Archive BacDiveID:10.13145/bacdive16898.20230509.8.1

Strain identifier

BacDive ID: 16898

Type strain:

Species: Thermodesulfobium narugense

Strain Designation: Na82

Strain history: K. Mori Na82.

NCBI tax ID(s): 747365 (strain), 184064 (species)

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

General

@ref: 5549

BacDive-ID: 16898

DSM-Number: 14796

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

description: Thermodesulfobium narugense Na82 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from narugo hot spring.

NCBI tax id

NCBI tax id	Matching level
184064	species
747365	strain

strain history

@ref	history
5549	<- K. Mori, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan; Na82 <- K. Mori {2001}
67770	K. Mori Na82.

doi: 10.13145/bacdive16898.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Thermoanaerobacterales
family: Thermodesulfobiaceae
genus: Thermodesulfobium
species: Thermodesulfobium narugense
full scientific name: Thermodesulfobium narugense Mori et al. 2004

@ref: 5549

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Thermoanaerobacterales

family: Thermodesulfobiaceae

genus: Thermodesulfobium

species: Thermodesulfobium narugense

full scientific name: Thermodesulfobium narugense Mori et al. 2004

strain designation: Na82

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.762

colony morphology

@ref: 5549
incubation period: 3-7 days

multimedia

@ref: 66793
multimedia content: EM_DSM_14796_1.jpg
caption: electron microscopic image
intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 5549
name: THERMODESULFOBIUM MEDIUM (DSMZ Medium 1005)
growth: yes
link: https://mediadive.dsmz.de/medium/1005
composition: Name: THERMODESULFOBIUM MEDIUM (DSMZ Medium 1005) Composition: Na2SO4 2.76954 g/l K2HPO4 0.771513 g/l KH2PO4 0.74184 g/l NH4Cl 0.49456 g/l L-Cysteine HCl x H2O 0.24728 g/l MgSO4 x 7 H2O 0.24728 g/l Na-acetate 0.148368 g/l Nitrilotriacetic acid 0.126607 g/l Na2-EDTA 0.0395648 g/l NaCl 0.0098912 g/l FeSO4 x 7 H2O 0.0098912 g/l FeCl2 x 4 H2O 0.0098912 g/l ZnCl2 0.00098912 g/l NiCl2 x 6 H2O 0.00098912 g/l CaCl2 x 2 H2O 0.00098912 g/l MnCl2 x 4 H2O 0.00098912 g/l Na2WO4 x 2 H2O 0.000395648 g/l Na2MoO4 x 2 H2O 0.000296736 g/l Na2SeO3 x 5 H2O 0.000296736 g/l CoCl2 x 6 H2O 0.000296736 g/l CuCl2 0.000197824 g/l H3BO3 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Vitamin B12 9.8912e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
5549	positive	growth	50	thermophilic
67770	positive	growth	50	thermophilic
69480				thermophilic	99.999

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
5549	anaerobe
69480	anaerobe	99.209

spore formation

@ref	spore formation	confidence
69481	no	99
69480	no	99.952

observation

@ref: 67770
observation: quinones: MK-7(H₂), MK-7, MK-7(H₄), MK-8

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
5549	narugo hot spring	Miyagi prefecture, near Katanuma Lake	Japan	JPN	Asia
67770	Microbial mat at Narugo hot spring	Miyagi Pref.	Japan	JPN	Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)

taxonmaps

@ref: 69479
File name: preview.99_8184.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_697;96_3767;97_4637;98_5953;99_8184&stattab=map
Last taxonomy: Thermodesulfobium narugense
16S sequence: AB077817
Sequence Identity:
Total samples: 115
soil counts: 9
aquatic counts: 64
animal counts: 34
plant counts: 8

Safety information

risk assessment

@ref: 5549
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 5549
description: Thermodesulfobium narugense gene for 16S rRNA, partial sequence
accession: AB077817
length: 1363
database: ena
NCBI tax ID: 747365

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Thermodesulfobium narugense DSM 14796	GCA_000212395	complete	ncbi	747365
66792	Thermodesulfobium narugense DSM 14796	747365.3	complete	patric	747365
66792	Thermodesulfobium narugense Na82, DSM 14796	2504756006	complete	img	747365

GC content

@ref: 5549
GC-content: 35.1
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	99	no
motile	yes	83.744	no
flagellated	no	91.183	no
gram-positive	no	97.819	no
anaerobic	yes	99.322	yes
aerobic	no	98.381	yes
halophile	no	93.918	no
spore-forming	no	93.758	no
thermophile	yes	99.622	yes
glucose-util	no	68.624	no
glucose-ferment	no	72.892	no

External links

@ref: 5549

culture collection no.: DSM 14796, JCM 11510, NBRC 100082

straininfo link

@ref: 85904
straininfo: 130853

literature

topic: Phylogeny
Pubmed-ID: 12910388
title: A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring.
authors: Mori K, Kim H, Kakegawa T, Hanada S
journal: Extremophiles
DOI: 10.1007/s00792-003-0320-0
year: 2003
mesh: Animals, Base Composition, Fresh Water/microbiology, Genes, Bacterial, Genes, rRNA, Gram-Negative Anaerobic Bacteria/*classification/genetics/isolation & purification/*physiology, *Hot Temperature, Hydrogen-Ion Concentration, Japan, Lipids/analysis, Microscopy, Electron, Oxidation-Reduction, Phenotype, *Phylogeny, RNA, Bacterial/chemistry/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfates/*metabolism, *Water Microbiology
topic2: Stress

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
5549	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14796)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-14796
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)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life	35: 676-683 2017	28604660
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)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
85904	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID130853.1	StrainInfo: A central database for resolving microbial strain identifiers