Calidithermus timidus (DSM 17022, CIP 108604, LMG 22897)

Name: Calidithermus timidus (DSM 17022, CIP 108604, LMG 22897)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16707

Type strain

Strain Designation SPS-243

Culture col. no. DSM 17022 CIP 108604 LMG 22897 NBRC 103207 SPS-243

NCBI tax ID(s) 1122223 307124

Special Collections DSMZ CIP

History <- M. da Costa, Univ. Coimbra, Dept. Bioquímica; SPS-243 <- A. Pires

Links

Calidithermus timidus SPS-243 is a bacterium that was isolated from Biofilm sample from a hot spring.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 134623

LMG 22897,CIP 108604,DSM 17022,NBRC 103207

@ref 20215

Last LPSN update 2026-02-09 11:22:02

Domain Bacteria

Phylum Deinococcota

Class Deinococci

Order Thermales

Family Thermaceae

Genus Calidithermus

Species Calidithermus timidus

Full scientific name Calidithermus timidus (Pires et al. 2005) Raposo et al. 2019

Synonyms (1)

Meiothermus timidus

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	92

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6688	THERMUS 162 MEDIUM (DSMZ Medium 878)		Medium recipe at MediaDive	Name: THERMUS 162 MEDIUM (DSMZ Medium 878) Composition: Agar 28.0 g/l Na2HPO4 x 12 H2O 4.3 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KH2PO4 0.544 g/l MgCl2 x 6 H2O 0.2 g/l Nitrilotriacetic acid 0.1 g/l CaSO4 x 2 H2O 0.04 g/l Fe(III) citrate 0.00122472 g/l MnSO4 x H2O 0.00114 g/l ZnSO4 x 7 H2O 0.00025 g/l H3BO3 0.00025 g/l CoCl2 x 6 H2O 2.25e-05 g/l CuSO4 x 5 H2O 1.25e-05 g/l Na2MoO4 x 2 H2O 1.25e-05 g/l H2SO4 Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
6688	positive	growth	50

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		93.1

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6688	Biofilm sample from a hot spring	São Pedro do Sul	Portugal	PRT	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ871168 (>99% sequence identity) for Calidithermus timidus from Microbeatlas

Aquatic Samples	174
Soil Samples	15
Animal Samples	188
Plant Samples	4
Total Samples	381

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6688	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM37320v1 assembly for Calidithermus timidus DSM 17022	scaffold	GCA_000373205	1122223.3	2515154081	1122223	73.08

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6688	Meiothermus timidus partial 16S rRNA gene, type strain SPS-243	AJ871168	1483		307124

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Calidithermus timidus DSM 17022
NCBI: GCA_000373205

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.10	no
125439	motility	BacteriaNetⓘ	yes	58.90	no
125439	gram_stain	BacteriaNetⓘ	negative	92.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	85.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Calidithermus timidus DSM 17022 DSM 17022
NCBI: GCA_000373205.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	67.94	no
125438	anaerobic	anaerobicⓘ	no	89.88	no
125438	aerobic	aerobicⓘ	yes	83.69	no
125438	spore-forming	spore-formingⓘ	no	69.59	no
125438	thermophilic	thermophileⓘ	yes	60.01	yes
125438	flagellated	motile2+ⓘ	no	73.76	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Structure-based interface engineering methodology in designing a thermostable amylose-forming transglucosylase.	Tian Y, Hou X, Ni D, Xu W, Guang C, Zhang W, Chen Q, Rao Y, Mu W.	J Biol Chem	10.1016/j.jbc.2022.102074	2022
Enzymology	Structural elements determining the transglycosylating activity of glycoside hydrolase family 57 glycogen branching enzymes.	Xiang G, Leemhuis H, van der Maarel MJEC.	Proteins	10.1002/prot.26200	2022
Enzymology	Thermostable Amylosucrase from Calidithermus timidus DSM 17022: Insight into Its Characteristics and Tetrameric Conformation.	Tian Y, Xu W, Guang C, Zhang W, Mu W	J Agric Food Chem	10.1021/acs.jafc.9b04023	2019
	Physiological Properties and Genome Structure of the Hyperthermophilic Filamentous Phage phiOH3 Which Infects Thermus thermophilus HB8.	Nagayoshi Y, Kumagae K, Mori K, Tashiro K, Nakamura A, Fujino Y, Hiromasa Y, Iwamoto T, Kuhara S, Ohshima T, Doi K	Front Microbiol	10.3389/fmicb.2016.00050	2016
Phylogeny	Meiothermus roseus sp. nov., a thermophilic bacterium isolated from a geothermal area.	Ming H, Duan YY, Guo QQ, Yin YR, Zhou EM, Liu L, Li S, Nie GX, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-015-0544-x	2015
Phylogeny	Meiothermus timidus sp. nov., a new slightly thermophilic yellow-pigmented species.	Pires AL, Albuquerque L, Tiago I, Nobre MF, Empadinhas N, Verissimo A, da Costa MS	FEMS Microbiol Lett	10.1016/j.femsle.2005.02.011	2005

References

#6688	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17022
#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) .
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Calidithermus timidus (DSM 17022, CIP 108604, LMG 22897)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000373205

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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