Name: Salinisphaera japonica YTM-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133949

Type strain:

Species: Salinisphaera japonica

Strain Designation: YTM-1

Culture col. no.: JCM 18087, CECT 8012

Strain history: Y. Shimane YTM-1.

NCBI tax ID(s): 1304270 (species)

SI-ID 388632

CECT 8012, JCM 18087

Special Collections

Section

Salinisphaera japonica YTM-1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from body surface of a deep-sea fish.

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	*Gammaproteobacteria*
	Order	*Nevskiales*
	Family	*Salinisphaeraceae*
	Genus	*Salinisphaera*
	Species	**Salinisphaera japonica**
	Full Scientific Name (LPSN)	Salinisphaera japonica Shimane et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30930]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.5

[Ref.: #30930]	Cell length	1.4 µm

[Ref.: #30930]	Cell width	1 µm

[Ref.: #30930]	Cell shape	rod-shaped

[Ref.: #30930]	Motility	no

[Ref.: #30930]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30930]	growth	04-30 °C
[Ref.: #30930]	optimum	22.5 °C
[Ref.: #67770]	growth	20 °C

	pH	Kind of pH		pH
[Ref.: #30930]			optimum	5.25
[Ref.: #30930]			growth	3.8-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30930]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30930]		NaCl		growth	01-30	%
[Ref.: #30930]		NaCl		optimum	8.75	%

[Ref.: #30930]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30930]	acetate ChEBI	+	carbon source
[Ref.: #30930]	citrate ChEBI	+	carbon source
[Ref.: #30930]	fructose ChEBI	+	carbon source
[Ref.: #30930]	galactose ChEBI	+	carbon source
[Ref.: #30930]	glucose ChEBI	+	carbon source
[Ref.: #30930]	glutamate ChEBI	+	carbon source
[Ref.: #30930]	glycerol ChEBI	+	carbon source
[Ref.: #30930]	lactate ChEBI	+	carbon source
[Ref.: #30930]	malate ChEBI	+	carbon source
[Ref.: #30930]	mannitol ChEBI	+	carbon source
[Ref.: #30930]	mannose ChEBI	+	carbon source
[Ref.: #30930]	pyruvate ChEBI	+	carbon source
[Ref.: #30930]	ribitol ChEBI	+	carbon source
[Ref.: #30930]	ribose ChEBI	+	carbon source
[Ref.: #30930]	sorbitol ChEBI	+	carbon source
[Ref.: #30930]	succinate ChEBI	+	carbon source
[Ref.: #30930]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30930]		acid phosphatase	+	3.1.3.2
[Ref.: #30930]		alkaline phosphatase	+	3.1.3.1

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

[Ref.: #30930]	Sample type/isolated from	body surface of a deep-sea fish

[Ref.: #67770]	Sample type/isolated from	Body surface of a deep-sea fish (Malacocottus gibber) collected from Nyuzen
[Ref.: #67770]	Host species	Malacocottus gibber
[Ref.: #67770]	Geographic location (country and/or sea, region)	Toyama Bay
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Host	#Fishes	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB735546 (>99% sequence identity) for Salinisphaera japonica subclade from Microbeatlas

Aquatic Samples	2401
Soil Samples	75
Animal Samples	426
Plant Samples	71
Total Samples	2973

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.: #30930]	Salinisphaera japonica YTM-1 gene for 16S ribosomal RNA, partial sequence	AB735546	1462	GenBank ENA	1209778 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Salinisphaera japonica YTM-1	GCA_003788585	contig	GenBank ENA	1209778 tax ID
[Ref.: #66792]	Salinisphaera japonica YTM-1	1209778.3	wgs	PATRIC	1209778 tax ID	*

[Ref.: #30930]	GC-content	67.3 mol%
[Ref.: #67770]	GC-content	67.3 mol%	high performance liquid chromatography (HPLC)

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: Salinisphaera japonica YTM-1 PATRIC: 1209778.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99.5	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.017	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.354	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	84.447	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	92.226	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	60.51	no

Availability in culture collections External links

[Ref.: #30930]

Culture collection no.

JCM 18087, CECT 8012

[Ref.: #91643]

SI-ID 388632

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Salifodinibacter halophilus gen. nov., sp. nov., a halophilic gammaproteobacterium in the family Salinisphaeraceae isolated from a salt mine in the Colombian Andes.	Parada-Pinilla MP, Diaz-Cardenas C, Lopez G, Diaz-Riano JI, Gonzalez LN, Restrepo S, Trujillo ME, Baena S	Int J Syst Evol Microbiol	10.1099/ijsem.0.004490	2020	*
Phylogeny	Salinisphaera japonica sp. nov., a moderately halophilic bacterium isolated from the surface of a deep-sea fish, Malacocottus gibber, and emended description of the genus Salinisphaera.	Shimane Y, Tsuruwaka Y, Miyazaki M, Mori K, Minegishi H, Echigo A, Ohta Y, Maruyama T, Grant WD, Hatada Y	Int J Syst Evol Microbiol	10.1099/ijs.0.047845-0	2012	*

References

#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 )

#30930

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 #27260 (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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#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) .

#91643

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-ID388632.1 )

#27260

IJSEM 2180 2013 ( DOI 10.1099/ijs.0.047845-0 , PubMed 23125319 )

* These data were automatically processed and therefore are not curated

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