Paludifilum halophilum (DSM 102817, CCUG 68698, SMBg3)

Name: Paludifilum halophilum (DSM 102817, CCUG 68698, SMBg3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132033

Type strain

Strain Designation SMBg3

Culture col. no. DSM 102817 CCUG 68698 SMBg3

NCBI tax ID(s) 1642702

Special Collections DSMZ CCUG Literature strains

Links

Paludifilum halophilum SMBg3 is an aerobe, chemoorganotroph, spore-forming prokaryote that forms filamentous colonies and was isolated from superficial sediment of a solar saltern.

spore-forming Gram-positive filament-shaped colony-forming aerobe chemoorganotroph thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404520

DSM 102817,CCUG 68698

@ref 20215

Last LPSN update 2025-12-16 10:01:24

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Thermoactinomycetaceae

Genus Paludifilum

Species Paludifilum halophilum

Full scientific name Paludifilum halophilum Frikha-Dammak et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell shape
25075	positive	filament-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25075	4.0-8.0 mm	pale yellow	filamentous	7 days	Bennett ’ s medium

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
25075	Bennett ’ s medium
23824	GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159) Composition: NaCl 100.0 g/l Agar 15.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
23824	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
23824	positive	growth	40	thermophilic
25075	positive	optimum	40.0-45.0	thermophilic
25075	positive	growth	30.0-55.0

Culture pH

@ref	Ability	Type	PH	PH range
25075	positive	optimum	8.0-9.0	alkaliphile
25075	positive	growth	5.0-11.0

Physiology and metabolism

Oxygen tolerance

25075

Oxygen toleranceaerobe

Nutrition type

25075

Typechemoorganotroph

Spore formation

@ref	Spore description	Type of spore	Confidence
25075	fluorescent,circular	spore
125438			93.957
125439			91.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration	Halophily level
25075	NaCl	positive	growth	5.0-20.0 %
25075	NaCl		optimum	10 %(w/v)	halophilic

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25075	22599 ChEBI	arabinose	+	carbon source
25075	29016 ChEBI	arginine	-	nitrogen source
25075		casein	+	hydrolysis
25075	62968 ChEBI	cellulose	-	hydrolysis
25075	16947 ChEBI	citrate	-	carbon source
25075	16991 ChEBI	dna	-	hydrolysis
25075	4853 ChEBI	esculin	+	hydrolysis
25075	28757 ChEBI	fructose	+	carbon source
25075	5291 ChEBI	gelatin	+	hydrolysis
25075	17234 ChEBI	glucose	-	fermentation
25075	17234 ChEBI	glucose	+	carbon source
25075	28300 ChEBI	glutamine	-	nitrogen source
25075	15428 ChEBI	glycine	+	nitrogen source
25075	17368 ChEBI	hypoxanthine	-	hydrolysis
25075	25017 ChEBI	leucine	-	nitrogen source
25075	18059 ChEBI	lipid	-	hydrolysis
25075	25094 ChEBI	lysine	+	nitrogen source
25075	17306 ChEBI	maltose	+	carbon source
25075	29864 ChEBI	mannitol	-	carbon source
25075	37684 ChEBI	mannose	+	carbon source
25075	17268 ChEBI	myo-inositol	+	carbon source
25075	17632 ChEBI	nitrate	-	reduction
25075	16301 ChEBI	nitrite	-	reduction
25075	18257 ChEBI	ornithine	+	nitrogen source
25075	28044 ChEBI	phenylalanine	-	nitrogen source
25075	26271 ChEBI	proline	+	nitrogen source
25075	30911 ChEBI	sorbitol	+	carbon source
25075	28017 ChEBI	starch	+	carbon source
25075	28017 ChEBI	starch	+	hydrolysis
25075	17992 ChEBI	sucrose	+	carbon source
25075	27897 ChEBI	tryptophan	-	energy source
25075	27897 ChEBI	tryptophan	-	nitrogen source
25075	18186 ChEBI	tyrosine	-	hydrolysis
25075	16199 ChEBI	urea	-	hydrolysis
25075	15318 ChEBI	xanthine	-	hydrolysis
25075	18222 ChEBI	xylose	+	carbon source

Antibiotic resistance

@ref	ChEBI	Metabolite	Is antibiotic	Is resistant
25075	15882	phenol
25075	53426	tween 80

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25075	15688 ChEBI	acetoin
25075	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Citrate test	Methylred-test	Indole test
25075	15688 ChEBI	acetoin	-
25075	16947 ChEBI	citrate		-
25075	17234 ChEBI	glucose			-
25075	35581 ChEBI	indole				-

Enzymes

@ref	Value	Activity	Ec
25075	catalase	+	1.11.1.6
25075	cytochrome oxidase	+	1.9.3.1
25075	tryptophan deaminase	-	4.1.99.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	aspartate and asparagine metabolism	100	9 of 9
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	lipoate biosynthesis	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	threonine metabolism	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	aerobactin biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	kanosamine biosynthesis II	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	degradation of sugar alcohols	93.75	15 of 16
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	vitamin B1 metabolism	92.31	12 of 13
66794	starch degradation	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	vitamin B12 metabolism	82.35	28 of 34
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	propionate fermentation	80	8 of 10
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	myo-inositol biosynthesis	80	8 of 10
66794	Entner Doudoroff pathway	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	flavin biosynthesis	73.33	11 of 15
66794	pyrimidine metabolism	73.33	33 of 45
66794	methionine metabolism	73.08	19 of 26
66794	proline metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	NAD metabolism	72.22	13 of 18
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	arginine metabolism	70.83	17 of 24
66794	glycolysis	70.59	12 of 17
66794	histidine metabolism	68.97	20 of 29
66794	tryptophan metabolism	68.42	26 of 38
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	alanine metabolism	65.52	19 of 29
66794	lipid metabolism	64.52	20 of 31
66794	degradation of pentoses	64.29	18 of 28
66794	citric acid cycle	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	oxidative phosphorylation	62.64	57 of 91
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	factor 420 biosynthesis	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	tyrosine metabolism	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	nitrate assimilation	55.56	5 of 9
66794	degradation of sugar acids	52	13 of 25
66794	degradation of hexoses	50	9 of 18
66794	butanoate fermentation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	toluene degradation	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	lactate fermentation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	sulfate reduction	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	cholesterol biosynthesis	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	d-mannose degradation	44.44	4 of 9
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	gallate degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	vitamin B6 metabolism	36.36	4 of 11
66794	phenol degradation	35	7 of 20
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	ascorbate metabolism	27.27	6 of 22
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	carnitine metabolism	25	2 of 8
66794	vitamin E metabolism	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature
23824	superficial sediment of a solar saltern	Sfax (thalossohaline natural ecosystem in the central eastern coast, about 34° 39' N 10° 42' E)	Tunisia	TUN	Africa	34.65	10.7 34.65/10.7
25075	superficial sediment of non-crystallizer M1 pond							Streptomyces isolation agar medium	containing l-1: 5 g glucose, 4 g sodium propionate, 2 g casein, 0.5 g K2HPO4 , 0.5 g MgSO4 .7H2O, 200 ml sterile soil extract, 150 g NaCl and 20 g agar, pH = 7.2, ampicillin (5 Âµg ml-1) and cycloheximide (50 Âµg ml-1)	21 days	37

Taxonmaps

69479

Global distribution of 16S sequence KP229518 (>99% sequence identity) for Paludifilum halophilum subclade from Microbeatlas

Aquatic Samples	62
Soil Samples	343
Animal Samples	149
Plant Samples	97
Total Samples	651

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
23824	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Paludifilum halophilum DSM 102817	complete			2784132154	1642702	91.91
66792	ASM224535v1 assembly for Paludifilum halophilum DSM 102817	contig	GCA_002245355	1642702.3	2802429553	1642702	23.91

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23824	Paludifilum halophilum strain SMBg3 16S ribosomal RNA gene, partial sequence	KP229518	1362		1642702

GC content

@ref	GC-content (mol%)	Method
23824	51.2	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: Paludifilum halophilum DSM 102817
NCBI: GCA_002245355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	91.10	no
125439	motility	BacteriaNetⓘ	yes	74.30	no
125439	gram_stain	BacteriaNetⓘ	variable	66.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	87.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paludifilum halophilum strain DSM 102817
PATRIC: 1642702.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	79.02	yes
125438	anaerobic	anaerobicⓘ	no	86.33	yes
125438	spore-forming	spore-formingⓘ	yes	93.96	yes
125438	aerobic	aerobicⓘ	yes	76.06	no
125438	thermophilic	thermophileⓘ	no	63.17	no
125438	flagellated	motile2+ⓘ	no	72.43	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Enhancement of Antibacterial Activity of Paludifilum halophilum and Identification of N-(1-Carboxy-ethyl)-phthalamic Acid as the Main Bioactive Compound.	Frikha-Dammak D, Fakhfakh J, Belhaj D, Bouattour E, Ayadi H, Chaabouni M, Ayadi H, Maalej S	Biomed Res Int	10.1155/2020/4805706	2020
Pathogenicity	Antagonistic Properties of Some Halophilic Thermoactinomycetes Isolated from Superficial Sediment of a Solar Saltern and Production of Cyclic Antimicrobial Peptides by the Novel Isolate Paludifilum halophilum.	Frikha Dammak D, Zarai Z, Najah S, Abdennabi R, Belbahri L, Rateb ME, Mejdoub H, Maalej S	Biomed Res Int	10.1155/2017/1205258	2017
Metabolism	Genome analysis of the salt-resistant Paludifilum halophilum DSM 102817(T) reveals genes involved in flux-tuning of ectoines and unexplored bioactive secondary metabolites.	Frikha-Dammak D, Ayadi H, Hakim-Rekik I, Belbahri L, Maalej S	World J Microbiol Biotechnol	10.1007/s11274-021-03147-7	2021
Stress	The saltern-derived Paludifilum halophilum DSM 102817(T) is a new high-yield ectoines producer in minimal medium and under salt stress conditions.	Ayadi H, Frikha-Dammak D, Fakhfakh J, Chamkha M, Hassairi I, Allouche N, Sayadi S, Maalej S	3 Biotech	10.1007/s13205-020-02512-x	2020
Phylogeny	Paludifilum halophilum gen. nov., sp. nov., a thermoactinomycete isolated from superficial sediment of a solar saltern.	Frikha-Dammak D, Fardeau ML, Cayol JL, Ben Fguira-Fourati L, Najeh S, Ollivier B, Maalej S	Int J Syst Evol Microbiol	10.1099/ijsem.0.001523	2016

References

#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 )
#23824	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102817
#25075	D. F. Frikha-Dammak, M. L.,Cayol, J. L.,Ben Fguira-Fourati, L.,Najeh, S.,Ollivier, B.,Maalej, S.: Paludifilum halophilum gen. nov., sp. nov., a thermoactinomycete isolated from superficial sediment of a solar saltern. IJSEM 66: 5371 - 5378 2016 ( DOI 10.1099/ijsem.0.001523 , PubMed 27671055 )
#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 )

Rate our new design

Content

About us

Paludifilum halophilum (DSM 102817, CCUG 68698, SMBg3)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

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_002245355

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media