Gelidibacter japonicus (LMG 30063, JCM 31967)

Name: Gelidibacter japonicus (LMG 30063, JCM 31967)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164163

Type strain

Culture col. no. LMG 30063 JCM 31967

NCBI tax ID(s) 1962232

Special Collections JCM

Links

Gelidibacter japonicus JCM 31967 is a mesophilic prokaryote that was isolated from Seawater collected from the Inland Sea in Japan.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 393834

JCM 31967

@ref 20215

Last LPSN update 2025-12-16 10:09:23

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Gelidibacter

Species Gelidibacter japonicus

Full scientific name Gelidibacter japonicus Doi and Osawa 2021

Morphology

Cell morphology

@ref	Confidence	Gram stain
125438	93.5
125438	98.481	negative
125439	99.4	negative

Culture and growth conditions

Culture temp

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

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.9

Spore formation

@ref	Spore formation	Confidence
125439		97.1

Isolation, sampling and environmental information

Isolation

67770

Sample typeSeawater collected from the Inland Sea (Setonaikai) in Japan

Taxonmaps

69479

Global distribution of 16S sequence LC341257 (>99% sequence identity) for Gelidibacter from Microbeatlas

Aquatic Samples	157
Soil Samples	82
Animal Samples	361
Plant Samples	23
Total Samples	623

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM1072505v1 assembly for Gelidibacter japonicus Bio7-1	scaffold	GCA_010725055	1962232.3	2890147465	1962232	64.01

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Gelidibacter japonicus Bio7-1 gene for 16S ribosomal RNA, partial sequence	LC217875	1448		1962232
67770	Gelidibacter sp. Bio7-1 gene for 16S ribosomal RNA, partial sequence, clone: 48	LC341257	1445		1962232

GC content

@ref	GC-content (mol%)	Method
67770	39.1	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: Gelidibacter japonicus Bio7-1
NCBI: GCA_010725055

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.10	no
125439	motility	BacteriaNetⓘ	no	74.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gelidibacter sp. Bio7-1
PATRIC: 1962232.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.48	no
125438	anaerobic	anaerobicⓘ	no	96.31	no
125438	spore-forming	spore-formingⓘ	no	89.64	no
125438	aerobic	aerobicⓘ	yes	83.57	no
125438	thermophilic	thermophileⓘ	no	99.96	yes
125438	flagellated	motile2+ⓘ	no	93.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of Gelidibacter japonicus sp. nov., isolated from the Inland Sea (Setonaikai) in Japan.	Doi H, Osawa I	Arch Microbiol	10.1007/s00203-019-01668-2	2019
Phylogeny	Gelidibacter maritimus sp. nov., isolated from marine sediment.	Gao C, Lun HY, Shang DD, Cai M, Ye MQ, Du ZJ	Arch Microbiol	10.1007/s00203-021-02478-1	2021
Phylogeny	Gelidibacter pelagius sp. nov., Isolated from Coastal Sediment.	Lun HY, Gao C, Shang DD, Gong Y, Du ZJ	Curr Microbiol	10.1007/s00284-021-02591-w	2021

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 )
#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 .
#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

Gelidibacter japonicus (LMG 30063, JCM 31967)

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

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_010725055

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media