Strain identifier

BacDive ID: 10460

Type strain: Yes

Species: Iodobacter fluviatilis

Strain Designation: 2236

Strain history: CIP <- 1989, LMG <- 1985, Surrey Univ., Guildford, UK: strain 2236 <- M.O. Moss: strain Sp3 (= strain 165), Chromobacterium fluviatile <- C. Ryal

NCBI tax ID(s): 537 (species)

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General

@ref: 1466

BacDive-ID: 10460

DSM-Number: 3764

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Iodobacter fluviatilis 2236 is a mesophilic, motile bacterium of the family Chromobacteriaceae.

NCBI tax id

  • NCBI tax id: 537
  • Matching level: species

strain history

@refhistory
1466<- NCTC <- M. Moss
67770IAM 13652 <-- NCTC 11159 <-- M. O. Moss 165.
119415CIP <- 1989, LMG <- 1985, Surrey Univ., Guildford, UK: strain 2236 <- M.O. Moss: strain Sp3 (= strain 165), Chromobacterium fluviatile <- C. Ryal

doi: 10.13145/bacdive10460.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Chromobacteriaceae
  • genus: Iodobacter
  • species: Iodobacter fluviatilis
  • full scientific name: Iodobacter fluviatilis corrig. (Moss et al. 1981) Logan 1989

  • synonyms

    @refsynonym
    20215Iodobacter fluviatile
    20215Chromobacterium fluviatile

@ref: 1466

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Chromobacteriaceae

genus: Iodobacter

species: Iodobacter fluviatilis

full scientific name: Iodobacter fluviatilis (Moss et al. 1981) Logan 1989

strain designation: 2236

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes97.968
6948099.997negative

pigmentation

  • @ref: 67770
  • production: yes
  • color: violet
  • name: violacein

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1466NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
1466BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
36471MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119415CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1466positivegrowth30mesophilic
36471positivegrowth22psychrophilic
49906positivegrowth25mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.942

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

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
49906---------------------

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typeisolation date
1466Surrey, River WeyUnited KingdomGBREurope
49906SurreyUnited KingdomGBREuropeRiver
67770Water sample from the River Wey
119415SurreyUnited KingdomGBREuropeEnvironment, Fresh water, Wey river1977

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #River (Creek)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
14661Risk group (German classification)
1194151Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.fluviatile 16S ribosomal RNA, complete cdsM225111473ena537
20218Iodobacter fluviatilis 16S rRNA gene, partialAJ247214451ena537
20218Iodobacter fluviatilis gene for 16S rRNA, partial sequence, strain: NBRC 102505AB6818391459ena537

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Iodobacter fluviatilis strain DSM 3764537.5wgspatric537
66792Iodobacter fluviatilis strain NCTC11159537.4wgspatric537
66792Iodobacter fluviatilis DSM 37642802428850draftimg537
66792Iodobacter fluviatilis NCTC 111592831541896draftimg537
67770Iodobacter fluviatilis DSM 3764GCA_004346505scaffoldncbi537
67770Iodobacter fluviatilis NCTC11159GCA_900451195contigncbi537

GC content

  • @ref: 67770
  • GC-content: 50-52
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno82no
gram-positiveno98.574no
anaerobicno98.48no
halophileno95.174no
spore-formingno94.77no
glucose-utilyes93.045no
thermophileno99.705yes
aerobicyes76.144no
motileyes90.296no
glucose-fermentno71.512no
flagellatedyes86.588no

External links

@ref: 1466

culture collection no.: DSM 3764, ATCC 33051, CCM 3308, NCTC 11159, CCUG 30103, JCM 9044, CIP 103351, IAM 13652, LMG 6630, NBRC 102505, NCIMB 2053

straininfo link

  • @ref: 79737
  • straininfo: 3023

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280319Chitinibacter tainanensis gen. nov., sp. nov., a chitin-degrading aerobe from soil in Taiwan.Chern LL, Stackebrandt E, Lee SF, Lee FL, Chen JK, Fu HMInt J Syst Evol Microbiol10.1099/ijs.0.02834-02004Bacterial Typing Techniques, Base Composition, Chitin/*metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Fatty Acids/analysis, Flagella/ultrastructure, Genes, rRNA, Microscopy, Electron, Microscopy, Phase-Contrast, Molecular Sequence Data, Neisseriaceae/*classification/cytology/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, *Soil Microbiology, Taiwan, TemperatureEnzymology
Phylogeny16280491Silvimonas terrae gen. nov., sp. nov., a novel chitin-degrading facultative anaerobe belonging to the 'Betaproteobacteria'.Yang HC, Im WT, An DS, Park WS, Kim IS, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63837-02005Bacteria, Anaerobic, Base Composition, Biodegradation, Environmental, Chitin/*metabolism, DNA, Bacterial/analysis/chemistry/isolation & purification, DNA, Ribosomal/analysis/chemistry, Molecular Sequence Data, Neisseriaceae/classification/genetics/*metabolism/ultrastructure, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Sequence Analysis, DNAMetabolism
Phylogeny17329799Deefgea rivuli gen. nov., sp. nov., a member of the class Betaproteobacteria.Stackebrandt E, Lang E, Cousin S, Pauker O, Brambilla E, Kroppenstedt R, Lunsdorf HInt J Syst Evol Microbiol10.1099/ijs.0.64771-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Genome, Bacterial, Germany, Molecular Sequence Data, Neisseriaceae/*classification/genetics/ultrastructure, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Water MicrobiologyGenetics
Phylogeny22888184Iodobacter limnosediminis sp. nov., isolated from Arctic lake sediment.Su W, Zhou Z, Jiang F, Chang X, Liu Y, Wang S, Kan W, Xiao M, Shao M, Peng F, Fang CInt J Syst Evol Microbiol10.1099/ijs.0.039982-02012Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Lakes/*microbiology, Molecular Sequence Data, Neisseriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water MicrobiologyGenetics
Phylogeny23291899Iodobacter arcticus sp. nov., a psychrotolerant bacterium isolated from meltwater stream sediment of an Arctic glacier.Srinivas TNR, Manasa P, Begum Z, Sunil B, Sailaja B, Singh SK, Prasad S, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.044776-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Ice Cover/*microbiology, Molecular Sequence Data, Neisseriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/microbiology, Sequence Analysis, DNA, Ubiquinone/analysis, *Water MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1466Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3764)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3764
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
36471Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15139
49906Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30103)https://www.ccug.se/strain?id=30103
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
79737Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3023.1StrainInfo: A central database for resolving microbial strain identifiers
119415Curators of the CIPCollection of Institut Pasteur (CIP 103351)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103351