Archive BacDiveID:10.13145/bacdive4041.20230509.8.1

Strain identifier

BacDive ID: 4041

Type strain:

Species: Desulfothermus okinawensis

Strain Designation: TFISO9

Strain history: T. Nunoura TFISO9.

NCBI tax ID(s): 1293588 (strain), 392842 (species)

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

General

@ref: 6843

BacDive-ID: 4041

DSM-Number: 17375

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, motile, rod-shaped

description: Desulfothermus okinawensis TFISO9 is an anaerobe, thermophilic, motile bacterium that was isolated from hydrothermal vent chimney.

NCBI tax id

NCBI tax id	Matching level
1293588	strain
392842	species

strain history

@ref	history
6843	<- T. Nunoura, Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC); TFISO9 <- T. Nunoura {2004}
67770	T. Nunoura TFISO9.

doi: 10.13145/bacdive4041.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfohalobiaceae
genus: Desulfothermus
species: Desulfothermus okinawensis
full scientific name: Desulfothermus okinawensis Nunoura et al. 2007

@ref: 6843

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfohalobiaceae

genus: Desulfothermus

species: Desulfothermus okinawensis

full scientific name: Desulfothermus okinawensis Nunoura et al. 2007

strain designation: TFISO9

type strain: yes

Morphology

cell morphology

@ref	cell length	cell width	cell shape	motility	confidence	gram stain
31997	3.75 µm	0.75 µm	rod-shaped	yes
69480				yes	95.312
69480					99.999	negative

Culture and growth conditions

culture medium

@ref: 6843
name: DESULFOTHERMUS MJ MEDIUM (H2/CO2) (DSMZ Medium 1011c)
growth: yes
link: https://mediadive.dsmz.de/medium/1011c
composition: Name: DESULFOTHERMUS MJ MEDIUM (H2/CO2) (DSMZ Medium 1011c) Composition: MgCl2 x 6 H2O 4.13043 g/l Na2S2O3 x 5 H2O 1.48221 g/l Na2CO3 1.48221 g/l Na-pyruvate 0.494071 g/l Na-lactate 0.494071 g/l KCl 0.326087 g/l NH4Cl 0.247036 g/l K2HPO4 0.13834 g/l Yeast extract 0.0988142 g/l Na2S2O4 0.0494071 g/l NaHCO3 0.0494071 g/l MgSO4 x 7 H2O 0.0296443 g/l Nitrilotriacetic acid 0.0148221 g/l NaCl 0.00988142 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00988142 g/l MnSO4 x H2O 0.00494071 g/l CoSO4 x 7 H2O 0.00177866 g/l ZnSO4 x 7 H2O 0.00177866 g/l FeSO4 x 7 H2O 0.000988142 g/l CaCl2 x 2 H2O 0.000988142 g/l NiCl2 x 6 H2O 0.000296443 g/l AlK(SO4)2 x 12 H2O 0.000197628 g/l H3BO3 9.88142e-05 g/l CuSO4 x 5 H2O 9.88142e-05 g/l Na2MoO4 x 2 H2O 9.88142e-05 g/l Pyridoxine hydrochloride 9.88142e-05 g/l (DL)-alpha-Lipoic acid 4.94071e-05 g/l Thiamine HCl 4.94071e-05 g/l p-Aminobenzoic acid 4.94071e-05 g/l Calcium D-(+)-pantothenate 4.94071e-05 g/l Riboflavin 4.94071e-05 g/l Nicotinic acid 4.94071e-05 g/l Folic acid 1.97628e-05 g/l Biotin 1.97628e-05 g/l Na2WO4 x 2 H2O 3.95257e-06 g/l Na2SeO3 x 5 H2O 2.96443e-06 g/l Vitamin B12 9.88142e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
6843	positive	growth	50	thermophilic
31997	positive	growth	35-60
31997	positive	optimum	50	thermophilic
67770	positive	growth	55	thermophilic
69480				thermophilic	94.658

culture pH

@ref	ability	type	pH
31997	positive	growth	5.4-7.9
31997	positive	optimum	6.15

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
6843	anaerobe
69480	anaerobe	99.343

spore formation

@ref: 69480
spore formation: no
confidence: 99.978

halophily

@ref	salt	growth	tested relation	concentration
31997	NaCl	positive	growth	1.5-4.5 %
31997	NaCl	positive	optimum	2.5 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
31997	30089	acetate	+	carbon source
31997	16947	citrate	+	carbon source
31997	16236	ethanol	+	carbon source
31997	15740	formate	+	carbon source
31997	17234	glucose	+	carbon source
31997	17754	glycerol	+	carbon source
31997	24996	lactate	+	carbon source
31997	25115	malate	+	carbon source
31997	17272	propionate	+	carbon source
31997	15361	pyruvate	+	carbon source
31997	30031	succinate	+	carbon source
31997	31011	valerate	+	carbon source

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
6843	hydrothermal vent chimney	Pacific Ocean, Yonaguni Knoll IV, Southern Okinawa Trough	Japan	JPN	Asia
67770	Deep-sea hydrothermal field at the Yonaguni Knoll IV in the Southern Okinawa Trough

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_7258.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16800;96_3390;97_4162;98_5323;99_7258&stattab=map
Last taxonomy: Desulfothermus okinawensis subclade
16S sequence: AB264617
Sequence Identity:
Total samples: 465
soil counts: 30
aquatic counts: 215
animal counts: 217
plant counts: 3

Safety information

risk assessment

@ref: 6843
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6843
description: Desulfothermus okinawensis gene for 16S rRNA, partial sequence
accession: AB264617
length: 1492
database: ena
NCBI tax ID: 1293588

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Desulfothermus okinawensis JCM 13304	1293588.5	wgs	patric	1293588
66792	Desulfothermus okinawensis JCM 13304	2728369691	draft	img	1293588
67770	Desulfothermus okinawensis JCM 13304	GCA_001311565	contig	ncbi	1293588

GC content

@ref	GC-content	method
6843	34.9
67770	34.9	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	88	no
motile	yes	89.325	yes
gram-positive	no	99.766	no
anaerobic	yes	100	no
aerobic	no	99.125	yes
halophile	no	80.397	no
spore-forming	no	96.625	no
thermophile	yes	99.483	yes
glucose-util	no	59.411	yes
flagellated	no	82.657	no
glucose-ferment	no	83.565	no

External links

@ref: 6843

culture collection no.: DSM 17375, JCM 13304

straininfo link

@ref: 73546
straininfo: 293886

literature

topic: Phylogeny
Pubmed-ID: 17911311
title: Desulfothermus okinawensis sp. nov., a thermophilic and heterotrophic sulfate-reducing bacterium isolated from a deep-sea hydrothermal field.
authors: Nunoura T, Oida H, Miyazaki M, Suzuki Y, Takai K, Horikoshi K
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.64781-0
year: 2007
mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deltaproteobacteria/*classification/genetics/*isolation & purification/physiology, Fatty Acids, Genes, rRNA, Hydrogen-Ion Concentration, Japan, Locomotion/physiology, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Sulfates/*metabolism, Temperature
topic2: Genetics

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
6843	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17375)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-17375
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
31997	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	28251	28776041
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)
73546	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID293886.1	StrainInfo: A central database for resolving microbial strain identifiers