Thiothrix caldifontis (DSM 21228, G1)

Name: Thiothrix caldifontis (DSM 21228, G1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17083

Type strain

Strain Designation G1

Culture col. no. DSM 21228 G1

NCBI tax ID(s) 1123398 525918

Special Collections DSMZ Literature strains

History <- G. Dubinina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; G1 <- M. Grabovich et al., Dept. Biology, Univ. Voronezh, Russia

Links

Thiothrix caldifontis G1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from bacterial mat from a sulfide spring at 33-40 °C.

Gram-negative rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 404309

VKM B-2520,DSM 21228

@ref 20215

Last LPSN update 2026-02-09 11:22:07

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Beggiatoales

Family Leucotrichaceae

Genus Thiothrix

Species Thiothrix caldifontis

Full scientific name Thiothrix caldifontis Chernousova et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
29249	negative	4.85 µm	1.55 µm	rod-shaped
125438	negative					98.5

Pigmentation

29249

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link
15527	Thiothrix medium II (DSMZ Medium 1774)		Medium recipe provided by DSMZ

Culture temp

@ref	Growth	Type	Temperature (°C)
15527	positive	growth	25
29249	positive	growth	07-37
29249	positive	optimum	25

Culture pH

@ref	Ability	Type	PH	PH range
29249	positive	optimum	8
29249	positive	growth	7-8.6	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29249	aerobe
125439	obligate aerobe	92.4

Spore formation

@ref	Spore formation	Confidence
125438		90.883
125439		96.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29249	NaCl	positive	growth	<3 %

Observation

29249

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29249	30089 ChEBI	acetate	+	carbon source
29249	35391 ChEBI	aspartate	+	carbon source
29249	24996 ChEBI	lactate	+	carbon source
29249	25017 ChEBI	leucine	+	carbon source
29249	17632 ChEBI	nitrate	+	reduction
29249	15361 ChEBI	pyruvate	+	carbon source
29249	30031 ChEBI	succinate	+	carbon source
29249	16199 ChEBI	urea	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29249	cytochrome oxidase	+	1.9.3.1
29249	urease	+	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	biotin biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	photosynthesis	100	14 of 14
66794	hydrogen production	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	lipid A biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	heme metabolism	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	pentose phosphate pathway	81.82	9 of 11
66794	cellulose degradation	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glutathione metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	alanine metabolism	75.86	22 of 29
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	purine metabolism	71.28	67 of 94
66794	starch degradation	70	7 of 10
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	glycolysis	64.71	11 of 17
66794	citric acid cycle	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	urea cycle	61.54	8 of 13
66794	pyrimidine metabolism	60	27 of 45
66794	propionate fermentation	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	oxidative phosphorylation	56.04	51 of 91
66794	metabolism of disaccharids	54.55	6 of 11
66794	d-xylose degradation	54.55	6 of 11
66794	proline metabolism	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	lipid metabolism	51.61	16 of 31
66794	cysteine metabolism	50	9 of 18
66794	glycine metabolism	50	5 of 10
66794	Entner Doudoroff pathway	50	5 of 10
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	selenocysteine biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	lysine metabolism	47.62	20 of 42
66794	sulfate reduction	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	tryptophan metabolism	44.74	17 of 38
66794	nitrate assimilation	44.44	4 of 9
66794	vitamin B12 metabolism	44.12	15 of 34
66794	propanol degradation	42.86	3 of 7
66794	degradation of pentoses	42.86	12 of 28
66794	glycine betaine biosynthesis	40	2 of 5
66794	elloramycin biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	ketogluconate metabolism	37.5	3 of 8
66794	carnitine metabolism	37.5	3 of 8
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	cyanate degradation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	degradation of sugar acids	32	8 of 25
66794	degradation of sugar alcohols	31.25	5 of 16
66794	polyamine pathway	30.43	7 of 23
66794	coenzyme M biosynthesis	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	myo-inositol biosynthesis	30	3 of 10
66794	degradation of hexoses	27.78	5 of 18
66794	chlorophyll metabolism	27.78	5 of 18
66794	ascorbate metabolism	27.27	6 of 22
66794	androgen and estrogen metabolism	25	4 of 16
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Spring
#Host	#Microbial	#Bacteria
#Condition	#Sulfuric	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15527	bacterial mat from a sulfide spring at 33-40 °C	Northern Caucasus, Petushok spring	Russia	RUS	Europe

Taxonmaps

69479

Global distribution of 16S sequence EU642573 (>99% sequence identity) for Thiothrix from Microbeatlas

Aquatic Samples	820
Soil Samples	27
Animal Samples	47
Plant Samples	7
Total Samples	901

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15527	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	IMG-taxon 2599185268 annotated assembly for Thiothrix caldifontis DSM 21228	scaffold	GCA_900107695	525918.3	2599185268	525918	63.84

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15527	Thiothrix caldifontis strain G1 16S ribosomal RNA gene, partial sequence	EU642573	1404		525918

GC content

@ref	GC-content (mol%)	Method
15527	52	thermal denaturation, midpoint method (Tm)
29249	52

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Thiothrix caldifontis DSM 21228
NCBI: GCA_900107695

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.10	no
125439	motility	BacteriaNetⓘ	no	67.40	no
125439	gram_stain	BacteriaNetⓘ	negative	88.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thiothrix caldifontis DSM 21228
NCBI: GCA_900107695.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	82.32	yes
125438	aerobic	aerobicⓘ	yes	64.23	yes
125438	spore-forming	spore-formingⓘ	no	90.88	no
125438	thermophilic	thermophileⓘ	no	95.82	yes
125438	flagellated	motile2+ⓘ	yes	67.97	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genome Analysis of the Genus Thiothrix Involving Three Novel Species, Thiothrix subterranea sp. nov. Ku-5, Thiothrix litoralis sp. nov. AS and "Candidatus Thiothrix anitrata" sp. nov. A52, Revealed the Conservation of the Pathways of Dissimilatory Sulfur Metabolism and Variations in the Genetic Inventory for Nitrogen Metabolism and Autotrophic Carbon Fixation.	Ravin NV, Rudenko TS, Smolyakov DD, Beletsky AV, Rakitin AL, Markov ND, Fomenkov A, Sun L, Roberts RJ, Novikov AA, Karnachuk OV, Grabovich MY.	Front Microbiol	10.3389/fmicb.2021.760289	2021
Phylogeny	Thiothrix caldifontis sp. nov. and Thiothrix lacustris sp. nov., gammaproteobacteria isolated from sulfide springs.	Chernousova E, Gridneva E, Grabovich M, Dubinina G, Akimov V, Rossetti S, Kuever J	Int J Syst Evol Microbiol	10.1099/ijs.0.009456-0	2009

References

#15527	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21228
#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 )
#25669	IJSEM 3128 2009 ( DOI 10.1099/ijs.0.009456-0 , PubMed 19643883 )
#29249	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25669
#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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Thiothrix caldifontis (DSM 21228, G1)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900107695

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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