Name: Paramaledivibacter caminithermalis DViRD3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2815

Type strain:

Species: Paramaledivibacter caminithermalis

Strain Designation: DViRD3

Culture col. no.: DSM 15212, CIP 107654

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

NCBI tax ID(s): 1121301 (strain), 191027 (species)

SI-ID 113585

DSM 15212, CIP 107654

Other strains from Paramaledivibacter caminithermalis

P. caminithermalis STI07646(IMET), IMET 07163, IMET ...
P. caminithermalis STI07679(IMET), IMRU 1692
P. caminithermalis STI07680(IMET), IMRU 1333
P. caminithermalis STI07681(IMET), F354, IMRU 1309
P. caminithermalis STI07684(IMET), IMRU 1701
P. caminithermalis STI07678(IMET), IMRU 1105
P. caminithermalis STI07682(IMET), IMRU 1300
P. caminithermalis STI07683(IMET), IMRU 1299

Section

Paramaledivibacter caminithermalis DViRD3 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from deep-sea hydrothermal vent, depth 800 m.

Gram-positive
motile
rod-shaped
spore-forming
anaerobe
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Peptostreptococcaceae*
	Genus	*Paramaledivibacter*
	Species	**Paramaledivibacter caminithermalis**
	Full Scientific Name (LPSN)	Paramaledivibacter caminithermalis (Brisbarre et al. 2003) Li et al. 2016

Synonym

Clostridium caminithermale

Information on morphological and physiological properties Morphology

[Ref.: #25020]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #25020]	Cell shape	rod-shaped

[Ref.: #25020]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.836

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5759]

Culture medium

PARAMALEDIVIBACTER MEDIUM (DSMZ Medium 986)

[Ref.: #5759]

Culture medium growth

[Ref.: #5759]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5759]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5759]			growth	42 °C

[Ref.: #5759]

Temperature range

thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5759]	Oxygen tolerance	anaerobe
[Ref.: #25020]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25020]	arabinose ChEBI	+	carbon source
[Ref.: #25020]	betaine ChEBI	+	electron acceptor
[Ref.: #25020]	cellobiose ChEBI	-	carbon source
[Ref.: #25020]	D-mannitol ChEBI	+	carbon source
[Ref.: #25020]	D-mannose ChEBI	+	carbon source
[Ref.: #25020]	esculin ferric citrate	+	carbon source
[Ref.: #25020]	gelatin ChEBI	+	carbon source
[Ref.: #25020]	glucose ChEBI	+	carbon source
[Ref.: #25020]	isoleucine ChEBI	+	electron donor
[Ref.: #25020]	melezitose ChEBI	+	carbon source
[Ref.: #25020]	methionine ChEBI	+	electron donor
[Ref.: #25020]	sucrose ChEBI	+	carbon source
[Ref.: #25020]	trehalose ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	purine metabolism	82.98	78 of 94
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	degradation of sugar acids	52	13 of 25
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	pentose phosphate pathway	45.45	5 of 11
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #5759]	Sample type/isolated from	deep-sea hydrothermal vent, depth 800 m
[Ref.: #5759]	Geographic location (country and/or sea, region)	Mid-Atlantic Ridge
[Ref.: #5759]	Country	Portugal
[Ref.: #5759]	Country ISO 3 Code	PRT
[Ref.: #5759]	Continent	Europe
[Ref.: #5759]	Geographic location	37.8333°/-31.5167°
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #5759]

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.: #5759]	Clostridium subatlanticum 16S ribosomal RNA gene, partial sequence	AF458779	1577	ENA	191027 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paramaledivibacter caminithermalis DSM 15212	GCA_900142245	scaffold	GenBank	1121301 tax ID	*
[Ref.: #66792]	Clostridium caminithermale DSM 15212	1121301.3	wgs	PATRIC	1121301 tax ID	*
[Ref.: #66792]	Paramaledivibacter caminithermalis DSM 15212	2585428176	draft	JGI IMG/M	1121301 tax ID	*

[Ref.: #5759]

GC-content

33.1 mol%

high performance liquid chromatography (HPLC)

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: Paramaledivibacter caminithermalis DSM 15212 DSM 15212 NCBI: GCA_900142245.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paramaledivibacter caminithermalis DSM 15212 DSM 15212 NCBI: GCA_900142245.1
[Ref.: #69480]	motile	yes	86.645	no
[Ref.: #69480]	flagellated	yes	54.714	no
[Ref.: #69480]	gram-positive	yes	57.575	yes
[Ref.: #69480]	anaerobic	yes	99.237	yes
[Ref.: #69480]	aerobic	no	97.806	yes
[Ref.: #69480]	halophile	no	87.919	no
[Ref.: #69480]	spore-forming	yes	94.185	no
[Ref.: #69480]	thermophile	yes	95.202	yes
[Ref.: #69480]	glucose-util	yes	90.592	yes
[Ref.: #69480]	glucose-ferment	yes	53.687	no

Availability in culture collections External links

[Ref.: #5759]

Culture collection no.

DSM 15212, CIP 107654

[Ref.: #72340]

SI-ID 113585

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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 )

#72340

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-ID113585.1 )

* These data were automatically processed and therefore are not curated

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Paramaledivibacter caminithermalis DSM 15212 DSM 15212

Paramaledivibacter caminithermalis DSM 15212 DSM 15212

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