Strain identifier

BacDive ID: 17326

Type strain: Yes

Species: Beneckea nigripulchritudo

Strain Designation: 164

Strain history: CIP <- 1988, NCIB <- 1972, P. Baumann: strain 164, Beneckea nigripulchrituda

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

@ref: 15841

BacDive-ID: 17326

DSM-Number: 21607

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

description: Beneckea nigripulchritudo 164 is a mesophilic, Gram-negative, motile bacterium that was isolated from Sea water.

NCBI tax id

NCBI tax idMatching level
28173species
1051649strain

strain history

@refhistory
15841<- NCIMB <- P. Baumann, University of Hawaii; 164
121300CIP <- 1988, NCIB <- 1972, P. Baumann: strain 164, Beneckea nigripulchrituda

doi: 10.13145/bacdive17326.20230509.8.1

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 nigripulchritudo
  • full scientific name: Beneckea nigripulchritudo corrig. Baumann et al. 1971 (Approved Lists 1980)
  • synonyms

    @refsynonym
    20215Beneckea nigrapulchrituda
    20215Beneckea nigrapulchritoda
    20215Vibrio nigripulchritudo

@ref: 15841

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio nigripulchritudo

full scientific name: Vibrio nigripulchritudo (Baumann et al. 1971) Baumann et al. 1981

strain designation: 164

type strain: yes

Morphology

cell morphology

  • @ref: 121300
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15841BACTO 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
35504Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121300CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
15841positivegrowth28mesophilic
35504positivegrowth25mesophilic
121300positivegrowth15-41
121300nogrowth5psychrophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
121300NaClpositivegrowth2-6 %
121300NaClnogrowth0 %
121300NaClnogrowth8 %
121300NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose+fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12130016947citrate-carbon source
1213004853esculin-hydrolysis
12130017632nitrate+reduction
12130016301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12130035581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12130015688acetoin-
12130017234glucose-

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121300oxidase+
121300beta-galactosidase+3.2.1.23
121300alcohol dehydrogenase-1.1.1.1
121300gelatinase+
121300amylase+
121300caseinase+3.4.21.50
121300catalase+1.11.1.6
121300tween esterase+
121300gamma-glutamyltransferase+2.3.2.2
121300lecithinase+
121300lipase+
121300lysine decarboxylase-4.1.1.18
121300ornithine decarboxylase-4.1.1.17
121300phenylalanine ammonia-lyase-4.3.1.24
121300protease+
121300tryptophan deaminase-
121300urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121300-+++-++---++-----+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15841+-+--+++--+/-+-+--+++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121300+--+--++---+-++---++----+-----++-+---------------+----+-------+--+---------+---++-----+--++--++----

Isolation, sampling and environmental information

isolation

@refsample type
15841Sea water
121300Environment, Seawater enriched with chitin

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_641.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_312;98_520;99_641&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: X74717
  • Sequence Identity:
  • Total samples: 231
  • soil counts: 22
  • aquatic counts: 192
  • animal counts: 17

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
158411Risk group (German classification)
1213002Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio nigripulchritudo DNA, 16S-23S rRNA intergenic spacer and 23S rRNA, partial sequence, strain: ATCC 27043AB255726291ena1051649
20218Vibrio nigripulchritudo DNA, 16S-23S ribosomal RNA intergenic spacer, type G, including tRNA-Glu, strain: ATCC 27043AB515338468ena1051649
20218Vibrio nigripulchritudo DNA, 16S-23S ribosomal RNA intergenic spacer, type GLV, including tRNA-Glu, tRNA-Lys, tRNA-Val, strain: ATCC 27043AB515339723ena1051649
20218Vibrio nigripulchritudo DNA, 16S-23S ribosomal RNA intergenic spacer, type GLAV, including tRNA-Glu, tRNA-Lys, tRNA-Ala, tRNA-Val, strain: ATCC 27043AB515340762ena1051649
20218Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu gene, complete sequenceAF413009492ena1051649
20218Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu and tRNA-Val genes, complete sequenceAF413010729ena1051649
20218Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu and tRNA-Val genes, complete sequenceAF413011766ena1051649
20218Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu, tRNA-Ala, and tRNA-Val genes, complete sequenceAF413012800ena1051649
20218Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Ala gene, complete sequenceAF413013472ena1051649
20218Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Ala gene, complete sequenceAF413014474ena1051649
20218Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequenceAF413015571ena1051649
20218Vibrio nigripulchritudo 16S rRNAD11213218ena1051649
20218Vibrio nigripulchritudo 16S rRNAD11262214ena1051649
20218Vibrio nigripulchritudo 16S rRNAD11311191ena1051649
20218Vibrio nigripulchritudo 16S ribosomal RNA gene, partial sequenceHM7713521470ena1051649
15841V.nigripulchritudo (ATCC 27043T) gene for 16S ribosomal RNAX747171434ena1051649

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio nigripulchritudo ATCC 27043GCA_000222685contigncbi1051649
66792Vibrio nigripulchritudo ATCC 270431051649.3wgspatric1051649
66792Vibrio nigripulchritudo ATCC 270432512047078draftimg1051649

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes92.233no
flagellatedyes92.928no
gram-positiveno98.682no
anaerobicno98.363no
aerobicyes81.535no
halophileno53.366no
spore-formingno94.411no
thermophileno99.687yes
glucose-utilyes92.395no
glucose-fermentyes85.412no

External links

@ref: 15841

culture collection no.: DSM 21607, ATCC 27043, CAIM 323, CCUG 16376, CCUG 28586, CIP 103195, LMG 3896, NCIMB 1904

straininfo link

  • @ref: 86326
  • straininfo: 5108

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15841Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21607)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21607
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
35504Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14965
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
68369Automatically annotated from API 20NE
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
86326Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5108.1StrainInfo: A central database for resolving microbial strain identifiers
121300Curators of the CIPCollection of Institut Pasteur (CIP 103195)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103195