Strain identifier

BacDive ID: 17339

Type strain: Yes

Species: Vibrio pacinii

Strain Designation: STD3 1057

Strain history: CIP <- 2003, CAIM <- LMG <- Xu

NCBI tax ID(s): 1123494 (strain), 170674 (species)

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General

@ref: 7836

BacDive-ID: 17339

DSM-Number: 19139

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

description: Vibrio pacinii STD3 1057 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from nauplii of shrimp Penaeus chinensis.

NCBI tax id

NCBI tax idMatching level
170674species
1123494strain

strain history

@refhistory
7836<- CAIM <- F. L. Thompson, Univ. Ghent
121504CIP <- 2003, CAIM <- LMG <- Xu

doi: 10.13145/bacdive17339.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Vibrio
  • species: Vibrio pacinii
  • full scientific name: Vibrio pacinii Gomez-Gil et al. 2003

@ref: 7836

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio pacinii

full scientific name: Vibrio pacinii Gomez-Gil et al. 2003

strain designation: STD3 1057

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
125438yes92.161
12543899.8negative
12543999.2negative
121504yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7836MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)yeshttps://mediadive.dsmz.de/medium/514fName: MARINE BROTH (ROTH CP73) (DSMZ Medium 514f) Composition: NaCl 19.4 g/l Agar 15.0 g/l MgCl2 8.8 g/l 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
33911Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121504CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121504CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
7836positivegrowth28
33911positivegrowth30
121504positivegrowth5-37
121504nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
121504facultative anaerobe
125439obligate aerobe97.7

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 98.6

halophily

@refsaltgrowthtested relationconcentration
121504NaClpositivegrowth2-10 %
121504NaClnogrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12150416947citrate-carbon source
1215044853esculin+hydrolysis
12150417234glucose+fermentation
12150417716lactose-fermentation
12150417632nitrate+reduction
12150416301nitrite+reduction
121504132112sodium thiosulfate-builds gas from
12150417234glucose-degradation
12150417632nitrate+respiration
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837117634D-glucose+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
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
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
6836935581indoleno
12150435581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12150415688acetoin-
12150417234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382alkaline phosphatase+3.1.3.1
121504oxidase+
121504beta-galactosidase+3.2.1.23
121504alcohol dehydrogenase-1.1.1.1
121504gelatinase+
121504amylase+
121504DNase+
121504caseinase+3.4.21.50
121504catalase+1.11.1.6
121504tween esterase-
121504gamma-glutamyltransferase+2.3.2.2
121504lecithinase-
121504lipase-
121504lysine decarboxylase-4.1.1.18
121504ornithine decarboxylase-4.1.1.17
121504phenylalanine ammonia-lyase+4.3.1.24
121504tryptophan deaminase-
121504urease-3.5.1.5
68369gelatinase+
68369urease-3.5.1.5
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68369cytochrome oxidase+1.9.3.1
68369beta-glucosidase+3.2.1.21
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
121504-++--++---++-+------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7836+-++-++++--+-++--+--+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121504---------+/-++/-------------+/------------------------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121504++++---+-+++++----++-----------+-+--------------+++--+-----++--------------+---++-+------++++++--+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
7836nauplii of shrimp Penaeus chinensisPenaeus chinensisLaizhouChinaCHNAsia
121504Shrimp, Penaeus drinensisLaizhou, ShandongChinaCHNAsia1996

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
78361Risk group (German classification)
1215042Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7836
  • description: Vibrio sp. LMG 19999 16S rRNA gene, strain LMG 19999
  • accession: AJ316194
  • length: 1494
  • database: nuccore
  • NCBI tax ID: 170674

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio pacinii DSM 19139GCA_000711795scaffoldncbi1123494
66792Vibrio pacinii DSM 191391123494.3wgspatric1123494
66792Vibrio pacinii DSM 191392565956518draftimg1123494

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.8no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.601yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no65.175yes
125438spore-formingspore-formingAbility to form endo- or exosporesno89.365no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.481yes
125438motile2+flagellatedAbility to perform flagellated movementyes92.161no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.6
125439BacteriaNetmotilityAbility to perform movementyes79.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.7

External links

@ref: 7836

culture collection no.: DSM 19139, CAIM 530, CIP 108197, LMG 19999

straininfo link

  • @ref: 86339
  • straininfo: 97596

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130050Vibrio pacinii sp. nov., from cultured aquatic organisms.Gomez-Gil B, Thompson FL, Thompson CC, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.02670-02003Acetoin/metabolism, Animals, Aquaculture, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Indoles/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Vibrio/classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny25964518Vibrio salilacus sp. nov., a new member of the Anguillarum clade with six alleles of the 16S rRNA gene from a saline lake.Zhong ZP, Liu Y, Liu HC, Wang F, Zhou YG, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.0003162015Alleles, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Lakes/*microbiology, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Sodium Chloride/analysis, Vibrio/*classification/genetics/isolation & purificationGenetics

Reference

@idauthorscataloguedoi/urltitle
7836Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19139)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19139
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
33911Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5792
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)
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
86339Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97596.1StrainInfo: A central database for resolving microbial strain identifiers
121504Curators of the CIPCollection of Institut Pasteur (CIP 108197)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108197
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