Tateyamaria omphalii (KCTC 12333, IAM 15108, JCM 21569)

Name: Tateyamaria omphalii (KCTC 12333, IAM 15108, JCM 21569)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 163231

Type strain

Culture col. no. KCTC 12333 IAM 15108 JCM 21569

NCBI tax ID(s) 299262

Special Collections JCM KCTC

Links

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

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 324006

IAM 15108,JCM 21569,KCTC 12333

@ref 20215

Last LPSN update 2025-12-16 10:09:10

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Tateyamaria

Species Tateyamaria omphalii

Full scientific name Tateyamaria omphalii Kurahashi and Yokota 2008

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	97.9
125438	negative	97.5

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	25	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	96.2

Spore formation

@ref	Spore formation	Confidence
125439		98.7

Observation

67770

Observationquinones: Q-10

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Host species
67770	Gastrointestinal tract of the molluscan top shell Omphalius pfeifferi pfeifferi collected on the coast of Japan	Omphalius pfeifferi pfeifferi

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1465137v1 assembly for Tateyamaria omphalii KCTC 12333	scaffold	GCA_014651375	299262.50	2995030257	299262	74.38

Genome browser: GCA_014651375

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
67770	Tateyamaria omphalii gene for 16S rRNA, partial sequence	AB193438	1386	299262
124043	Tateyamaria omphalii strain KCTC 12333 16S ribosomal RNA gene, partial sequence.	MT758056	1282	299262
124043	Tateyamaria omphalii strain KCTC 12333 16S ribosomal RNA gene, partial sequence.	MT759916	1279	299262

GC content

@ref	GC-content (mol%)	Method
67770	61.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Tateyamaria omphalii KCTC 12333
NCBI: GCA_014651375

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.70	no
125439	motility	BacteriaNetⓘ	yes	77.70	no
125439	gram_stain	BacteriaNetⓘ	negative	97.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Tateyamaria omphalii KCTC 12333
NCBI: GCA_014651375.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	no
125438	anaerobic	anaerobicⓘ	no	95.58	no
125438	aerobic	aerobicⓘ	yes	85.92	no
125438	spore-forming	spore-formingⓘ	no	89.20	no
125438	thermophilic	thermophileⓘ	no	98.39	yes
125438	flagellated	motile2+ⓘ	no	52.67	no

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 .
#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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Tateyamaria omphalii (KCTC 12333, IAM 15108, JCM 21569)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_014651375

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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