Chitiniphilus shinanonensis SAY3 | Type strain | DSM 23277, NBRC 104970, NCIMB 14509 | BacDiveID:10528

Strain identifier

BacDive ID: 10528

Type strain:

Species: Chitiniphilus shinanonensis

Strain Designation: SAY3

Culture col. no.: DSM 23277, NBRC 104970, NCIMB 14509

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

NCBI tax ID(s): 1121280 (strain), 553088 (species)

SI-ID 398868

DSM 23277

Special Collections

DSMZ

Section

Chitiniphilus shinanonensis SAY3 is a Gram-negative bacterium that was isolated from moat water.

Gram-negative
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Neisseriales*
	Family	*Chromobacteriaceae*
	Genus	*Chitiniphilus*
	Species	**Chitiniphilus shinanonensis**
	Full Scientific Name (LPSN)	Chitiniphilus shinanonensis Sato et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %97.494

Multimedia content

Intellectual property rights:

© Leibniz-Institut DSMZ

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #16773]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]	Ability of spore formation	no Confidence in %90.109
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #16773]	Sample type/isolated from	moat water
[Ref.: #16773]	Geographic location (country and/or sea, region)	Nagano Prefecture, Ueda Castle
[Ref.: #16773]	Country	Japan
[Ref.: #16773]	Country ISO 3 Code	JPN
[Ref.: #16773]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

-

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

Biosafety level

1

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16773]	Chitiniphilus shinanonensis gene for 16S rRNA, partial sequence, strain: SAY3	AB453176	1494	GenBank ENA	553088 tax ID
[Ref.: #20218]	Chitiniphilus shinanonensis gene for 16S rRNA, partial sequence, strain: NBRC 104970	AB682233	1459	GenBank ENA	553088 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Chitiniphilus shinanonensis DSM 23277	GCA_000374805	scaffold	GenBank ENA	1121280 tax ID	*
[Ref.: #66792]	Chitiniphilus shinanonensis DSM 23277	1121280.3	wgs	PATRIC	1121280 tax ID	*
[Ref.: #66792]	Chitiniphilus shinanonensis DSM 23277	2517572136	draft	JGI IMG/M	1121280 tax ID	*

GC-content

67.6 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Chitiniphilus shinanonensis DSM 23277 DSM 23277 NCBI: GCA_000374805.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Chitiniphilus shinanonensis DSM 23277 DSM 23277 NCBI: GCA_000374805.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.494	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	90.93	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	50.86	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	90.109	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.73	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	76.776	no

Availability in culture collections External links

Culture collection no.

DSM 23277, NBRC 104970, NCIMB 14509

SI-ID 398868

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chitiniphilus shinanonensis gen. nov., sp. nov., a novel chitin-degrading bacterium belonging to Betaproteobacteria.	Sato K, Kato Y, Taguchi G, Nogawa M, Yokota A, Shimosaka M	J Gen Appl Microbiol	10.2323/jgam.55.147	2009	*

References

#16773

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23277

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#79804

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID398868.1 )

* These data were automatically processed and therefore are not curated

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