Strain identifier

BacDive ID: 17251

Type strain: Yes

Species: Aliivibrio logei

Strain Designation: 584, Baumann584

Strain history: CIP <- 1996, ATCC <- P. Baumann: strain 584, Photobacterium logei <- K.H. Nealson <- J. Baboss

NCBI tax ID(s): 688 (species)

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General

@ref: 15793

BacDive-ID: 17251

DSM-Number: 21555

keywords: 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, motile, rod-shaped, animal pathogen

description: Aliivibrio logei 584 is an aerobe, psychrophilic, Gram-negative animal pathogen that was isolated from gut of Arctic mussel.

NCBI tax id

  • NCBI tax id: 688
  • Matching level: species

strain history

@refhistory
15793<- NCIMB <- ATCC <- P. Baumann; 584 <- K. H. Nealson <- J. Baboss
120642CIP <- 1996, ATCC <- P. Baumann: strain 584, Photobacterium logei <- K.H. Nealson <- J. Baboss

doi: 10.13145/bacdive17251.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Aliivibrio
  • species: Aliivibrio logei
  • full scientific name: Aliivibrio logei (Harwood et al. 1980 ex Bang et al. 1978) Urbanczyk et al. 2007

  • synonyms

    @refsynonym
    20215Photobacterium logei
    20215Vibrio logei

@ref: 15793

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Aliivibrio

species: Aliivibrio logei

full scientific name: Aliivibrio logei (Harwood et al. 1980) Urbanczyk et al. 2007

strain designation: 584, Baumann584

type strain: yes

Morphology

cell morphology

  • @ref: 120642
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15793REACTIVATION WITH LIQUID MEDIUM 246 (DSMZ Medium 246a)yeshttps://mediadive.dsmz.de/medium/246aName: REACTIVATION WITH LIQUID MEDIUM 246 (DSMZ Medium 246a) Composition: Agar 20.0 g/l Beef extract 10.0 g/l Peptone 10.0 g/l Tap water Sea water
39153Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120642CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
15793positivegrowth15
39153positivegrowth15
47121positivegrowth14
120642positivegrowth15
120642nogrowth5
120642nogrowth22
120642nogrowth30
120642nogrowth37
120642nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
47121aerobe
120642facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
120642NaClnogrowth0 %
120642NaClnogrowth2 %
120642NaClnogrowth4 %
120642NaClnogrowth6 %
120642NaClnogrowth8 %
120642NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12064216947citrate-carbon source
1206424853esculin-hydrolysis
12064217234glucose-fermentation
12064217716lactose-fermentation
12064217632nitrate-reduction
12064216301nitrite-reduction
120642132112sodium thiosulfate-builds gas from
12064217234glucose+degradation
68371Potassium 5-ketogluconate+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
68371Potassium 2-ketogluconate-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
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
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
12064235581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12064215688acetoin-
12064217234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
120642oxidase+
120642beta-galactosidase-3.2.1.23
120642alcohol dehydrogenase-1.1.1.1
120642gelatinase-
120642catalase+1.11.1.6
120642gamma-glutamyltransferase-2.3.2.2
120642lysine decarboxylase-4.1.1.18
120642ornithine decarboxylase-4.1.1.17
120642phenylalanine ammonia-lyase-4.3.1.24
120642tryptophan deaminase-
120642urease+3.5.1.5
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucuronidase-3.2.1.31
68382cystine arylamidase-3.4.11.3
68382esterase (C 4)+
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
120642-+++------++---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15793+-+--+--+-+++++--+--+
15793+-+--+--+-++-++--++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120642-----------------+/-----------------------------+/--+

Isolation, sampling and environmental information

isolation

@refsample typecountrycontinent
15793gut of Arctic mussel
47121Gut of arctic mussel
120642Arctic mussel, gutArcticArctic

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1172.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_201;97_796;98_922;99_1172&stattab=map
  • Last taxonomy: Aliivibrio
  • 16S sequence: AJ437616
  • Sequence Identity:
  • Total samples: 4496
  • soil counts: 147
  • aquatic counts: 2162
  • animal counts: 1349
  • plant counts: 838

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
15793yes1Risk group (German classification)
1206422Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Aliivibrio logei strain ATCC 29985 16S ribosomal RNA gene, partial sequenceEU2212731467nuccore688
15793Vibrio logei 16S rRNA gene, strain NCIMB 2252AJ4376161377nuccore688

External links

@ref: 15793

culture collection no.: DSM 21555, ATCC 29985, CCUG 20283, CIP 104991, KCTC 52966, LMG 21012, NCIMB 2252

straininfo link

  • @ref: 86249
  • straininfo: 323293

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12383519Cloning, characterisation and phylogenetic analysis of the fur gene in Vibrio salmonicida and Vibrio logei.Colquhoun DJ, Sorum HGene10.1016/s0378-1119(02)00863-62002Amino Acid Sequence, Bacterial Proteins/*genetics, Base Sequence, Blotting, Southern, Cloning, Molecular, DNA, Bacterial/chemistry/genetics/metabolism, Deoxyribonuclease EcoRI/metabolism, Escherichia coli/genetics, Genetic Complementation Test, Molecular Sequence Data, Mutation, *Phylogeny, Repressor Proteins/*genetics, Sequence Analysis, DNA, Species Specificity, Vibrio/classification/*geneticsEnzymology
Phylogeny18048732Reclassification of Vibrio fischeri, Vibrio logei, Vibrio salmonicida and Vibrio wodanis as Aliivibrio fischeri gen. nov., comb. nov., Aliivibrio logei comb. nov., Aliivibrio salmonicida comb. nov. and Aliivibrio wodanis comb. nov.Urbanczyk H, Ast JC, Higgins MJ, Carson J, Dunlap PVInt J Syst Evol Microbiol10.1099/ijs.0.65081-02007Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Genes, rRNA, Molecular Sequence Data, Nucleoside-Phosphate Kinase/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vibrio/*classification/genetics/metabolismGenetics
Phylogeny19481895Multi-gene analysis reveals previously unrecognized phylogenetic diversity in Aliivibrio.Ast JC, Urbanczyk H, Dunlap PVSyst Appl Microbiol10.1016/j.syapm.2009.04.0052009Bacterial Proteins/*genetics, Bacterial Typing Techniques, Evolution, Molecular, Genes, rRNA/*genetics, *Genetic Variation, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Sequence Analysis, DNA/methods, Species Specificity, Symbiosis, Vibrionaceae/*classification/geneticsGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15793Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21555)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21555
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
39153Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16960
47121Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 20283)https://www.ccug.se/strain?id=20283
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
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
86249Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323293.1StrainInfo: A central database for resolving microbial strain identifiers
120642Curators of the CIPCollection of Institut Pasteur (CIP 104991)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104991