Cite this strain

Vibrio sp. (JCM 18904)

Name: Vibrio sp. (JCM 18904)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 162331

Type strain

Culture col. no. JCM 18904

NCBI tax ID(s) 1298599

Special Collections JCM

History T. Kudo C141.

Links

JCM 18904 is a bacterium that was isolated from Sea cucumber Holothuria leucospilota.

genome sequence Bacteria

Name and taxonomic classification

SI-ID 131662

JCM 18904

@ref 20215

Last LPSN update 2026-02-09 11:39:22

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Vibrio

Full scientific name Vibrio Pacini 1854 (Approved Lists 1980)

Synonyms (4)

Allomonas
"Allomonas"
Lucibacterium
Beneckea

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99
125439	negative	98.3

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	95.4

Spore formation

@ref	Spore formation	Confidence
125439		96.9

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Host species
67770	Sea cucumber Holothuria leucospilota	Holothuria leucospilota

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM69503v1 assembly for Vibrio sp. JCM 18904	contig	GCA_000695035	1298599.3	2579778626	1298599	13.96
66792	ASM131518v1 assembly for Vibrio sp. JCM 18904	contig	GCA_001315185	1298599.4	8033305015	1298599	7.73

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vibrio sp. JCM 18904
NCBI: GCA_001315185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.90	no
125439	motility	BacteriaNetⓘ	yes	75.80	no
125439	gram_stain	BacteriaNetⓘ	negative	98.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Vibrio sp. JCM 18904
PATRIC: 1298599.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	96.20	no
125438	spore-forming	spore-formingⓘ	no	87.24	no
125438	aerobic	aerobicⓘ	no	57.86	no
125438	thermophilic	thermophileⓘ	no	99.50	yes
125438	flagellated	motile2+ⓘ	yes	87.12	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft Genome Sequences of Vibrio sp. Strains Isolated from Tetrodotoxin-Bearing Scavenging Gastropod.	Kudo T, Kawauchi A, Nakahara T, Zhang X, Taniyama S, Takatani T, Arakawa O, Oshima K, Suda W, Kitamura K, Iida T, Iino T, Inoue T, Hongoh Y, Hattori M, Ohkuma M	Genome Announc	10.1128/genomeA.00623-14	2014

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;
#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 )

Rate our new design

Content

About us

Vibrio sp. (JCM 18904)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_000695035

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media