Clostridium halophilum (DSM 5387, ATCC 49637, M1)

Name: Clostridium halophilum (DSM 5387, ATCC 49637, M1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2740

Type strain

Strain Designation M1

Culture col. no. DSM 5387 ATCC 49637 M1

NCBI tax ID(s) 1121317 36842

Special Collections DSMZ Literature strains

History DSMZ <- C. Fendrich, Universität Göttingen, Institut für Mikrobiologie, Germany; M1 <- C. Fendrich {1986}

Links

Clostridium halophilum M1 is an anaerobe, chemoorganotroph, Gram-positive bacterium that was isolated from anoxic hypersaline sediment.

Gram-positive motile rod-shaped anaerobe chemoorganotroph genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 42595

ATCC 49637,DSM 5387

@ref 20215

Last LPSN update 2026-05-29 08:25:32

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium halophilum

Full scientific name Clostridium halophilum corrig. Fendrich et al. 1991

Synonyms (2)

Clostridium halophilium
Maledivibacter halophilus

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
2131	MALEDIVIBACTER MEDIUM (BETAINE) (DSMZ Medium 104d)		Medium recipe at MediaDive	Name: MALEDIVIBACTER MEDIUM (BETAINE) (DSMZ Medium 104d) Composition: NaCl 60.0 g/l Yeast extract 10.0 g/l Betaine x H2O 6.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l MgSO4 x 7 H2O 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
2131	positive	growth	35

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
2131	anaerobe
25020	anaerobe
125439	anaerobe	98.295

Nutrition type

25020

Typechemoorganotroph

Halophily

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25020	16763 ChEBI	2-oxobutanoate	-	carbon source
25020	37054 ChEBI	3-hydroxybutyrate	-	carbon source
25020	22599 ChEBI	arabinose	-	carbon source
25020	17057 ChEBI	cellobiose	+	carbon source
25020	15824 ChEBI	D-fructose	-	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	15978 ChEBI	glycerol 3-phosphate	-	carbon source
25020	18287 ChEBI	L-fucose	-	carbon source
25020	18050 ChEBI	L-glutamine	+	carbon source
25020	62345 ChEBI	L-rhamnose	-	carbon source
25020	16857 ChEBI	L-threonine	+	carbon source
25020	6731 ChEBI	melezitose	-	carbon source
25020	51850 ChEBI	methyl pyruvate	-	carbon source
25020	18394 ChEBI	palatinose	-	carbon source
25020	15361 ChEBI	pyruvate	+	carbon source
25020	17992 ChEBI	sucrose	-	carbon source
25020	27082 ChEBI	trehalose	+	carbon source

Antibiotic resistance

@ref	ChEBI	Metabolite	Is resistant
25020	17698	chloramphenicol

Enzymes

@ref	Value	Activity	Ec
25020	catalase	-	1.11.1.6
25020	cytochrome oxidase	-	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	propanol degradation	100	7 of 7
66794	suberin monomers biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	lipoate biosynthesis	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	threonine metabolism	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	isoleucine metabolism	100	8 of 8
66794	degradation of sugar alcohols	93.75	15 of 16
66794	vitamin B1 metabolism	92.31	12 of 13
66794	pyrimidine metabolism	91.11	41 of 45
66794	propionate fermentation	90	9 of 10
66794	alanine metabolism	89.66	26 of 29
66794	purine metabolism	89.36	84 of 94
66794	d-mannose degradation	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	flavin biosynthesis	86.67	13 of 15
66794	citric acid cycle	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	vitamin B12 metabolism	85.29	29 of 34
66794	urea cycle	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	NAD metabolism	83.33	15 of 18
66794	glycolysis	82.35	14 of 17
66794	pentose phosphate pathway	81.82	9 of 11
66794	hydrogen production	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	starch degradation	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	tryptophan metabolism	78.95	30 of 38
66794	photosynthesis	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	butanoate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	phenol degradation	75	15 of 20
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	histidine metabolism	72.41	21 of 29
66794	arginine metabolism	70.83	17 of 24
66794	methionine metabolism	69.23	18 of 26
66794	non-pathway related	68.42	26 of 38
66794	degradation of sugar acids	68	17 of 25
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	degradation of hexoses	66.67	12 of 18
66794	acetoin degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	oxidative phosphorylation	64.84	59 of 91
66794	glutathione metabolism	64.29	9 of 14
66794	degradation of pentoses	64.29	18 of 28
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	heme metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	gluconeogenesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	creatinine degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	lysine metabolism	59.52	25 of 42
66794	nitrate assimilation	55.56	5 of 9
66794	proline metabolism	54.55	6 of 11
66794	vitamin B6 metabolism	54.55	6 of 11
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	tyrosine metabolism	50	7 of 14
66794	pantothenate biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	lactate fermentation	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	metabolism of disaccharids	45.45	5 of 11
66794	allantoin degradation	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	ascorbate metabolism	40.91	9 of 22
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	IAA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	sulfate reduction	30.77	4 of 13
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	cyclohexanol degradation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	carnitine metabolism	25	2 of 8
66794	alginate biosynthesis	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	#Terrestrial	#Sediment
#Condition	#Anoxic (anaerobic)	-
#Condition	#Saline	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
2131	anoxic hypersaline sediment	Maldives	MDV	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2131	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 2524614863 annotated assembly for Maledivibacter halophilus M1	scaffold	GCA_900167445	36842.3	2524614863	36842	67.59

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2131	Clostridium halophilum 16S rRNA gene, strain DSM 5387	X77837	1480		36842

GC content

2131

GC-content (mol%)27.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2524614863 annotated assembly for Maledivibacter halophilus M1
NCBI: GCA_900167445

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.30	no
125439	gram_stain	BacteriaNetⓘ	variable	50.41	no
125439	motility	BacteriaNetⓘ	yes	68.25	no
125439	spore_formation	BacteriaNetⓘ	yes	65.48	no

Literature

References

#2131	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5387
#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 )
#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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