Caldichromatium japonicum (DSM 110881, JCM 39101, No.7)

Name: Caldichromatium japonicum (DSM 110881, JCM 39101, No.7)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164869

Type strain

Strain Designation No.7

Culture col. no. DSM 110881 JCM 39101 No.7

NCBI tax ID(s) 2699430

Special Collections DSMZ JCM

Links

Caldichromatium japonicum No.7 is a thermophilic prokaryote that was isolated from Nakabusa hot springs is located in the Japanese Alps in Nagano Prefecture.

thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 403101

JCM 39101,DSM 110881

@ref 20215

Last LPSN update 2025-12-16 10:09:33

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Chromatiales

Family Chromatiaceae

Genus Caldichromatium

Species Caldichromatium japonicum

Full scientific name Caldichromatium japonicum Saini et al. 2020

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99.494

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
68694	PFENNIG'S MEDIUM III (DSMZ Medium 1761)		Medium recipe at MediaDive	Name: PFENNIG'S MEDIUM III (DSMZ Medium 1761) Composition: NaHCO3 1.5 g/l MgSO4 x 7 H2O 0.500001 g/l Ammonium chloride 0.4 g/l Na2S x 9 H2O 0.385185 g/l KCl 0.339999 g/l KH2PO4 0.339999 g/l Ammonium acetate 0.25 g/l CaCl2 x 2 H2O 0.25 g/l Magnesium acetate 0.25 g/l Na2-EDTA 0.003 g/l Resazurin 0.00225 g/l FeSO4 x 7 H2O 0.0011 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 2 H2O 5e-05 g/l ZnCl2 4.2e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Vitamin B12 2e-05 g/l Na2MoO4 x 2 H2O 1.8e-05 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water H2O

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	50	thermophilic
68694	positive	growth	50	thermophilic

Physiology and metabolism

Observation

67770

Observationquinones: Q-8

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
67770	Nakabusa hot springs is located in the Japanese Alps in Nagano Prefecture		Japan	JPN	Asia
68694	hot spring microbial mat	Nakabusa Hot Spring site B, Nagano Prefecture	Japan	JPN	Asia	36.3942	137.747 36.3942/137.747

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM1129048v1 assembly for Caldichromatium japonicum No.7	complete	GCA_011290485	2699430.3	2964078231	2699430	98.49

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Caldichromatium japonicum strain No.7 16S ribosomal RNA gene, partial sequence	MN999710	1486		2699430

GC content

@ref	GC-content (mol%)	Method
67770	61.2	genome sequence analysis
68694	61.2	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Caldichromatium japonicum No.7
NCBI: GCA_011290485

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	80.00	no
125439	motility	BacteriaNetⓘ	no	74.70	no
125439	gram_stain	BacteriaNetⓘ	negative	53.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	59.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Caldichromatium japonicum No.7
NCBI: GCA_011290485.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.49	no
125438	anaerobic	anaerobicⓘ	yes	74.15	no
125438	aerobic	aerobicⓘ	no	81.47	no
125438	spore-forming	spore-formingⓘ	no	87.65	no
125438	thermophilic	thermophileⓘ	no	61.24	yes
125438	flagellated	motile2+ⓘ	yes	72.44	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Caldichromatium japonicum gen. nov., sp. nov., a novel thermophilic phototrophic purple sulphur bacterium of the Chromatiaceae isolated from Nakabusa hot springs, Japan.	Saini MK, ChihChe W, Soulier N, Sebastian A, Albert I, Thiel V, Bryant DA, Hanada S, Tank M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004465	2020

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;
#68694	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 110881
#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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Caldichromatium japonicum (DSM 110881, JCM 39101, No.7)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Observation

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_011290485

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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