Gracilinema caldarium (DSM 7334, ATCC 51460, H1)

Name: Gracilinema caldarium (DSM 7334, ATCC 51460, H1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14324

Type strain

Strain Designation H1

Culture col. no. DSM 7334 ATCC 51460 H1

NCBI tax ID(s) 744872 215591

Special Collections DSMZ Literature strains

History <- M. Pohlschroeder, University of Massachusetts, Department of Microbiology, USA; H1 <- M. Pohlschroeder {1990}

Links

Gracilinema caldarium H1 is an anaerobe, thermophilic, Gram-negative prokaryote that was isolated from cyanobacterial mat of freshwater hot spring.

Gram-negative motile spiral-shaped anaerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 41060

ATCC 35405,CIP 103919,ATCC 51460,DSM 7334,DSM 14222,JCM 8153

@ref 20215

Last LPSN update 2025-12-16 09:50:19

Domain Pseudomonadati

Phylum Spirochaetota

Class Spirochaetia

Order Spirochaetales

Family Breznakiellaceae

Genus Gracilinema

Species Gracilinema caldarium

Full scientific name Gracilinema caldarium (Pohlschröder et al. 1995) Brune et al. 2022

Synonyms (4)

Spirochaeta caldaria
Treponema caldarium
Treponema caldaria
Spirochaeta caldarium

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
43420	negative	15-25 µm	0.2-0.3 µm	spiral-shaped
125439	negative					98.2

Colony morphology

@ref	Colony color	Colony shape	Incubation period
2903			2-3 days
43420	white, fluffy, cotton-ball like	circular

Multimedia

@ref:	66793
multimedia content:	EM_DSM_7334_1.jpg
multimedia.multimedia content:	EM_DSM_7334_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2903	GRACILINEMA MEDIUM (DSMZ Medium 635)		Medium recipe at MediaDive	Name: GRACILINEMA MEDIUM (DSMZ Medium 635) Composition: D-Glucose 1.98807 g/l Tryptone 1.98807 g/l L-Cysteine HCl x H2O 0.248509 g/l MgSO4 x 7 H2O 0.0745527 g/l Nitrilotriacetic acid 0.0372763 g/l HCl 0.0248509 g/l NaCl 0.0248509 g/l FeCl2 x 4 H2O 0.0149105 g/l MnSO4 x H2O 0.0124254 g/l ZnSO4 x 7 H2O 0.00447316 g/l CoSO4 x 7 H2O 0.00447316 g/l CaCl2 x 2 H2O 0.00248509 g/l FeSO4 x 7 H2O 0.00248509 g/l CoCl2 x 6 H2O 0.00188867 g/l MnCl2 x 4 H2O 0.000994036 g/l NiCl2 x 6 H2O 0.000745527 g/l ZnCl2 0.000695825 g/l AlK(SO4)2 x 12 H2O 0.000497018 g/l Sodium resazurin 0.000497018 g/l CuSO4 x 5 H2O 0.000248509 g/l H3BO3 0.000248509 g/l Na2MoO4 x 2 H2O 0.000248509 g/l Pyridoxine hydrochloride 9.94036e-05 g/l Thiamine HCl 4.97018e-05 g/l Nicotinic acid 4.97018e-05 g/l Calcium D-(+)-pantothenate 4.97018e-05 g/l (DL)-alpha-Lipoic acid 4.97018e-05 g/l p-Aminobenzoic acid 4.97018e-05 g/l Riboflavin 4.97018e-05 g/l Folic acid 1.98807e-05 g/l CuCl2 x 2 H2O 1.98807e-05 g/l Biotin 1.98807e-05 g/l Na2WO4 x 2 H2O 9.94036e-06 g/l Na2SeO3 x 5 H2O 7.45527e-06 g/l Vitamin B12 9.94036e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2903	positive	growth	50	thermophilic
43420	negative	growth	25
43420	negative	growth	60
43420	positive	optimum	48-52	thermophilic

Culture pH

@ref	Ability	Type	PH	PH range
43420	positive	optimum	7.2-7.5
43420	positive	growth	5.8-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
2903	anaerobe
43420	obligate anaerobe
125438	anaerobe	91.005
125439	anaerobe	97.9

Spore formation

@ref	Spore formation	Confidence
43420
125439		96.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43420	NaCl	positive	growth	0.25 %(w/v)
43420	NaCl		growth	0.4 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
43420		casein hydrolysate	-	assimilation
43420	17057 ChEBI	cellobiose	+	fermentation
43420	62974 ChEBI	cellotetraose	+	fermentation
43420	3528 ChEBI	cellotriose	+	fermentation
43420	62968 ChEBI	cellulose	-	assimilation
43420	15824 ChEBI	D-fructose	+	fermentation
43420	12936 ChEBI	D-galactose	+	fermentation
43420	17634 ChEBI	D-glucose	+	fermentation
43420	16024 ChEBI	D-mannose	+	fermentation
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
43420	16988 ChEBI	D-ribose	-	assimilation
43420	65327 ChEBI	D-xylose	+	fermentation
43420	17234 ChEBI	glucose	+	fermentation
43420	17754 ChEBI	glycerol	-	assimilation
43420	30849 ChEBI	L-arabinose	+	fermentation
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
43420	17716 ChEBI	lactose	+	fermentation
43420	17306 ChEBI	maltose	+	fermentation
43420	29864 ChEBI	mannitol	-	assimilation
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
43420		peptone	-	assimilation
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
43420	32954 ChEBI	sodium acetate	-	assimilation
43420	28017 ChEBI	starch	+	fermentation
43420	17992 ChEBI	sucrose	+	fermentation
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
43420	37166 ChEBI	xylan	-	assimilation

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
43420	17698	chloramphenicol	10 µg/mL
43420	7507	neomycin	10 µg/mL
43420	18208	penicillin g	10 µg/mL
43420	28077	rifampicin		100 µg/mL
43420	27902	tetracycline	10 µg/mL

Metabolite production

@ref	Chebi-ID	Metabolite
43420	30089 ChEBI	acetate
43420	16526 ChEBI	carbon dioxide
43420	18276 ChEBI	dihydrogen
43420	24996 ChEBI	DL-lactate
43420	16236 ChEBI	ethanol
68380	35581 ChEBI	indole	from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ppGpp biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	lipoate biosynthesis	100	5 of 5
66794	acetoin degradation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	cellulose degradation	100	5 of 5
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	degradation of sugar alcohols	81.25	13 of 16
66794	glycogen metabolism	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	d-mannose degradation	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	acetate fermentation	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	glutamate and glutamine metabolism	75	21 of 28
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	flavin biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	purine metabolism	72.34	68 of 94
66794	photosynthesis	71.43	10 of 14
66794	pyrimidine metabolism	71.11	32 of 45
66794	Entner Doudoroff pathway	70	7 of 10
66794	NAD metabolism	66.67	12 of 18
66794	UDP-GlcNAc biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	oxidative phosphorylation	65.93	60 of 91
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	leucine metabolism	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	degradation of pentoses	60.71	17 of 28
66794	bacilysin biosynthesis	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	methylglyoxal degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	citric acid cycle	57.14	8 of 14
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	non-pathway related	52.63	20 of 38
66794	histidine metabolism	51.72	15 of 29
66794	glycine metabolism	50	5 of 10
66794	biotin biosynthesis	50	2 of 4
66794	adipate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	ribulose monophosphate pathway	50	1 of 2
66794	propionate fermentation	50	5 of 10
66794	arginine metabolism	50	12 of 24
66794	methionine metabolism	50	13 of 26
66794	coenzyme A metabolism	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	tryptophan metabolism	47.37	18 of 38
66794	proline metabolism	45.45	5 of 11
66794	lysine metabolism	45.24	19 of 42
66794	cysteine metabolism	44.44	8 of 18
66794	polyamine pathway	43.48	10 of 23
66794	tyrosine metabolism	42.86	6 of 14
66794	ascorbate metabolism	40.91	9 of 22
66794	degradation of sugar acids	40	10 of 25
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	degradation of hexoses	38.89	7 of 18
66794	urea cycle	38.46	5 of 13
66794	vitamin B6 metabolism	36.36	4 of 11
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	sulfate reduction	30.77	4 of 13
66794	lipid metabolism	29.03	9 of 31
66794	ubiquinone biosynthesis	28.57	2 of 7
66794	carotenoid biosynthesis	27.27	6 of 22
66794	cyclohexanol degradation	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	vitamin B12 metabolism	23.53	8 of 34
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	lipid A biosynthesis	22.22	2 of 9
66794	glutathione metabolism	21.43	3 of 14

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
2903	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
2903	cyanobacterial mat of freshwater hot spring		Oregon, Lakeview, Hunter's hot spring	USA	USA	North America
43420	Hot Spring	1990-08	Hunter'2 Hot Spring, Oregon	USA	USA	North America	42.222	-120.368 42.222/-120.368

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2903	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	ASM21972v1 assembly for Gracilinema caldarium DSM 7334	complete	GCA_000219725	744872.15	2505679006	744872	98.82
66792	Treponema caldaria DSM 7334	complete		744872.3		744872	64.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
124043	Treponema caldarium DSM 7334 16S ribosomal RNA gene, partial sequence.	EU580141	1535		744872

GC content

@ref	GC-content (mol%)	Method
2903	45.6	sequence analysis
2903	45.0	thermal denaturation, midpoint method (Tm)
43420	46

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Gracilinema caldarium DSM 7334
NCBI: GCA_000219725

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.70	no
125439	motility	BacteriaNetⓘ	no	67.40	no
125439	gram_stain	BacteriaNetⓘ	negative	98.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Treponema caldarium DSM 7334 DSM 7334
NCBI: GCA_000219725.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	82.03	yes
125438	anaerobic	anaerobicⓘ	yes	91.01	no
125438	aerobic	aerobicⓘ	no	95.67	no
125438	spore-forming	spore-formingⓘ	no	72.47	yes
125438	thermophilic	thermophileⓘ	yes	54.31	yes
125438	flagellated	motile2+ⓘ	yes	59.43	no

Literature

References

#2903	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7334
#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 )
#43420	Birte Abt, Markus Goeker, Carmen Scheuner, Cliff Han, Megan Lu, Monica Misra, Alla Lapidus, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia, Lynne A. Goodwin, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Marcel Huntemann, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Cynthia D. Jeffries, Manfred Rohde, Stefan Spring, Sabine Gronow, John C. Detter, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Tanja Woyke, Hans-Peter Klenk: Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1 T ), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema. Stand Genomic Sci 8: 88 - 105 2013 ( DOI 10.4056/sigs.3096473 , PubMed 23961314 )
#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) .
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#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 )
#68380	Automatically annotated from API rID32A .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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