Name: Shinella yambaruensis MS-4
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13905

Type strain:

Species: Shinella yambaruensis

Strain Designation: MS-4

Culture col. no.: DSM 18801, NBRC 102122

Strain history: <- T. Matsui, Center of Molecular Biosciences, University of the Ryukyus; MS-4

NCBI tax ID(s): 415996 (species)

SI-ID 397399

DSM 18801

Special Collections

Section

Shinella yambaruensis MS-4 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

Gram-negative
rod-shaped
aerobe
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Rhizobiaceae*
	Genus	*Shinella*
	Species	**Shinella yambaruensis**
	Full Scientific Name (LPSN)	Shinella yambaruensis Matsui et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #32445]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.5

[Ref.: #32445]	Cell length	1.6-2.1 µm

[Ref.: #32445]	Cell width	1.0-1.2 µm

[Ref.: #32445]	Cell shape	rod-shaped

[Ref.: #32445]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7706]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #7706]

Culture medium growth

[Ref.: #7706]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7706]

Culture medium composition

expand / minimize

[Ref.: #7706]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7706]

Culture medium growth

[Ref.: #7706]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7706]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7706]	growth	28 °C
[Ref.: #32445]	growth	15-42 °C
[Ref.: #32445]	optimum	28.5 °C

	pH	Kind of pH		pH
[Ref.: #32445]			optimum	6.5
[Ref.: #32445]			growth	4-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32445]

Oxygen tolerance

aerobe

[Ref.: #32445]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %93.236

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32445]		NaCl		growth	0-2	%
[Ref.: #32445]		NaCl		optimum	1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32445]	arabinose ChEBI	+	carbon source
[Ref.: #32445]	cellobiose ChEBI	+	carbon source
[Ref.: #32445]	esculin ChEBI	+	hydrolysis
[Ref.: #32445]	fructose ChEBI	+	carbon source
[Ref.: #32445]	fucose ChEBI	+	carbon source
[Ref.: #32445]	galactose ChEBI	+	carbon source
[Ref.: #32445]	glucose ChEBI	+	carbon source
[Ref.: #32445]	glycerol ChEBI	+	carbon source
[Ref.: #32445]	L-arabitol ChEBI	+	carbon source
[Ref.: #32445]	maltose ChEBI	+	carbon source
[Ref.: #32445]	mannitol ChEBI	+	carbon source
[Ref.: #32445]	mannose ChEBI	+	carbon source
[Ref.: #32445]	rhamnose ChEBI	+	carbon source
[Ref.: #32445]	ribitol ChEBI	+	carbon source
[Ref.: #32445]	ribose ChEBI	+	carbon source
[Ref.: #32445]	sorbitol ChEBI	+	carbon source
[Ref.: #32445]	sucrose ChEBI	+	carbon source
[Ref.: #32445]	trehalose ChEBI	+	carbon source
[Ref.: #32445]	xylitol ChEBI	+	carbon source
[Ref.: #32445]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32445]		catalase	+	1.11.1.6
[Ref.: #32445]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #7706]	Sample type/isolated from	soil
[Ref.: #7706]	Geographic location (country and/or sea, region)	Okinawa main island, Yambaru area, Ryukyu Archipelago
[Ref.: #7706]	Country	Japan
[Ref.: #7706]	Country ISO 3 Code	JPN
[Ref.: #7706]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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

[Ref.: #7706]

Biosafety level

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.: #7706]	Shinella yambaruensis gene for 16S rRNA, partial sequence, strain: MS4	AB285481	1443	GenBank ENA	415996 tax ID
[Ref.: #20218]	Shinella yambaruensis gene for 16S rRNA, partial sequence, strain: NBRC 102122	AB681707	1411	GenBank ENA	415996 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Shinella yambaruensis DSM 18801	GCA_022899355	scaffold	GenBank ENA	415996 tax ID	*
[Ref.: #66792]	Shinella yambaruensis DSM 18801	GCA_025656855	scaffold	GenBank ENA	415996 tax ID	*

[Ref.: #7706]

GC-content

66.4 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Shinella yambaruensis DSM 18801 NCBI: GCA_022899355.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.5	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.326	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	85.278	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	93.236	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.75	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	68.309	no

Availability in culture collections External links

[Ref.: #7706]

Culture collection no.

DSM 18801, NBRC 102122

[Ref.: #83080]

SI-ID 397399

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Shinella yambaruensis sp. nov., a 3-methyl-sulfolane-assimilating bacterium isolated from soil.	Matsui T, Shinzato N, Tamaki H, Muramatsu M, Hanada S	Int J Syst Evol Microbiol	10.1099/ijs.0.65510-0	2009	*

References

#7706

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18801

#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 )

#32445

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28667 (see below)

#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) .

#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) .

#83080

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-ID397399.1 )

#28667

IJSEM 536 2009 ( DOI 10.1099/ijs.0.65510-0 , PubMed 19244436 )

* These data were automatically processed and therefore are not curated

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Shinella yambaruensis DSM 18801

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