Calidithermus roseus (DSM 29972, KCTC 42495, NBRC 110900)

Name: Calidithermus roseus (DSM 29972, KCTC 42495, NBRC 110900)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132336

Type strain

Culture col. no. DSM 29972 KCTC 42495 NBRC 110900 YIM 71031 JCM 30647

NCBI tax ID(s) 1644118

Special Collections DSMZ JCM KCTC

History <- W.-J. Li, YIM; YIM 71031 <- Y. Duan W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 71031.

Links

Calidithermus roseus DSM 29972 is a bacterium that was isolated from geothermally heated sediment from a hot spring.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 404729

KCTC 42495,NBRC 110900,DSM 29972

@ref 20215

Last LPSN update 2026-02-09 11:31:41

Domain Bacteria

Phylum Deinococcota

Class Deinococci

Order Thermales

Family Thermaceae

Genus Calidithermus

Species Calidithermus roseus

Full scientific name Calidithermus roseus (Ming et al. 2016) Raposo et al. 2019

Synonyms (1)

Meiothermus roseus

BacDive ID	Other strains from **Calidithermus roseus** (1)	Type strain
132337	C. roseus DSM 29973, NBRC 110899, YIM 71039, JCM 30648

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24125	T 5 MEDIUM (DSMZ Medium 1573)		Medium recipe at MediaDive	Name: T 5 MEDIUM (DSMZ Medium 1573) Composition: Yeast extract 2.0 g/l Peptone 1.0 g/l D(+)-Glucose 1.0 g/l CaCO3 1.0 g/l Tryptone 0.5 g/l MgSO4 x 7 H2O 0.003 g/l Nitrilotriacetic acid 0.0015 g/l NaCl 0.001 g/l MnSO4 x H2O 0.0005 g/l CoSO4 x 7 H2O 0.00018 g/l ZnSO4 x 7 H2O 0.00018 g/l FeSO4 x 7 H2O 0.0001 g/l CaCl2 x 2 H2O 0.0001 g/l NiCl2 x 6 H2O 3e-05 g/l AlK(SO4)2 x 12 H2O 2e-05 g/l H3BO3 1e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l CuSO4 x 5 H2O 1e-05 g/l Na2WO4 x 2 H2O 4e-07 g/l Na2SeO3 x 5 H2O 3e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
24125	positive	growth	50
67770	positive	growth	50

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		90.9

Observation

67770

Observationquinones: MK-8

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	glycogen metabolism	100	5 of 5
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	allantoin degradation	100	9 of 9
66794	adipate degradation	100	2 of 2
66794	kanosamine biosynthesis II	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	denitrification	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	palmitate biosynthesis	95.45	21 of 22
66794	photosynthesis	92.86	13 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	purine metabolism	85.11	80 of 94
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	alanine metabolism	82.76	24 of 29
66794	pyrimidine metabolism	82.22	37 of 45
66794	pentose phosphate pathway	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	Entner Doudoroff pathway	80	8 of 10
66794	3-chlorocatechol degradation	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	starch degradation	80	8 of 10
66794	myo-inositol biosynthesis	80	8 of 10
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	heme metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	sulfopterin metabolism	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	tryptophan metabolism	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	degradation of sugar acids	72	18 of 25
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	methionine metabolism	69.23	18 of 26
66794	histidine metabolism	68.97	20 of 29
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	lipid A biosynthesis	66.67	6 of 9
66794	oxidative phosphorylation	65.93	60 of 91
66794	polyamine pathway	65.22	15 of 23
66794	glycolysis	64.71	11 of 17
66794	d-xylose degradation	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	urea cycle	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	coenzyme M biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	cardiolipin biosynthesis	57.14	4 of 7
66794	degradation of pentoses	57.14	16 of 28
66794	tyrosine metabolism	57.14	8 of 14
66794	glutathione metabolism	57.14	8 of 14
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	sulfate reduction	53.85	7 of 13
66794	lysine metabolism	52.38	22 of 42
66794	lipid metabolism	51.61	16 of 31
66794	phenol degradation	50	10 of 20
66794	phenylmercury acetate degradation	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	propanol degradation	42.86	3 of 7
66794	glycine betaine biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	vitamin B12 metabolism	38.24	13 of 34
66794	carotenoid biosynthesis	36.36	8 of 22
66794	vitamin B6 metabolism	36.36	4 of 11
66794	bile acid biosynthesis, neutral pathway	35.29	6 of 17
66794	IAA biosynthesis	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	pantothenate biosynthesis	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	androgen and estrogen metabolism	25	4 of 16
66794	cyclohexanol degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	arachidonic acid metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
24125	geothermally heated sediment from a hot spring	Yunnan province, Tengchong county	China	CHN	Asia
67770	Hot spring in Tengchong county	Yunnan Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KP232921 (>99% sequence identity) for Calidithermus roseus from Microbeatlas

Aquatic Samples
Soil Samples
Animal Samples	4
Plant Samples
Total Samples	4

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24125	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM357409v1 assembly for Calidithermus roseus NBRC 110900	contig	GCA_003574095	1644118.3	2887030614	1644118	39.8

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24125	Calidithermus roseus strain YIM 71031 16S ribosomal RNA gene, partial sequence	KP232921	1538		1644118

GC content

@ref	GC-content (mol%)	Method
24125	64.0	high performance liquid chromatography (HPLC)
67770	64	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Calidithermus roseus NBRC 110900
NCBI: GCA_003574095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	90.90	no
125439	motility	BacteriaNetⓘ	no	53.20	no
125439	gram_stain	BacteriaNetⓘ	negative	80.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	69.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Meiothermus roseus strain NBRC 110900
PATRIC: 1644118.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	67.88	no
125438	anaerobic	anaerobicⓘ	no	91.70	no
125438	spore-forming	spore-formingⓘ	no	70.97	no
125438	aerobic	aerobicⓘ	yes	79.36	no
125438	thermophilic	thermophileⓘ	yes	57.54	yes
125438	flagellated	motile2+ⓘ	no	76.48	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Transfer of Meiothermus chliarophilus (Tenreiro et al.1995) Nobre et al. 1996, Meiothermus roseus Ming et al. 2016, Meiothermus terrae Yu et al. 2014 and Meiothermus timidus Pires et al. 2005, to Calidithermus gen. nov., as Calidithermus chliarophilus comb. nov., Calidithermus roseus comb. nov., Calidithermus terrae comb. nov. and Calidithermus timidus comb. nov., respectively, and emended description of the genus Meiothermus.	Raposo P, Viver T, Albuquerque L, Froufe H, Barroso C, Egas C, Rossello-Mora R, da Costa MS.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003270	2019
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

References

#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 )
#24125	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29972
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 roseus (DSM 29972, KCTC 42495, NBRC 110900)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003574095

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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