Archive BacDiveID:10.13145/bacdive17794.20230509.8.1

Strain identifier

BacDive ID: 17794

Type strain:

Species: Rhodothermus marinus

Strain Designation: OKD7

Strain history: K. Takai OKD7.

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

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 4543

BacDive-ID: 17794

DSM-Number: 12399

keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative

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

NCBI tax id

NCBI tax id	Matching level
1295135	strain
29549	species

strain history

@ref	history
4543	<- JCM/RIKEN; JCM 9785
67770	K. Takai OKD7.

doi: 10.13145/bacdive17794.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/rhodothermota
domain: Bacteria
phylum: Rhodothermota
class: Rhodothermia
order: Rhodothermales
family: Rhodothermaceae
genus: Rhodothermus
species: Rhodothermus marinus
full scientific name: Rhodothermus marinus Alfredsson et al. 1995
synonyms
- @ref: 20215
- synonym: Rhodothermus obamensis

@ref: 4543

domain: Bacteria

phylum: Rhodothermaeota

class: Rhodothermia

order: Cytophagales

family: Rhodothermaceae

genus: Rhodothermus

species: Rhodothermus marinus

full scientific name: Rhodothermus marinus Alfredsson et al. 1995 emend. Park et al. 2019

strain designation: OKD7

type strain: no

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.917

Culture and growth conditions

culture medium

@ref: 4543
name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
growth: yes
link: https://mediadive.dsmz.de/medium/514
composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
4543	positive	growth	70	thermophilic
67770	positive	growth	70	thermophilic
69480				thermophilic	98.744

Physiology and metabolism

spore formation

@ref: 69480
spore formation: no
confidence: 99.989

observation

@ref: 67770
observation: quinones: MK-7

enzymes

@ref: 67770
value: cellobiose epimerase
ec: 5.1.3.11

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
4543	Hydrothermal vent at a depth of 22 m	Tachibana Bay, Nagasaki Pref	Japan	JPN	Asia
67770	Hydrothermal vent at a depth of 22 m (120-125°C)	Tachibana Bay, Nagasaki Pref.	Japan	JPN	Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Condition	#Thermophilic (>45°C)

taxonmaps

@ref: 69479
File name: preview.99_7548.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_302;96_1200;97_1415;98_1722;99_7548&stattab=map
Last taxonomy: Rhodothermus marinus
16S sequence: AF217493
Sequence Identity:
Total samples: 601
soil counts: 193
aquatic counts: 243
animal counts: 134
plant counts: 31

Safety information

risk assessment

@ref: 4543
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
4543	R.obamae 16S ribosomal RNA	X95071	1520	ena	29549
4543	Rhodothermus obamensis strain JCM 9785T 16S ribosomal RNA gene, partial sequence	AF217493	1471	ena	518766

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Rhodothermus marinus JCM 9785	GCA_001312245	contig	ncbi	1295135
66792	Rhodothermus marinus JCM 9785	1295135.3	wgs	patric	1295135
66792	Rhodothermus marinus JCM 9785	2728369716	draft	img	1295135

GC content

@ref: 67770
GC-content: 66.6
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	60	no
motile	yes	72.035	no
gram-positive	no	96.653	no
anaerobic	no	95.604	no
aerobic	yes	62.706	no
halophile	no	59.989	no
spore-forming	no	93.694	no
thermophile	yes	99.686	no
glucose-util	yes	88.142	no
flagellated	no	88.72	no
glucose-ferment	no	78.227	no

External links

@ref: 4543

culture collection no.: DSM 12399, JCM 9785, CGMCC 1.3047

straininfo link

@ref	straininfo
86785	65980
86786	312195

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	8863442	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	Base Sequence, Fatty Acids/analysis, Gram-Negative Aerobic Bacteria/classification/isolation & purification, Hydrogen-Ion Concentration, Molecular Sequence Data, Quinones/analysis, Temperature, Water Microbiology	Genetics
Phylogeny	10939650	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	Cloning, Molecular, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gram-Negative Aerobic Bacteria/chemistry/classification/genetics, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/analysis, Temperature, Water Microbiology	Enzymology
Phylogeny	20851913	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	Aerobiosis, Bacteroidetes/classification/genetics/isolation & purification/physiology, Base Composition, Carbon/metabolism, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Heterotrophic Processes, Japan, Molecular Sequence Data, Nitrogen/metabolism, Pacific Ocean, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature	Metabolism
Enzymology	22056431	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	Amino Acid Sequence, Cellobiose/chemistry/genetics/isolation & purification, Cloning, Molecular, Disaccharides/metabolism, Enzyme Stability, Hydrogen-Ion Concentration, Molecular Sequence Data, Racemases and Epimerases/chemistry/genetics/isolation & purification, Recombinant Proteins/chemistry, Rhodothermus/*enzymology, Substrate Specificity, Temperature	Phylogeny
Enzymology	22878201	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	Bacterial Proteins/chemistry/genetics, Biocatalysis, Bioreactors, Cellobiose/chemistry, Disaccharides/chemical synthesis, Enzyme Stability, Escherichia coli/genetics, Hot Temperature, Hydrogen-Ion Concentration, Immobilized Proteins/chemistry/genetics, Kinetics, Lactose/chemistry, Racemases and Epimerases/chemistry/genetics, Recombinant Proteins/chemistry/genetics, Rhodothermus/chemistry/*enzymology, Substrate Specificity	Stress
Enzymology	25472442	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	Amino Acid Oxidoreductases/chemistry/genetics/metabolism, Bacterial Proteins/chemistry/genetics/metabolism, Enzyme Stability, Escherichia coli/genetics/metabolism, Hydrogen-Ion Concentration, Isomerism, Kinetics, Proline/chemistry/metabolism, Rhodothermus/chemistry/enzymology/genetics, Substrate Specificity	Metabolism

Reference

@id	authors	catalogue	doi/url	title
4543	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12399)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-12399
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
86785	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID65980.1	StrainInfo: A central database for resolving microbial strain identifiers
86786	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID312195.1	StrainInfo: A central database for resolving microbial strain identifiers

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

spore formation

observation

enzymes

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference