Name: Rhodothermus marinus OKD7
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17794

Type strain:

Species: Rhodothermus marinus

Strain Designation: OKD7

Culture col. no.: DSM 12399, JCM 9785, CGMCC 1.3047

Strain history: K. Takai OKD7.

NCBI tax ID(s): 1295135 (strain), 29549 (species)

SI-ID 65980

JCM 9785, DSM 12399

Special Collections

DSMZ
JCM

Other strains from Rhodothermus marinus

Section

Rhodothermus marinus OKD7 is a Gram-negative bacterium that was isolated from Hydrothermal vent at a depth of 22 m.

Gram-negative
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Rhodothermota*
	Class	*Rhodothermia*
	Order	*Rhodothermales*
	Family	*Rhodothermaceae*
	Genus	*Rhodothermus*
	Species	**Rhodothermus marinus**
	Full Scientific Name (LPSN)	Rhodothermus marinus Alfredsson et al. 1995

Synonym

Rhodothermus obamensis

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %94.234

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4543]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #4543]

Culture medium growth

[Ref.: #4543]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4543]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4543]			growth	70 °C
[Ref.: #67770]			growth	70 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Ability of spore formation

no Confidence in %90.551

[Ref.: #67770]

Observation

quinones: MK-7

	Enzymes	Enzyme	EC number
[Ref.: #67770]		cellobiose epimerase	5.1.3.11

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

[Ref.: #4543]	Sample type/isolated from	Hydrothermal vent at a depth of 22 m
[Ref.: #4543]	Geographic location (country and/or sea, region)	Tachibana Bay, Nagasaki Pref
[Ref.: #4543]	Country	Japan
[Ref.: #4543]	Country ISO 3 Code	JPN
[Ref.: #4543]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Hydrothermal vent at a depth of 22 m (120-125°C)
[Ref.: #67770]	Geographic location (country and/or sea, region)	Tachibana Bay, Nagasaki Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF217493 (>99% sequence identity) for Rhodothermus marinus from Microbeatlas

Aquatic Samples	243
Soil Samples	193
Animal Samples	134
Plant Samples	31
Total Samples	601

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #4543]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #4543]	Rhodothermus obamensis strain JCM 9785T 16S ribosomal RNA gene, partial sequence	AF217493	1471	GenBank ENA	518766 tax ID
[Ref.: #4543]	R.obamae 16S ribosomal RNA	X95071	1520	GenBank ENA	29549 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodothermus marinus JCM 9785	GCA_001312245	contig	GenBank ENA	1295135 tax ID	*
[Ref.: #66792]	Rhodothermus marinus JCM 9785	1295135.3	wgs	PATRIC	1295135 tax ID	*
[Ref.: #66792]	Rhodothermus marinus JCM 9785	2728369716	draft	JGI IMG/M	1295135 tax ID	*

[Ref.: #67770]

GC-content

66.6 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 GenomeNet Sporulation v. 1 based on: Rhodothermus marinus JCM 9785 PATRIC: 1295135.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	60	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodothermus marinus JCM 9785 PATRIC: 1295135.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	94.234	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	85.616	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	90.551	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	72.842	no
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	61.108	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	57.024	no

Availability in culture collections External links

[Ref.: #4543]

Culture collection no.

DSM 12399, JCM 9785, CGMCC 1.3047

[Ref.: #86785]	SI-ID 65980	*
[Ref.: #86786]	SI-ID 312195	*

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Dye-linked D-amino acid dehydrogenase from the thermophilic bacterium Rhodothermus marinus JCM9785: characteristics and role in trans-4-hydroxy-L-proline catabolism.	Satomura T, Ishikura M, Koyanagi T, Sakuraba H, Ohshima T, Suye S	Appl Microbiol Biotechnol	10.1007/s00253-014-6263-9	2014	*
Enzymology	Immobilization of a thermostable cellobiose 2-epimerase from Rhodothermus marinus JCM9785 and continuous production of epilactose.	Sato H, Saburi W, Ojima T, Taguchi H, Mori H, Matsui H	Biosci Biotechnol Biochem	10.1271/bbb.120284	2012	*
Phylogeny	Rubricoccus marinus gen. nov., sp. nov., of the family 'Rhodothermaceae', isolated from seawater.	Park S, Yoshizawa S, Kogure K, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.026294-0	2010	*
Phylogeny	Rhodothermus obamensis sp. nov., a modern lineage of extremely thermophilic marine bacteria.	Sako Y, Takai K, Ishida Y, Uchida A, Katayama Y	Int J Syst Bacteriol	10.1099/00207713-46-4-1099	1996	*
Enzymology	Biochemical characterization of a thermophilic cellobiose 2-epimerase from a thermohalophilic bacterium, Rhodothermus marinus JCM9785.	Ojima T, Saburi W, Sato H, Yamamoto T, Mori H, Matsui H	Biosci Biotechnol Biochem	10.1271/bbb.110456	2011	*
Phylogeny	Polyphasic evidence for the reclassification of Rhodothermus obamensis Sako et al. 1996 as a member of the species Rhodothermus marinus Alfredsson et al. 1988.	Silva Z, Horta C, da Costa MS, Chung AP, Rainey FA	Int J Syst Evol Microbiol	10.1099/00207713-50-4-1457	2000	*

References

#4543

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12399

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86785

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-ID65980.1 )

#86786

* These data were automatically processed and therefore are not curated

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