Strain identifier

BacDive ID: 17290

Type strain: Yes

Species: Vibrio penaeicida

Strain Designation: KH-1

Strain history: CIP <- 1995, K. Muroga, Hiroshima Univ., Hiroshima, Japan: strain KH-1 <- K. Momoyama

NCBI tax ID(s): 1123495 (strain), 104609 (species)

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General

@ref: 5335

BacDive-ID: 17290

DSM-Number: 14398

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

description: Vibrio penaeicida KH-1 is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from kuruma prawns .

NCBI tax id

NCBI tax idMatching level
104609species
1123495strain

strain history

@refhistory
5335<- IFO <- K. Ishimaru; KH-1
67770K. Muroga KH-1 <-- K. Momoyama.
121659CIP <- 1995, K. Muroga, Hiroshima Univ., Hiroshima, Japan: strain KH-1 <- K. Momoyama

doi: 10.13145/bacdive17290.20230509.8.1

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 penaeicida
  • full scientific name: Vibrio penaeicida Ishimaru et al. 1995

@ref: 5335

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio penaeicida

full scientific name: Vibrio penaeicida Ishimaru et al. 1995

strain designation: KH-1

type strain: yes

Morphology

cell morphology

  • @ref: 121659
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5335BACTO 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
40146Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121659CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5335positivegrowth28mesophilic
40146positivegrowth22psychrophilic
67770positivegrowth26mesophilic
121659positivegrowth22-30
121659nogrowth5psychrophilic
121659nogrowth37mesophilic
121659nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121659
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
121659NaClpositivegrowth2-4 %
121659NaClnogrowth0 %
121659NaClnogrowth6 %
121659NaClnogrowth8 %
121659NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68368L-arabinose-fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol-fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
121659citrate-carbon source16947
121659glucose-fermentation17234
121659lactose-fermentation17716
121659nitrate+reduction17632
121659nitrite-reduction16301
121659sodium thiosulfate-builds gas from132112
121659glucose+degradation17234

antibiotic resistance

  • @ref: 121659
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12165935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12165915688acetoin-
12165917234glucose-

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
121659oxidase+
121659beta-galactosidase+3.2.1.23
121659alcohol dehydrogenase-1.1.1.1
121659gelatinase+
121659DNase+
121659caseinase+3.4.21.50
121659catalase+1.11.1.6
121659tween esterase-
121659lecithinase+
121659lipase+
121659lysine decarboxylase-4.1.1.18
121659ornithine decarboxylase-4.1.1.17
121659urease-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
121659-+++-++-+-++---+-+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
5335+----------+-----++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121659+/----+----+/-+++--------+--+/--+++/---+---++------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121659+++++-+--++--+++--++----+-----++-----+----------++---------++-+------------+--+++-+------+++-++---+

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic locationisolation date
5335kuruma prawns (Penaeus japonicus)Penaeus japonicusJapanJPNAsia
67770Kuruma prawn (Penaeus japonicus)Penaeus japonicusJapanJPNAsiaKagoshima Pref.
121659Animal, Fish, Penaeus japonicusJapanJPNAsiaTanegashima Island1989

isolation source categories

  • Cat1: #Host
  • Cat2: #Arthropoda
  • Cat3: #Crustacea

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
5335yes1Risk group (German classification)
1216592Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio penaeicida 16S rRNA gene, strain DSM 14398TAJ4214441504ena104609
20218Vibrio penaeicida partial 16S rRNA gene, strain LMG 19663TAJ4371911493ena104609
20218Vibrio penaeicida gene for 16S rRNA, partial sequence, strain: NBRC 15640AB6809261466ena104609

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio penaeicida IFO 15640TGCA_019977755completencbi104609
66792Vibrio penaeicida strain CAIM 285104609.6wgspatric104609
66792Vibrio penaeicida strain IFO 15640 strain IFO 15640T104609.11wgspatric104609
67770Vibrio penaeicida CAIM 285GCA_003970425scaffoldncbi104609
66792Vibrio penaeicida strain IFO 15640 strain IFO 15640T104609.26wgspatric104609
66792Vibrio penaeicida strain IFO 15640 strain IFO 15640T104609.16wgspatric104609
66792Vibrio penaeicida strain IFO 15640 strain IFO 15640T104609.21wgspatric104609

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes91.095no
gram-positiveno98.641no
anaerobicno97.416no
aerobicyes80.588no
halophileno55.005no
spore-formingno94.121no
motileyes92.45no
thermophileno99.746no
glucose-utilyes88.789no
glucose-fermentyes86.364yes

External links

@ref: 5335

culture collection no.: DSM 14398, IFO 15640, JCM 9123, NBRC 15640, ATCC 51841, CAIM 285, CIP 104417, LMG 19663, LMG 19518

straininfo link

  • @ref: 86291
  • straininfo: 12998

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology16408835Pathogenicity of Vibrio penaeicida for white shrimp Litopenaeus vannamei: a cysteine protease-like exotoxin as a virulence factor.Aguirre-Guzman G, Ascencio F, Saulnier DDis Aquat Organ10.3354/dao0672012005Animals, Chromatography, Liquid, Copper, Cysteine Endopeptidases/isolation & purification/*toxicity, Electrophoresis, Polyacrylamide Gel, Endopeptidase K, Hot Temperature, Lethal Dose 50, Leucine/analogs & derivatives, Penaeidae/*drug effects/*microbiology, Vibrio/chemistry/*pathogenicity, Virulence Factors/isolation & purification/*toxicityPhylogeny
Phylogeny34874245Vibrio ulleungensis sp. nov., isolated from Mytilus coruscus.Moon YL, Park JSInt J Syst Evol Microbiol10.1099/ijsem.0.0051362021Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mytilus/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry, *Vibrio/classification/isolation & purificationTranscriptome
Genetics35171089Comparative genome analyses of five Vibrio penaeicida strains provide insights into their virulence-related factors.Ragab W, Kawato S, Nozaki R, Kondo H, Hirono IMicrob Genom10.1099/mgen.0.0007662022Aquaculture, Base Composition, Comparative Genomic Hybridization/*methods, Drug Resistance, Bacterial/genetics, Genome, Bacterial, Genomic Islands, Genomics/methods, Interspersed Repetitive Sequences, Multigene Family, Nanopore Sequencing/methods, Phylogeny, Prophages/genetics, Vibrio/classification/*genetics, Vibrio Infections, Virulence/genetics, Virulence Factors/*genetics, Whole Genome SequencingPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5335Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14398)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14398
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
40146Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16324
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
86291Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12998.1StrainInfo: A central database for resolving microbial strain identifiers
121659Curators of the CIPCollection of Institut Pasteur (CIP 104417)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104417