Strain identifier

BacDive ID: 17335

Type strain: Yes

Species: Vibrio rumoiensis

Strain history: CIP <- 2007, DSMZ <- CAIM <- LMG <- I. Yumoto, Nat. Industr. Res. Inst., Sapporo, Japan: S-1

NCBI tax ID(s): 76258 (species)

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General

@ref: 7838

BacDive-ID: 17335

DSM-Number: 19141

keywords: 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, rod-shaped

description: Vibrio rumoiensis DSM 19141 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from drain pool of fish processing plant.

NCBI tax id

  • NCBI tax id: 76258
  • Matching level: species

strain history

@refhistory
7838<- CAIM <- LMG <- ? <- I. Yumoto, Natl. Industrial Research Institute, Sapporo; S-1
122314CIP <- 2007, DSMZ <- CAIM <- LMG <- I. Yumoto, Nat. Industr. Res. Inst., Sapporo, Japan: S-1

doi: 10.13145/bacdive17335.20230509.8.1

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 rumoiensis
  • full scientific name: Vibrio rumoiensis Yumoto et al. 1999

@ref: 7838

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio rumoiensis

full scientific name: Vibrio rumoiensis Yumoto et al. 1999

type strain: yes

Morphology

cell morphology

  • @ref: 122314
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7838BACTO 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
37661Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122314CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7838positivegrowth28mesophilic
37661positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122314
  • oxygen tolerance: obligate aerobe

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
68371raffinose-builds acid from16634
68371melezitose+builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
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
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
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68369malate+assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369maltose-assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose-assimilation17634
68369gelatin-hydrolysis5291
68369esculin-hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate+reduction17632
122314nitrate+reduction17632
122314nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12231435581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

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
122314oxidase+
122314catalase+1.11.1.6
122314urease-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
122314-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7838+----------------++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122314+/---++/-+---++++----+/----+--+/-+/-++--+--+-+/--------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7838drain pool of fish processing plantJapanJPNAsia
122314Fish processing plant, drain poolJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Water reservoir (Aquarium/pool)
#Engineered#Food production#Aquaculture
#Engineered#Industrial#Plant (Factory)
#Host#Fishes

taxonmaps

  • @ref: 69479
  • File name: preview.99_13390.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_982;97_1142;98_1364;99_13390&stattab=map
  • Last taxonomy: Vibrio rumoiensis
  • 16S sequence: AB013297
  • Sequence Identity:
  • Total samples: 330
  • soil counts: 16
  • aquatic counts: 229
  • animal counts: 63
  • plant counts: 22

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
78381Risk group (German classification)
1223142Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7838
  • description: Vibrio rumoiensis gene for 16S rRNA, complete sequence
  • accession: AB013297
  • length: 1494
  • database: ena
  • NCBI tax ID: 76258

External links

@ref: 7838

culture collection no.: DSM 19141, CAIM 598, CIP 109752, FERM P-14531, LMG 20038

straininfo link

  • @ref: 86335
  • straininfo: 93881

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9872761Characterization of a facultatively psychrophilic bacterium, vibrio rumoiensis sp. nov., that exhibits high catalase activityYumoto I I, Iwata H, Sawabe T, Ueno K, Ichise N, Matsuyama H, Okuyama H, Kawasaki KAppl Environ Microbiol10.1128/AEM.65.1.67-72.19991999
Phylogeny17329785Vibrio litoralis sp. nov., isolated from a Yellow Sea tidal flat in Korea.Nam YD, Chang HW, Park JR, Kwon HY, Quan ZX, Park YH, Kim BC, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.64653-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Vibrio/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny19749036Vibrio casei sp. nov., isolated from the surfaces of two French red smear soft cheeses.Bleicher A, Neuhaus K, Scherer SInt J Syst Evol Microbiol10.1099/ijs.0.016493-02009Cheese/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Oxidoreductases/genetics/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Vibrio/*classification/enzymology/genetics/*isolation & purification, beta-Galactosidase/genetics/metabolismEnzymology
Phylogeny20382785Vibrio marisflavi sp. nov., isolated from seawater.Wang H, Liu J, Wang Y, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.022285-02010Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydroxybutyrates/analysis, Molecular Sequence Data, Phylogeny, Polyesters/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vibrio/*classification/genetics/*isolation & purification/physiologyGenetics
Phylogeny27199227Vibrio algivorus sp. nov., an alginate- and agarose-assimilating bacterium isolated from the gut flora of a turban shell marine snail.Doi H, Chinen A, Fukuda H, Usuda YInt J Syst Evol Microbiol10.1099/ijsem.0.0011652016Alginates, Animals, Aquatic Organisms/microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gastrointestinal Microbiome, Glucuronic Acid, Hexuronic Acids, Japan, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sepharose, Sequence Analysis, DNA, Snails/*microbiology, Ubiquinone/chemistry, Vibrio/*classification/genetics/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitle
7838Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19141)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19141
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
37661Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7530
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
86335Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID93881.1StrainInfo: A central database for resolving microbial strain identifiers
122314Curators of the CIPCollection of Institut Pasteur (CIP 109752)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109752