Caldimonas thermodepolymerans (DSM 15344, LMG 21644, CCUG 50333)

Name: Caldimonas thermodepolymerans (DSM 15344, LMG 21644, CCUG 50333)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2995

Type strain

Strain Designation R-16654, K14

Culture col. no. DSM 15344 LMG 21644 CCUG 50333 R-16654 K14

NCBI tax ID(s) 215580

Special Collections DSMZ CCUG

History <- D. Janssens <- S. Van Trappen, Univ. Ghent, Belgium; R-16654 <- A. Steinbüchel, Univ. Münster

Links

Caldimonas thermodepolymerans R-16654 is an aerobe, thermophilic prokaryote that was isolated from activated sludge.

aerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 85530

LMG 21644,DSM 15344,CCUG 50333,KCTC 12177,VTT E-072690

@ref 20215

Last LPSN update 2026-02-09 11:18:24

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Sphaerotilaceae

Genus Caldimonas

Species Caldimonas thermodepolymerans

Full scientific name Caldimonas thermodepolymerans (Elbanna et al. 2003) Liu et al. 2023

Synonyms (2)

Schlegelella thermodepolymerans
Caenibacterium thermophilum

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.5
125439	negative	97.7

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5859	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5859	positive	growth	50	thermophilic
58845	positive	growth	42

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
58845	aerobe
125439	obligate aerobe	99.3

Spore formation

@ref	Spore formation	Confidence
125439		96.8

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	methylglyoxal degradation	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	cyanate degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	taurine degradation	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	palmitate biosynthesis	90.91	20 of 22
66794	starch degradation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	peptidoglycan biosynthesis	80	12 of 15
66794	phenol degradation	80	16 of 20
66794	threonine metabolism	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	purine metabolism	79.79	75 of 94
66794	serine metabolism	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	tryptophan metabolism	76.32	29 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	biotin biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	metabolism of disaccharids	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	tyrosine metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	lysine metabolism	71.43	30 of 42
66794	glutathione metabolism	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	methionine metabolism	69.23	18 of 26
66794	urea cycle	69.23	9 of 13
66794	non-pathway related	68.42	26 of 38
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	allantoin degradation	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	lipid metabolism	64.52	20 of 31
66794	pyrimidine metabolism	64.44	29 of 45
66794	citric acid cycle	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	hydrogen production	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	oxidative phosphorylation	59.34	54 of 91
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	degradation of sugar alcohols	56.25	9 of 16
66794	nitrate assimilation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	pentose phosphate pathway	54.55	6 of 11
66794	sulfate reduction	53.85	7 of 13
66794	quinate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	arginine metabolism	50	12 of 24
66794	toluene degradation	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	resorcinol degradation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	carotenoid biosynthesis	45.45	10 of 22
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	propanol degradation	42.86	3 of 7
66794	bile acid biosynthesis, neutral pathway	41.18	7 of 17
66794	glycine metabolism	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	vitamin K metabolism	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	cholesterol biosynthesis	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	vitamin B12 metabolism	29.41	10 of 34
66794	degradation of sugar acids	28	7 of 25
66794	arachidonic acid metabolism	27.78	5 of 18
66794	ascorbate metabolism	27.27	6 of 22
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4

Fatty acid profile

Metadata FA analysis

@ref

58845

Fatty acid	Percentage	ECL
C16:0	30.9	16
C17:0 CYCLO	20	16.888
C18:1 ω7c /12t/9t	20	17.824
C16:1 ω7c	17.4	15.819
C10:0 3OH	3.3	11.423
C18:0	2.4	18
C12:0	1.5	12
C12:0 3OH	1.4	13.455
C10:0	1.2	10
C19:0 CYCLO ω8c	0.7	18.9
C16:0 iso	0.6	15.626
C14:0	0.2	14
Unidentified	0.2	11.08
Unidentified	0.2	17.749
unk. 18.846/19:1 ω6c	0.2	18.846

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Activated sludge

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
5859	activated sludge	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence AY152824 (>99% sequence identity) for Schlegelella thermodepolymerans subclade from Microbeatlas

Aquatic Samples	726
Soil Samples	630
Animal Samples	2814
Plant Samples	134
Total Samples	4304

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5859	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	ASM1547623v1 assembly for Caldimonas thermodepolymerans DSM 15344	complete	GCA_015476235	215580.7	8001698186	215580	99.5
66792	ASM334982v1 assembly for Caldimonas thermodepolymerans DSM 15344	scaffold	GCA_003349825	215580.4	2770939503	215580	73.19
66792	ASM293341v1 assembly for Caldimonas thermodepolymerans DSM 15344	contig	GCA_002933415	215580.3	2832556195	215580	70.03

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Schlegelella thermodepolymerans strain K14 16S ribosomal RNA gene, partial sequence	AY152824	1517		215580

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Caldimonas thermodepolymerans DSM 15344
NCBI: GCA_015476235

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.80	no
125439	motility	BacteriaNetⓘ	yes	80.70	no
125439	gram_stain	BacteriaNetⓘ	negative	97.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Schlegelella thermodepolymerans DSM 15344
NCBI: GCA_015476235.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	91.60	no
125438	aerobic	aerobicⓘ	yes	82.04	yes
125438	spore-forming	spore-formingⓘ	no	89.90	no
125438	thermophilic	thermophileⓘ	no	67.13	yes
125438	flagellated	motile2+ⓘ	yes	79.65	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	An Initial Genome Editing Toolset for Caldimonas thermodepolymerans, the First Model of Thermophilic Polyhydroxyalkanoates Producer.	Grybchuk-Ieremenko A, Lipovska K, Kourilova X, Obruca S, Dvorak P.	Microb Biotechnol	10.1111/1751-7915.70103	2025
Biotechnology	Genomic and phenotypic comparison of polyhydroxyalkanoates producing strains of genus Caldimonas/Schlegelella.	Musilova J, Kourilova X, Hermankova K, Bezdicek M, Ieremenko A, Dvorak P, Obruca S, Sedlar K.	Comput Struct Biotechnol J	10.1016/j.csbj.2023.10.051	2023
Genetics	First Complete Genome of the Thermophilic Polyhydroxyalkanoates-Producing Bacterium Schlegelella thermodepolymerans DSM 15344.	Musilova J, Kourilova X, Bezdicek M, Lengerova M, Obruca S, Skutkova H, Sedlar K	Genome Biol Evol	10.1093/gbe/evab007	2021
Biotechnology	Production of polyhydroxyalkanoates (PHA) by a thermophilic strain of Schlegelella thermodepolymerans from xylose rich substrates.	Kourilova X, Pernicova I, Sedlar K, Musilova J, Sedlacek P, Kalina M, Koller M, Obruca S	Bioresour Technol	10.1016/j.biortech.2020.123885	2020
Phylogeny	Schlegelella thermodepolymerans gen. nov., sp. nov., a novel thermophilic bacterium that degrades poly(3-hydroxybutyrate-co-3-mercaptopropionate).	Elbanna K, Lutke-Eversloh T, Van Trappen S, Mergaert J, Swings J, Steinbuchel A	Int J Syst Evol Microbiol	10.1099/ijs.0.02562-0	2003

References

#5859	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15344
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#58845	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 50333
#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) .
#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 )
#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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Caldimonas thermodepolymerans (DSM 15344, LMG 21644, CCUG 50333)

Name and taxonomic classification