

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.9
125439BacteriaNetmotilityAbility to perform movementyes81.3
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.4
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.495yes
125438spore-formingspore-formingAbility to form endo- or exosporesno93.393no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no66.889no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes90.836no

External links

@ref: 8193

culture collection no.: DSM 19584, ATCC 25917, CCUG 28585, CECT 595, CIP 75.05, LMG 3895, NCMB 1897, CIP 103194, JCM 21190, BCRC 12914, CAIM 322, IAM 14407, IFO 15637, JCM 1141, KCTC 12677, KCTC 2722, NBRC 15637, NCCB 73020, NCIMB 1897

straininfo link

  • @ref: 86325
  • straininfo: 5105

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8193Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19584)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19584
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
40558Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14964
49289Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28585)https://www.ccug.se/strain?id=28585
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)
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
86325Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5105.1StrainInfo: A central database for resolving microbial strain identifiers
121274Curators of the CIPCollection of Institut Pasteur (CIP 103194)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103194
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1