Name: Caldimonas thermodepolymerans R-16654
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2995

Type strain:

Species: Caldimonas thermodepolymerans

Strain Designation: R-16654, K14

Culture col. no.: DSM 15344, LMG 21644, CCUG 50333

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

NCBI tax ID(s): 215580 (species)

SI-ID 85530

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

Section

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

motile
aerobe
thermophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Caldimonas*
	Species	**Caldimonas thermodepolymerans**
	Full Scientific Name (LPSN)	Caldimonas thermodepolymerans (Elbanna et al. 2003) Liu et al. 2023

	Synonym	Schlegelella thermodepolymerans
	Synonym	Caenibacterium thermophilum

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #69480]	Motility	yes Confidence in %92.34

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5859]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #5859]

Culture medium growth

[Ref.: #5859]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5859]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5859]			growth	50 °C
[Ref.: #58845]			growth	42 °C

[Ref.: #5859]

Temperature range

thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #58845]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.954

Fatty acid profile

Metadata FA analysis

Reference

[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

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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #5859]	Sample type/isolated from	activated sludge
[Ref.: #5859]	Country	Germany
[Ref.: #5859]	Country ISO 3 Code	DEU
[Ref.: #5859]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Activated sludge

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #5859]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Schlegelella thermodepolymerans strain K14 16S ribosomal RNA gene, partial sequence	AY152824	1517	ENA	215580 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Schlegelella thermodepolymerans DSM 15344	2832556195	draft	JGI IMG/M	215580 tax ID	*
[Ref.: #66792]	Caldimonas thermodepolymerans DSM 15344	GCA_003349825	scaffold	GenBank	215580 tax ID	*
[Ref.: #66792]	Caldimonas thermodepolymerans DSM 15344	GCA_002933415	contig	GenBank	215580 tax ID	*
[Ref.: #66792]	Schlegelella thermodepolymerans strain DSM 15344	215580.4	wgs	PATRIC	215580 tax ID	*
[Ref.: #66792]	Schlegelella thermodepolymerans strain DSM 15344	215580.3	wgs	PATRIC	215580 tax ID	*
[Ref.: #66792]	Schlegelella thermodepolymerans strain DSM 15344	215580.7	complete	PATRIC	215580 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Schlegelella thermodepolymerans DSM 15344 NCBI: GCA_015476235.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Schlegelella thermodepolymerans DSM 15344 NCBI: GCA_015476235.1
[Ref.: #69480]	motile	yes	84.447	no
[Ref.: #69480]	flagellated	yes	68.155	no
[Ref.: #69480]	gram-positive	no	99.234	no
[Ref.: #69480]	anaerobic	no	97.017	yes
[Ref.: #69480]	aerobic	yes	87.24	yes
[Ref.: #69480]	halophile	no	91.256	no
[Ref.: #69480]	spore-forming	no	94.911	no
[Ref.: #69480]	glucose-util	yes	55.687	no
[Ref.: #69480]	thermophile	yes	64.067	yes
[Ref.: #69480]	glucose-ferment	no	90.994	no

Availability in culture collections External links

[Ref.: #5859]

Culture collection no.

DSM 15344, LMG 21644, CCUG 50333

[Ref.: #72517]

SI-ID 85530

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#72517

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID85530.1 )

* These data were automatically processed and therefore are not curated

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Schlegelella thermodepolymerans DSM 15344

Schlegelella thermodepolymerans DSM 15344

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