Fontimonas thermophila (DSM 23609, CCUG 59713, HA-01)

Name: Fontimonas thermophila (DSM 23609, CCUG 59713, HA-01)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23456

Type strain

Strain Designation HA-01

Culture col. no. DSM 23609 CCUG 59713 HA-01

NCBI tax ID(s) 1076937

Special Collections DSMZ CCUG Literature strains

Links

Fontimonas thermophila HA-01 is an aerobe, thermophilic, Gram-negative prokaryote that was isolated from freshwater hot spring.

Gram-negative motile rod-shaped aerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 405672

DSM 23609,CCUG 59713

@ref 20215

Last LPSN update 2025-12-16 09:52:40

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Nevskiales

Family Nevskiaceae

Genus Fontimonas

Species Fontimonas thermophila

Full scientific name Fontimonas thermophila Losey et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
30484	negative	rod-shaped
125439	negative		98.5
125439			96.4
125438	negative		98.494

Pigmentation

30484

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19194	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
19194	positive	growth	50	thermophilic
30484	positive	growth	37-60
30484	positive	optimum	47.5	thermophilic
62085	positive	growth	56	thermophilic

Culture pH

@ref	Ability	Type	PH	PH range
30484	positive	optimum	6.75
30484	positive	growth	6.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
30484	aerobe
62085	aerobe

Spore formation

@ref	Spore formation	Confidence
30484
125439		97
125438		91.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30484	NaCl	positive	growth	0-1 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30484	28644 ChEBI	2-oxopentanoate	+	carbon source
30484	16449 ChEBI	alanine	+	carbon source
30484	35391 ChEBI	aspartate	+	carbon source
30484	29987 ChEBI	glutamate	+	carbon source
30484	15428 ChEBI	glycine	+	carbon source
30484	21217 ChEBI	L-alaninamide	+	carbon source
30484	25017 ChEBI	leucine	+	carbon source
30484	51850 ChEBI	methyl pyruvate	+	carbon source
30484	26271 ChEBI	proline	+	carbon source
30484	53423 ChEBI	tween 40	+	carbon source
30484	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30484	alkaline phosphatase	+	3.1.3.1
30484	catalase	+	1.11.1.6
30484	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	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	lipid A biosynthesis	88.89	8 of 9
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	gluconeogenesis	87.5	7 of 8
66794	NAD metabolism	83.33	15 of 18
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	citric acid cycle	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	phenylalanine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	methionine metabolism	73.08	19 of 26
66794	propanol degradation	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	vitamin B1 metabolism	69.23	9 of 13
66794	purine metabolism	69.15	65 of 94
66794	alanine metabolism	68.97	20 of 29
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	peptidoglycan biosynthesis	66.67	10 of 15
66794	lipid metabolism	64.52	20 of 31
66794	proline metabolism	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	tryptophan metabolism	60.53	23 of 38
66794	threonine metabolism	60	6 of 10
66794	flavin biosynthesis	60	9 of 15
66794	cellulose degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	pyrimidine metabolism	60	27 of 45
66794	arachidonate biosynthesis	60	3 of 5
66794	non-pathway related	57.89	22 of 38
66794	tyrosine metabolism	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	glutathione metabolism	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	histidine metabolism	55.17	16 of 29
66794	arginine metabolism	54.17	13 of 24
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	lysine metabolism	52.38	22 of 42
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	glycogen biosynthesis	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	oxidative phosphorylation	48.35	44 of 91
66794	sulfate reduction	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of sugar alcohols	43.75	7 of 16
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	glycine metabolism	40	4 of 10
66794	Entner Doudoroff pathway	40	4 of 10
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	vitamin K metabolism	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	carnitine metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	cholesterol biosynthesis	36.36	4 of 11
66794	pentose phosphate pathway	36.36	4 of 11
66794	bile acid biosynthesis, neutral pathway	35.29	6 of 17
66794	phenol degradation	35	7 of 20
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	degradation of pentoses	32.14	9 of 28
66794	urea cycle	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	starch degradation	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	ppGpp biosynthesis	25	1 of 4

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	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Sampling date
19194	freshwater hot spring	Arkansas, Hot Springs National Park, Hale Bathhouse (W 93° 3' 13'', N 34° 30' 47'')	USA	USA	North America	34.5131	-93.0536 34.5131/-93.0536
62085	Hot spring water	Arkansas,Hale Bath House	USA	USA	North America			2010-01-20

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19194	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 2622736503 annotated assembly for Fontimonas thermophila DSM 23609	scaffold	GCA_900113085	1076937.3	2622736503	1076937	63.69

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19194	Fontimonas thermophila strain HA-01 16S ribosomal RNA gene, partial sequence	JN415769	1468		1076937

GC content

@ref	GC-content (mol%)	Method
19194	64.4	high performance liquid chromatography (HPLC)
30484	64.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Fontimonas thermophila DSM 23609
NCBI: GCA_900113085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.00	no
125439	motility	BacteriaNetⓘ	yes	96.40	no
125439	gram_stain	BacteriaNetⓘ	negative	98.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	88.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Fontimonas thermophila DSM 23609
NCBI: GCA_900113085.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	yes
125438	anaerobic	anaerobicⓘ	no	94.73	yes
125438	aerobic	aerobicⓘ	yes	78.63	yes
125438	spore-forming	spore-formingⓘ	no	91.80	yes
125438	thermophilic	thermophileⓘ	no	66.28	yes
125438	flagellated	motile2+ⓘ	yes	66.17	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Assembly strategies for rubber-degrading microbial consortia based on omics tools.	Cui C, Jiang M, Zhang C, Zhang N, Jin FJ, Li T, Lee HG, Jin L.	Front Bioeng Biotechnol	10.3389/fbioe.2023.1326395	2023
Genetics	Comprehensive genomic and phenotypic characterization of thermophilic bacterium Sinimarinibacterium thermocellulolyticum sp. nov. HSW-8^T, a cellulase-producing bacterium isolated from hot spring water in South Korea.	Jiang Y, Li Z.	Antonie Van Leeuwenhoek	10.1007/s10482-024-02055-8	2024
Phylogeny	Flagellatimonas centrodinii gen. nov., sp. nov., a novel member of the family Nevskiaceae isolated from toxin-producing dinoflagellate Centrodinium punctatum.	Jiang Y, Jiang L, Peng Y, Kim KH, Shin HH, Kim YM, Lee J, Li Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.005084	2021
Phylogeny	Fontimonas thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a freshwater hot spring, and proposal of Solimonadaceae fam. nov. to replace Sinobacteraceae Zhou et al. 2008.	Losey NA, Stevenson BS, Verbarg S, Rudd S, Moore ERB, Lawson PA	Int J Syst Evol Microbiol	10.1099/ijs.0.037127-0	2012

References

#19194	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23609
#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 )
#26818	IJSEM 254 2013 ( DOI 10.1099/ijs.0.037127-0 , PubMed 22407788 )
#30484	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 #26818
#62085	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 59713
#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 )
#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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Fontimonas thermophila (DSM 23609, CCUG 59713, HA-01)

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

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900113085

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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