Shinella yambaruensis (DSM 18801, NBRC 102122, MS-4)

Name: Shinella yambaruensis (DSM 18801, NBRC 102122, MS-4)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13905

Type strain

Strain Designation MS-4

Culture col. no. DSM 18801 NBRC 102122 MS-4

NCBI tax ID(s) 415996

Special Collections DSMZ Literature strains

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

Links

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

Gram-negative rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397399

NBRC 102122,DSM 18801

@ref 20215

Last LPSN update 2026-02-09 11:21:16

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Shinella

Species Shinella yambaruensis

Full scientific name Shinella yambaruensis Matsui et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32445	negative	1.6-2.1 µm	1.0-1.2 µm	rod-shaped
125439	negative				93.1
125438	negative				98.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7706	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Glucose 10.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
7706	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7706	positive	growth	28
32445	positive	growth	15-42
32445	positive	optimum	28.5

Culture pH

@ref	Ability	Type	PH	PH range
32445	positive	optimum	6.5
32445	positive	growth	4-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

32445

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
32445
125439		96.6
125438		93.236

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32445	NaCl	positive	growth	0-2 %
32445	NaCl	positive	optimum	1 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32445	22599 ChEBI	arabinose	+	carbon source
32445	17057 ChEBI	cellobiose	+	carbon source
32445	4853 ChEBI	esculin	+	hydrolysis
32445	28757 ChEBI	fructose	+	carbon source
32445	33984 ChEBI	fucose	+	carbon source
32445	28260 ChEBI	galactose	+	carbon source
32445	17234 ChEBI	glucose	+	carbon source
32445	17754 ChEBI	glycerol	+	carbon source
32445	18403 ChEBI	L-arabitol	+	carbon source
32445	17306 ChEBI	maltose	+	carbon source
32445	29864 ChEBI	mannitol	+	carbon source
32445	37684 ChEBI	mannose	+	carbon source
32445	26546 ChEBI	rhamnose	+	carbon source
32445	15963 ChEBI	ribitol	+	carbon source
32445	33942 ChEBI	ribose	+	carbon source
32445	30911 ChEBI	sorbitol	+	carbon source
32445	17992 ChEBI	sucrose	+	carbon source
32445	27082 ChEBI	trehalose	+	carbon source
32445	17151 ChEBI	xylitol	+	carbon source
32445	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32445	catalase	+	1.11.1.6
32445	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7706	soil	Okinawa main island, Yambaru area, Ryukyu Archipelago	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7706	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2289935v1 assembly for Shinella yambaruensis DSM 18801	scaffold	GCA_022899355	415996.4		415996	66.44
66792	ASM2565685v1 assembly for Shinella yambaruensis DSM 18801	scaffold	GCA_025656855	415996.5	8047840540	415996	61.66
124043	ASM3016057v1 assembly for Shinella yambaruensis NBRC 102122	scaffold	GCA_030160575	415996.6	8116712186	415996	56.52

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Shinella yambaruensis gene for 16S rRNA, partial sequence, strain: NBRC 102122	AB681707	1411		415996
7706	Shinella yambaruensis gene for 16S rRNA, partial sequence, strain: MS4	AB285481	1443		415996

GC content

7706

GC-content (mol%)66.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Shinella yambaruensis DSM 18801
NCBI: GCA_022899355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.60	no
125439	motility	BacteriaNetⓘ	yes	64.90	no
125439	gram_stain	BacteriaNetⓘ	negative	93.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	86.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Shinella yambaruensis DSM 18801
NCBI: GCA_022899355.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	97.33	yes
125438	aerobic	aerobicⓘ	yes	85.28	yes
125438	spore-forming	spore-formingⓘ	no	93.24	yes
125438	thermophilic	thermophileⓘ	no	98.75	yes
125438	flagellated	motile2+ⓘ	yes	68.31	no

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 )
#28667	IJSEM 536 2009 ( DOI 10.1099/ijs.0.65510-0 , PubMed 19244436 )
#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
#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) .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Shinella yambaruensis (DSM 18801, NBRC 102122, MS-4)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_022899355

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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