Archive BacDiveID:10.13145/bacdive14323.20230509.8.1

Strain identifier

BacDive ID: 14323

Type strain:

Species: Spirochaeta thermophila

Strain Designation: Z-1203

Strain history: <- F. A. Rainey; Z-1203 <- H. Y. Aksenova

NCBI tax ID(s): 869211 (strain), 154 (species)

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

General

@ref: 2738

BacDive-ID: 14323

DSM-Number: 6578

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

description: Spirochaeta thermophila Z-1203 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from marine hot spring.

NCBI tax id

NCBI tax id	Matching level
869211	strain
154	species

strain history

@ref: 2738
history: <- F. A. Rainey; Z-1203 <- H. Y. Aksenova

doi: 10.13145/bacdive14323.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/spirochaetota
domain: Bacteria
phylum: Spirochaetota
class: Spirochaetia
order: Spirochaetales
family: Spirochaetaceae
genus: Spirochaeta
species: Spirochaeta thermophila
full scientific name: Spirochaeta thermophila Aksenova et al. 1992

@ref: 2738

domain: Bacteria

phylum: Spirochaetes

class: Spirochaetia

order: Spirochaetales

family: Spirochaetaceae

genus: Spirochaeta

species: Spirochaeta thermophila

full scientific name: Spirochaeta thermophila Aksenova et al. 1992

strain designation: Z-1203

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.901

multimedia

@ref: 66793
multimedia content: EM_DSM_6578_1.jpg
caption: electron microscopic image
intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 2738
name: SPIROCHAETA THERMOPHILA MEDIUM (DSMZ Medium 509)
growth: yes
link: https://mediadive.dsmz.de/medium/509
composition: Name: SPIROCHAETA THERMOPHILA MEDIUM (DSMZ Medium 509) Composition: NaCl 14.9402 g/l MgCl2 x 6 H2O 2.29084 g/l Na2CO3 1.49402 g/l Starch 0.996016 g/l Yeast extract 0.996016 g/l KCl 0.498008 g/l Na2S x 9 H2O 0.298805 g/l NH4Cl 0.298805 g/l KH2PO4 0.199203 g/l CaCl2 x 2 H2O 0.0298805 g/l HCl 0.00249004 g/l FeCl2 x 4 H2O 0.00149402 g/l Sodium resazurin 0.000498008 g/l NaOH 0.000498008 g/l CoCl2 x 6 H2O 0.000189243 g/l Pyridoxine hydrochloride 9.96016e-05 g/l MnCl2 x 4 H2O 9.96016e-05 g/l ZnCl2 6.97211e-05 g/l Thiamine HCl 4.98008e-05 g/l Nicotinic acid 4.98008e-05 g/l Calcium D-(+)-pantothenate 4.98008e-05 g/l p-Aminobenzoic acid 4.98008e-05 g/l (DL)-alpha-Lipoic acid 4.98008e-05 g/l Riboflavin 4.98008e-05 g/l Na2MoO4 x 2 H2O 3.58566e-05 g/l NiCl2 x 6 H2O 2.39044e-05 g/l Folic acid 1.99203e-05 g/l Biotin 1.99203e-05 g/l H3BO3 5.9761e-06 g/l Na2WO4 x 2 H2O 3.98406e-06 g/l Na2SeO3 x 5 H2O 2.98805e-06 g/l CuCl2 x 2 H2O 1.99203e-06 g/l Vitamin B12 9.96016e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
2738	positive	growth	65	thermophilic
69480				thermophilic	98.476

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
2738	anaerobe
69480	anaerobe	99.998

spore formation

@ref: 69480
spore formation: no
confidence: 99.984

Isolation, sampling and environmental information

isolation

@ref: 2738
sample type: marine hot spring
geographic location: Kurils, Shiashkoten island
country: Russia
origin.country: RUS
continent: Europe

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_3133.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_374;96_1633;97_1955;98_2404;99_3133&stattab=map
Last taxonomy: Spirochaeta thermophila subclade
16S sequence: FR749903
Sequence Identity:
Total samples: 1014
soil counts: 56
aquatic counts: 191
animal counts: 727
plant counts: 40

Safety information

risk assessment

@ref: 2738
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 20218
description: Spirochaeta thermophila partial 16S rRNA gene, type strain DSM 6578T
accession: FR749903
length: 1538
database: ena
NCBI tax ID: 154

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Spirochaeta thermophila DSM 6578	GCA_000184345	complete	ncbi	869211
66792	Spirochaeta thermophila DSM 6578	869211.3	wgs	patric	869211
66792	Spirochaeta thermophila Z-1203, DSM 6578	2506381022	complete	img	869211

GC content

@ref: 2738
GC-content: 60.9
method: sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	70	no
motile	yes	89.463	no
flagellated	no	70.26	no
gram-positive	no	94.022	no
anaerobic	yes	98.949	yes
aerobic	no	97.253	yes
halophile	no	79.28	no
spore-forming	no	90.121	no
thermophile	yes	98.39	yes
glucose-util	yes	87.749	no
glucose-ferment	yes	55.207	no

External links

@ref: 2738

culture collection no.: DSM 6578, ATCC 700085

straininfo link

@ref: 83472
straininfo: 43763

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Metabolism	1556064	Glucose catabolism by Spirochaeta thermophila RI 19.B1.	Janssen PH, Morgan HW	J Bacteriol	10.1128/jb.174.8.2449-2453.1992	1992	Fermentation, Glucose/metabolism, Spirochaeta/enzymology/metabolism	Enzymology
Enzymology	33135681	Insight into the potential factors influencing the catalytic direction in cellobiose 2-epimerase by crystallization and mutagenesis.	Feng Y, Hua X, Shen Q, Matthews M, Zhang Y, Fisher AJ, Lyu X, Yang R	Acta Crystallogr D Struct Biol	10.1107/S205979832001222X	2020	Bacillus/enzymology, Bacterial Proteins/chemistry/genetics, Biocatalysis, Caldicellulosiruptor/enzymology, Carbohydrate Epimerases/chemistry/genetics, Catalytic Domain, Isomerism, Mutagenesis, Site-Directed, Spirochaeta/*enzymology, Substrate Specificity

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
2738	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6578)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-6578
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
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
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
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
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)
83472	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID43763.1	StrainInfo: A central database for resolving microbial strain identifiers