Name: Tateyamaria omphalii JCM 21569
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 163231

Type strain:

Species: Tateyamaria omphalii

Culture col. no.: JCM 21569, IAM 15108, KCTC 12333

Strain history: IAM 15108 <-- M. Kurahashi MKT107.

NCBI tax ID(s): 299262 (species)

SI-ID 324006

IAM 15108, JCM 21569, KCTC 12333

Special Collections

JCM
KCTC

Section

Tateyamaria omphalii JCM 21569 is a mesophilic, Gram-negative bacterium that was isolated from Gastrointestinal tract of the molluscan top shell Omphalius pfeifferi pfeifferi collected on the coast of Japan.

Gram-negative
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Tateyamaria*
	Species	**Tateyamaria omphalii**
	Full Scientific Name (LPSN)	Tateyamaria omphalii Kurahashi and Yokota 2008

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %97.5

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #67770]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67770]

Observation

quinones: Q-10

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

[Ref.: #67770]	Sample type/isolated from	Gastrointestinal tract of the molluscan top shell Omphalius pfeifferi pfeifferi collected on the coast of Japan
[Ref.: #67770]	Host species	Omphalius pfeifferi pfeifferi
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence AB193438 (>99% sequence identity) for Tateyamaria omphalii subclade from Microbeatlas

Aquatic Samples	557
Soil Samples	5
Animal Samples	30
Plant Samples	4
Total Samples	596

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.: #67770]	Tateyamaria omphalii gene for 16S rRNA, partial sequence	AB193438	1386	GenBank ENA	299262 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Tateyamaria omphalii KCTC 12333	GCA_014651375	scaffold	GenBank ENA	299262 tax ID	*
[Ref.: #66792]	Tateyamaria omphalii strain KCTC 12333	299262.50	wgs	PATRIC	299262 tax ID	*

[Ref.: #67770]

GC-content

61.6 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: Tateyamaria omphalii KCTC 12333 NCBI: GCA_014651375.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.5	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.576	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	85.918	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.199	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.393	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	52.666	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 21569, IAM 15108, KCTC 12333

[Ref.: #113973]

SI-ID 324006

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Isolation and polyphasic identification of Tateyamaria armeniaca sp. nov.	Yoon J	FEMS Microbiol Lett	10.1093/femsle/fnz182	2019	*
Phylogeny	Tateyamaria omphalii gen. nov., sp. nov., an alpha-Proteobacterium isolated from a top shell Omphalius pfeifferi pfeifferi.	Kurahashi M, Yokota A	Syst Appl Microbiol	10.1016/j.syapm.2006.11.007	2007	*

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 )

#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) .

#113973

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-ID324006.1 )

* These data were automatically processed and therefore are not curated

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Tateyamaria omphalii KCTC 12333

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