Paramaledivibacter caminithermalis (DSM 15212, CIP 107654, DViRD3)

Name: Paramaledivibacter caminithermalis (DSM 15212, CIP 107654, DViRD3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2815

Type strain

Strain Designation DViRD3

Culture col. no. DSM 15212 CIP 107654 DViRD3

NCBI tax ID(s) 1121301 191027

Special Collections DSMZ CIP Literature strains

History <- M.-L. Fardeau, Universités de Provence et de la Méditerranée, ESIL, Marseille, France; DViRD3 <- N. Brisbarre {2000}

Links

Paramaledivibacter caminithermalis DViRD3 is an anaerobe, thermophilic, Gram-positive prokaryote that was isolated from deep-sea hydrothermal vent, depth 800 m.

Gram-positive motile rod-shaped anaerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 113585

DSM 15212,CIP 107654

@ref 20215

Last LPSN update 2026-02-09 11:18:21

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Peptostreptococcales

Family Peptostreptococcaceae

Genus Paramaledivibacter

Species Paramaledivibacter caminithermalis

Full scientific name Paramaledivibacter caminithermalis (Brisbarre et al. 2003) Li et al. 2016

Synonyms (1)

Clostridium caminithermale

BacDive ID	Other strains from **Paramaledivibacter caminithermalis** (8)	Type strain
100549	P. caminithermalis STI07646(IMET), IMET 07163, IMET 7163, IMET ...
100550	P. caminithermalis STI07679(IMET), IMRU 1692
100551	P. caminithermalis STI07680(IMET), IMRU 1333
100552	P. caminithermalis STI07681(IMET), F354, IMRU 1309
100553	P. caminithermalis STI07684(IMET), IMRU 1701
100554	P. caminithermalis STI07678(IMET), IMRU 1105
100555	P. caminithermalis STI07682(IMET), IMRU 1300
100556	P. caminithermalis STI07683(IMET), IMRU 1299

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
25020	positive	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5759	PARAMALEDIVIBACTER MEDIUM (DSMZ Medium 986)		Medium recipe at MediaDive	Name: PARAMALEDIVIBACTER MEDIUM (DSMZ Medium 986) Composition: Sea Salt 29.97 g/l D-Glucose 3.996 g/l NaHCO3 1.998 g/l NH4Cl 0.999001 g/l Peptone 0.499501 g/l Yeast extract 0.499501 g/l KH2PO4 0.2997 g/l K2HPO4 0.2997 g/l L-Cysteine HCl x H2O 0.24975 g/l Na2S x 9 H2O 0.24975 g/l Sodium resazurin 0.0004995 g/l Pyridoxine hydrochloride 9.99001e-05 g/l Calcium D-(+)-pantothenate 4.995e-05 g/l Thiamine HCl 4.995e-05 g/l Riboflavin 4.995e-05 g/l Nicotinic acid 4.995e-05 g/l (DL)-alpha-Lipoic acid 4.995e-05 g/l p-Aminobenzoic acid 4.995e-05 g/l Folic acid 1.998e-05 g/l Biotin 1.998e-05 g/l Vitamin B12 9.99001e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5759	positive	growth	42	thermophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
5759	anaerobe
25020	anaerobe
125438	anaerobe	94.882
125439	anaerobe	99.5

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25020	22599 ChEBI	arabinose	+	carbon source
25020	17750 ChEBI	betaine	+	electron acceptor
25020	17057 ChEBI	cellobiose	-	carbon source
25020	16899 ChEBI	D-mannitol	+	carbon source
25020	16024 ChEBI	D-mannose	+	carbon source
25020		esculin ferric citrate	+	carbon source
25020	5291 ChEBI	gelatin	+	carbon source
25020	17234 ChEBI	glucose	+	carbon source
25020	24898 ChEBI	isoleucine	+	electron donor
25020	6731 ChEBI	melezitose	+	carbon source
25020	16811 ChEBI	methionine	+	electron donor
25020	17992 ChEBI	sucrose	+	carbon source
25020	27082 ChEBI	trehalose	-	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	aspartate and asparagine metabolism	100	9 of 9
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	threonine metabolism	90	9 of 10
66794	d-mannose degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	NAD metabolism	83.33	15 of 18
66794	purine metabolism	82.98	78 of 94
66794	vitamin B12 metabolism	82.35	28 of 34
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	starch degradation	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	alanine metabolism	79.31	23 of 29
66794	photosynthesis	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	urea cycle	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	histidine metabolism	75.86	22 of 29
66794	pyrimidine metabolism	75.56	34 of 45
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	acetoin degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	octane oxidation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	flavin biosynthesis	66.67	10 of 15
66794	heme metabolism	64.29	9 of 14
66794	gluconeogenesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	oxidative phosphorylation	61.54	56 of 91
66794	lipoate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	lipid metabolism	58.06	18 of 31
66794	tryptophan metabolism	57.89	22 of 38
66794	non-pathway related	57.89	22 of 38
66794	lysine metabolism	54.76	23 of 42
66794	proline metabolism	54.55	6 of 11
66794	sulfate reduction	53.85	7 of 13
66794	degradation of sugar acids	52	13 of 25
66794	pantothenate biosynthesis	50	3 of 6
66794	isoprenoid biosynthesis	50	13 of 26
66794	toluene degradation	50	2 of 4
66794	lactate fermentation	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	phenylmercury acetate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	tyrosine metabolism	50	7 of 14
66794	glycogen biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	pentose phosphate pathway	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	polyamine pathway	43.48	10 of 23
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	degradation of pentoses	42.86	12 of 28
66794	ascorbate metabolism	40.91	9 of 22
66794	factor 420 biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	metabolism of disaccharids	36.36	4 of 11
66794	lipid A biosynthesis	33.33	3 of 9
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	glutathione metabolism	28.57	4 of 14
66794	d-xylose degradation	27.27	3 of 11
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	degradation of sugar alcohols	25	4 of 16
66794	cyclohexanol degradation	25	1 of 4
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
5759	deep-sea hydrothermal vent, depth 800 m	Mid-Atlantic Ridge	Portugal	PRT	Europe	37.8333	-31.5167 37.8333/-31.5167

Taxonmaps

69479

Global distribution of 16S sequence AF458779 (>99% sequence identity) for Wukongibacter from Microbeatlas

Aquatic Samples	86
Soil Samples	10
Animal Samples	40
Plant Samples	4
Total Samples	140

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5759	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 2585428176 annotated assembly for Paramaledivibacter caminithermalis DSM 15212	scaffold	GCA_900142245	1121301.3	2585428176	1121301	46.95

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5759	Clostridium subatlanticum 16S ribosomal RNA gene, partial sequence	AF458779	1577		191027

GC content

@ref	GC-content (mol%)	Method
5759	33.1	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paramaledivibacter caminithermalis DSM 15212
NCBI: GCA_900142245

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	84.00	no
125439	motility	BacteriaNetⓘ	yes	80.80	no
125439	gram_stain	BacteriaNetⓘ	variable	73.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paramaledivibacter caminithermalis DSM 15212 DSM 15212
NCBI: GCA_900142245.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	64.35	yes
125438	anaerobic	anaerobicⓘ	yes	94.88	yes
125438	aerobic	aerobicⓘ	no	94.40	no
125438	spore-forming	spore-formingⓘ	yes	72.39	no
125438	thermophilic	thermophileⓘ	no	69.66	no
125438	flagellated	motile2+ⓘ	yes	81.91	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Detailed description of Senegalia massiliensis strain SIT17^T , a bacterium isolated from the human gut.	Traore SI, Ngom II, Lo CI, Di Pinto F, Sokhna C, Fournier PE, Raoult D, Fenollar F.	New Microbes New Infect	10.1016/j.nmni.2020.100700	2020
	Structural, Biochemical, and Bioinformatic Basis for Identifying Radical SAM Cyclopropyl Synthases.	Lien Y, Lachowicz JC, Mendauletova A, Zizola C, Ngendahimana T, Kostenko A, Eaton SS, Latham JA, Grove TL.	ACS Chem Biol	10.1021/acschembio.3c00583	2024
Phylogeny	Clostridium caminithermale sp. nov., a slightly halophilic and moderately thermophilic bacterium isolated from an Atlantic deep-sea hydrothermal chimney.	Brisbarre N, Fardeau ML, Cueff V, Cayol JL, Barbier G, Cilia V, Ravot G, Thomas P, Garcia JL, Ollivier B	Int J Syst Evol Microbiol	10.1099/ijs.0.02471-0	2003

References

#5759	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15212
#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 )
#25020	G. Z. Li, X.,Liu, X.,Zhang, X.,Shao, Z.: Wukongibacter baidiensis gen. nov., sp. nov., an anaerobic bacterium isolated from hydrothermal sulfides, and proposal for the reclassification of the closely related Clostridium halophilum and Clostridium caminithermale within Maledivibacter gen. nov. and Paramaledivibacter gen. nov., respectively. IJSEM 66: 4355 - 4361 2016 ( DOI 10.1099/ijsem.0.001355 , PubMed 27473553 )
#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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Paramaledivibacter caminithermalis (DSM 15212, CIP 107654, DViRD3)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900142245

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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