Strain identifier
BacDive ID: 10528
Type strain:
Species: Chitiniphilus shinanonensis
Strain Designation: SAY3
Strain history: <- M. Shimosaka, Shinshu Univ., Ueda, Japan; SAY3 <- K. Sato and Y. Kato
NCBI tax ID(s): 1121280 (strain), 553088 (species)
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 id | Matching level |
---|---|
553088 | species |
1121280 | strain |
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
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 96.878 | |
69480 | 99.952 | negative |
multimedia
@ref | multimedia content | intellectual property rights | caption |
---|---|---|---|
16773 | https://www.dsmz.de/microorganisms/photos/DSM_23277.jpg | © Leibniz-Institut DSMZ | |
66793 | EM_DSM_23277_1.jpg | © HZI/Manfred Rohde | electron microscopic image |
66793 | EM_DSM_23277_2.jpg | © HZI/Manfred Rohde | electron microscopic image |
66793 | EM_DSM_23277_3.jpg | © HZI/Manfred Rohde | electron microscopic image |
66793 | EM_DSM_23277_4.jpg | © HZI/Manfred Rohde | electron microscopic image |
66793 | EM_DSM_23277_5.jpg | © HZI/Manfred Rohde | electron microscopic image |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16773 | REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) | yes | https://mediadive.dsmz.de/medium/535b | Name: 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 |
16773 | REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) | yes | https://mediadive.dsmz.de/medium/1a | Name: 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
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.748 |
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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Chitiniphilus shinanonensis gene for 16S rRNA, partial sequence, strain: NBRC 104970 | AB682233 | 1459 | ena | 553088 |
16773 | Chitiniphilus shinanonensis gene for 16S rRNA, partial sequence, strain: SAY3 | AB453176 | 1494 | ena | 553088 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Chitiniphilus shinanonensis DSM 23277 | GCA_000374805 | scaffold | ncbi | 1121280 |
66792 | Chitiniphilus shinanonensis DSM 23277 | 1121280.3 | wgs | patric | 1121280 |
66792 | Chitiniphilus shinanonensis DSM 23277 | 2517572136 | draft | img | 1121280 |
GC content
- @ref: 16773
- GC-content: 67.6
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 93.466 | no |
flagellated | yes | 83.198 | no |
gram-positive | no | 98.718 | no |
anaerobic | no | 98.419 | no |
aerobic | yes | 57.745 | no |
halophile | no | 94.613 | no |
spore-forming | no | 92.836 | no |
glucose-util | yes | 84.498 | no |
thermophile | no | 99.201 | yes |
glucose-ferment | no | 80.077 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16773 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23277) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23277 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
79804 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398868.1 | StrainInfo: A central database for resolving microbial strain identifiers |