Strain identifier

BacDive ID: 17309

Type strain: Yes

Species: Vibrio neonatus

Strain Designation: HDD 3-1, HDD3-1

Strain history: CIP <- 2004, IAM <- T. Sawabe, Univ. Hokkaido, Sapporo, Japan: strain HDD3-1

NCBI tax ID(s): 278860 (species)

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General

@ref: 7045

BacDive-ID: 17309

DSM-Number: 17531

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

description: Vibrio neonatus HDD 3-1 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from gut of abalone Haliotis discus discus.

NCBI tax id

  • NCBI tax id: 278860
  • Matching level: species

strain history

@refhistory
7045<- T. Sawabe
67770IAM 15060 <-- T. Sawabe HDD3-1.
121269CIP <- 2004, IAM <- T. Sawabe, Univ. Hokkaido, Sapporo, Japan: strain HDD3-1

doi: 10.13145/bacdive17309.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Vibrio
  • species: Vibrio neonatus
  • full scientific name: Vibrio neonatus Sawabe et al. 2005

@ref: 7045

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio neonatus

full scientific name: Vibrio neonatus Sawabe et al. 2005

strain designation: HDD 3-1, HDD3-1

type strain: yes

Morphology

cell morphology

  • @ref: 121269
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7045BACTO 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
33247Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121269CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7045positivegrowth28mesophilic
33247positivegrowth25mesophilic
67770positivegrowth25mesophilic
121269positivegrowth15-30
121269nogrowth5psychrophilic
121269nogrowth37mesophilic
121269nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121269
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
121269NaClpositivegrowth2-4 %
121269NaClnogrowth0 %
121269NaClnogrowth6 %
121269NaClnogrowth8 %
121269NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12126916947citrate-carbon source
1212694853esculin-hydrolysis
12126917632nitrate+reduction
12126916301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno
12126935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole+
12126915688acetoin-
12126917234glucose-

enzymes

@refvalueactivityec
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
121269oxidase+
121269beta-galactosidase-3.2.1.23
121269alcohol dehydrogenase-1.1.1.1
121269gelatinase-
121269amylase-
121269DNase-
121269caseinase-3.4.21.50
121269catalase+1.11.1.6
121269tween esterase-
121269lecithinase-
121269lipase-
121269lysine decarboxylase-4.1.1.18
121269ornithine decarboxylase-4.1.1.17
121269phenylalanine ammonia-lyase-4.3.1.24
121269tryptophan deaminase-
121269urease-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
121269-++--+----+------+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7045--------++-++-------+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
7045gut of abalone Haliotis discus discusHaliotis discus discusKanagawaJapanJPNAsia
67770Gut of abalone (Haliotis discus discus)Haliotis discus discusKanagawa Pref.JapanJPNAsia
121269Other, Japonese abalone (Haliotis discus discus), gutJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Mollusca
#Host Body-Site#Gastrointestinal tract#Stomach

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70451Risk group (German classification)
1212692Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7045
  • description: Vibrio neonatus strain HDD3-1 16S ribosomal RNA gene, partial sequence
  • accession: AY426979
  • length: 1406
  • database: ena
  • NCBI tax ID: 278860

Genome sequences

  • @ref: 66792
  • description: Vibrio neonatus JCM 21521
  • accession: GCA_024346975
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 278860

GC content

  • @ref: 67770
  • GC-content: 43.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno80.193no
gram-positiveno98.424no
anaerobicno96.965no
aerobicyes76.131no
halophileyes87.387no
spore-formingno96.264no
motileno82.774no
glucose-fermentyes86.895yes
thermophileno99.412yes
glucose-utilyes87.053no

External links

@ref: 7045

culture collection no.: DSM 17531, IAM 15060, LMG 19973, JCM 21521, CIP 108521

straininfo link

  • @ref: 86309
  • straininfo: 85092

literature

  • topic: Phylogeny
  • Pubmed-ID: 15490553
  • title: Vibrio neonatus sp. nov. and Vibrio ezurae sp. nov. isolated from the gut of Japanese abalones.
  • authors: Sawabe T, Hayashi K, Moriwaki J, Fukui Y, Thompson FL, Swings J, Christen R
  • journal: Syst Appl Microbiol
  • DOI: 10.1078/0723202041748154
  • year: 2004
  • mesh: Aerobiosis, Alginates/metabolism, Anaerobiosis, Animals, DNA Fingerprinting, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Flagella, Gastrointestinal Tract/microbiology, Genes, rRNA, Gluconates/metabolism, Glucuronic Acid/metabolism, Glyceraldehyde-3-Phosphate Dehydrogenase (NADP+)(Phosphorylating)/genetics, Glycerol/metabolism, Hexuronic Acids/metabolism, Mannose/metabolism, Molecular Sequence Data, Mollusca/*microbiology, Movement, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Vibrio/*classification/cytology/*isolation & purification/physiology, beta-Galactosidase/analysis
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
7045Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17531)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17531
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
33247Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6153
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/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
86309Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID85092.1StrainInfo: A central database for resolving microbial strain identifiers
121269Curators of the CIPCollection of Institut Pasteur (CIP 108521)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108521