Strain identifier

BacDive ID: 10528

Type strain: Yes

Species: Chitiniphilus shinanonensis

Strain Designation: SAY3

Strain history: <- M. Shimosaka, Shinshu Univ., Ueda, Japan; SAY3 <- K. Sato and Y. Kato

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16773

BacDive-ID: 10528

DSM-Number: 23277

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

description: Chitiniphilus shinanonensis SAY3 is a mesophilic, motile bacterium that was isolated from moat water.

NCBI tax id

NCBI tax idMatching level
553088species
1121280strain

strain history

  • @ref: 16773
  • history: <- M. Shimosaka, Shinshu Univ., Ueda, Japan; SAY3 <- K. Sato and Y. Kato

doi: 10.13145/bacdive10528.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Chromobacteriaceae
  • genus: Chitiniphilus
  • species: Chitiniphilus shinanonensis
  • full scientific name: Chitiniphilus shinanonensis Sato et al. 2009

@ref: 16773

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Chromobacteriaceae

genus: Chitiniphilus

species: Chitiniphilus shinanonensis

full scientific name: Chitiniphilus shinanonensis Sato et al. 2009

strain designation: SAY3

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes96.878
6948099.952negative

multimedia

@refmultimedia contentintellectual property rightscaption
16773https://www.dsmz.de/microorganisms/photos/DSM_23277.jpg© Leibniz-Institut DSMZ
66793EM_DSM_23277_1.jpg© HZI/Manfred Rohdeelectron microscopic image
66793EM_DSM_23277_2.jpg© HZI/Manfred Rohdeelectron microscopic image
66793EM_DSM_23277_3.jpg© HZI/Manfred Rohdeelectron microscopic image
66793EM_DSM_23277_4.jpg© HZI/Manfred Rohdeelectron microscopic image
66793EM_DSM_23277_5.jpg© HZI/Manfred Rohdeelectron microscopic image

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16773REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)yeshttps://mediadive.dsmz.de/medium/535bName: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) Composition: Trypticase soy broth 30.0 g/l Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l K2HPO4 2.5 g/l D(+)-Glucose 2.5 g/l Distilled water
16773REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

  • @ref: 16773
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.748

Isolation, sampling and environmental information

isolation

  • @ref: 16773
  • sample type: moat water
  • geographic location: Nagano Prefecture, Ueda Castle
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

Safety information

risk assessment

  • @ref: 16773
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Chitiniphilus shinanonensis gene for 16S rRNA, partial sequence, strain: NBRC 104970AB6822331459ena553088
16773Chitiniphilus shinanonensis gene for 16S rRNA, partial sequence, strain: SAY3AB4531761494ena553088

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chitiniphilus shinanonensis DSM 23277GCA_000374805scaffoldncbi1121280
66792Chitiniphilus shinanonensis DSM 232771121280.3wgspatric1121280
66792Chitiniphilus shinanonensis DSM 232772517572136draftimg1121280

GC content

  • @ref: 16773
  • GC-content: 67.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes93.466no
flagellatedyes83.198no
gram-positiveno98.718no
anaerobicno98.419no
aerobicyes57.745no
halophileno94.613no
spore-formingno92.836no
glucose-utilyes84.498no
thermophileno99.201yes
glucose-fermentno80.077no

External links

@ref: 16773

culture collection no.: DSM 23277, NBRC 104970, NCIMB 14509

straininfo link

  • @ref: 79804
  • straininfo: 398868

literature

  • topic: Phylogeny
  • Pubmed-ID: 19436131
  • title: Chitiniphilus shinanonensis gen. nov., sp. nov., a novel chitin-degrading bacterium belonging to Betaproteobacteria.
  • authors: Sato K, Kato Y, Taguchi G, Nogawa M, Yokota A, Shimosaka M
  • journal: J Gen Appl Microbiol
  • DOI: 10.2323/jgam.55.147
  • year: 2009
  • mesh: Chemotaxis, Chitin/*metabolism, Microscopy, Electron, Transmission, Molecular Sequence Data, Neisseriaceae/*classification/enzymology/genetics/*metabolism/ultrastructure, Phylogeny, RNA, Ribosomal, 16S/genetics, Water Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16773Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23277)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23277
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
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
79804Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398868.1StrainInfo: A central database for resolving microbial strain identifiers