Strain identifier

BacDive ID: 132033

Type strain: Yes

Species: Paludifilum halophilum

Strain Designation: SMBg3

Strain history: <- M. L. Fardeau, IRD/ESIL, Marseille, France; SMBg3 <- D. F. Dammak, University of Sfax, Tunisis; SMBg3

NCBI tax ID(s): 1642702 (species)

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General

@ref: 23824

BacDive-ID: 132033

DSM-Number: 102817

keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, spore-forming, thermophilic, Gram-positive, filament-shaped, colony-forming

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

NCBI tax id

  • NCBI tax id: 1642702
  • Matching level: species

strain history

  • @ref: 23824
  • history: <- M. L. Fardeau, IRD/ESIL, Marseille, France; SMBg3 <- D. F. Dammak, University of Sfax, Tunisis; SMBg3

doi: 10.13145/bacdive132033.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Thermoactinomycetaceae
  • genus: Paludifilum
  • species: Paludifilum halophilum
  • full scientific name: Paludifilum halophilum Frikha-Dammak et al. 2016

@ref: 23824

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Thermoactinomycetaceae

genus: Paludifilum

species: Paludifilum halophilum

full scientific name: Paludifilum halophilum Frikha-Dammak et al. 2016

strain designation: SMBg3

type strain: yes

Morphology

cell morphology

@refgram staincell shapeconfidence
25075positivefilament-shaped
69480positive100

colony morphology

  • @ref: 25075
  • colony size: 4.0-8.0 mm
  • colony color: pale yellow
  • colony shape: filamentous
  • incubation period: 7 days
  • medium used: Bennett ’ s medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25075Bennett ’ s mediumyes
23824GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159)yeshttps://mediadive.dsmz.de/medium/1159Name: 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
23824BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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

@refgrowthtypetemperaturerangeconfidence
25075positiveoptimum40.0-45.0thermophilic
25075positivegrowth30.0-55.0
23824positivegrowth40thermophilic
69480thermophilic94.119

culture pH

@refabilitytypepHPH range
25075positiveoptimum8.0-9.0alkaliphile
25075positivegrowth5.0-11.0

Physiology and metabolism

oxygen tolerance

  • @ref: 25075
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 25075
  • type: chemoorganotroph

spore formation

@refspore descriptiontype of sporespore formationconfidence
25075fluorescent,circularsporeyes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentrationhalophily level
25075NaClpositivegrowth5.0-20.0 %
25075NaCloptimum10 %(w/v)halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2507529016arginine-nitrogen source
2507562968cellulose-hydrolysis
2507516947citrate-carbon source
2507516991dna-hydrolysis
2507517234glucose-fermentation
2507528300glutamine-nitrogen source
2507517368hypoxanthine-hydrolysis
2507525017leucine-nitrogen source
2507518059lipid-hydrolysis
2507529864mannitol-carbon source
2507517632nitrate-reduction
2507516301nitrite-reduction
2507528044phenylalanine-nitrogen source
2507527897tryptophan-energy source
2507527897tryptophan-nitrogen source
2507518186tyrosine-hydrolysis
2507516199urea-hydrolysis
2507515318xanthine-hydrolysis
2507522599arabinose+carbon source
25075casein+hydrolysis
250754853esculin+hydrolysis
2507528757fructose+carbon source
250755291gelatin+hydrolysis
2507517234glucose+carbon source
2507515428glycine+nitrogen source
2507517268myo-inositol+carbon source
2507525094lysine+nitrogen source
2507517306maltose+carbon source
2507537684mannose+carbon source
2507518257ornithine+nitrogen source
2507526271proline+nitrogen source
2507530911sorbitol+carbon source
2507528017starch+carbon source
2507528017starch+hydrolysis
2507517992sucrose+carbon source
2507518222xylose+carbon source

antibiotic resistance

@refChEBImetaboliteis antibioticis resistant
2507553426tween 80yesyes
2507515882phenolyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2507515688acetoinno
2507535581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole testcitrate test
2507517234glucose-
2507515688acetoin-
2507535581indole-
2507516947citrate-

enzymes

@refvalueactivityec
25075catalase+1.11.1.6
25075cytochrome oxidase+1.9.3.1
25075tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
23824superficial sediment of a solar salternSfax (thalossohaline natural ecosystem in the central eastern coast, about 34° 39' N 10° 42' E)TunisiaTUNAfrica34.6510.7
25075superficial sediment of non-crystallizer M1 pondStreptomyces isolation agar mediumcontaining 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 µg ml-1) and cycloheximide (50 µg ml-1)21 days37

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Pond (small)
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_25809.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_358;96_12919;97_15680;98_19404;99_25809&stattab=map
  • Last taxonomy: Paludifilum halophilum subclade
  • 16S sequence: KP229518
  • Sequence Identity:
  • Total samples: 651
  • soil counts: 343
  • aquatic counts: 62
  • animal counts: 149
  • plant counts: 97

Safety information

risk assessment

  • @ref: 23824
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23824
  • description: Paludifilum halophilum strain SMBg3 16S ribosomal RNA gene, partial sequence
  • accession: KP229518
  • length: 1362
  • database: ena
  • NCBI tax ID: 1642702

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paludifilum halophilum DSM 102817GCA_002245355contigncbi1642702
66792Paludifilum halophilum strain DSM 1028171642702.3wgspatric1642702
66792Paludifilum halophilum DSM 1028172784132154draftimg1642702
66792Paludifilum halophilum DSM 1028172802429553draftimg1642702

GC content

  • @ref: 23824
  • GC-content: 51.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno82.742no
gram-positiveyes90.18no
anaerobicno97.929yes
aerobicyes95.273yes
halophileno71.926no
spore-formingyes95.281no
thermophileyes99.107yes
glucose-utilyes93.925yes
flagellatedno93.367no
glucose-fermentno91.243yes

External links

@ref: 23824

culture collection no.: DSM 102817, CCUG 68698

straininfo link

  • @ref: 90401
  • straininfo: 404520

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27671055Paludifilum 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 SInt J Syst Evol Microbiol10.1099/ijsem.0.0015232016Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Tunisia, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Pathogenicity28819625Antagonistic 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 SBiomed Res Int10.1155/2017/12052582017Agrobacterium tumefaciens/drug effects/pathogenicity, Escherichia coli/drug effects/pathogenicity, Geologic Sediments/*microbiology, Humans, Peptides, Cyclic/*biosynthesis/chemistry/isolation & purification/*pharmacology, Pseudomonas aeruginosa/drug effects/pathogenicity, RNA, Ribosomal, 16S/genetics, Salmonella enterica/drug effects/pathogenicity, Staphylococcus aureus/drug effects/pathogenicity, Thermoactinomyces/*chemistry/genetics/isolation & purificationPhylogeny
Metabolism32104693Enhancement 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 SBiomed Res Int10.1155/2020/48057062020*Anti-Bacterial Agents/chemistry/metabolism/pharmacology, Bacillales/*metabolism, Pseudomonas aeruginosa/*growth & development, Salmonella enterica/*growth & development
Stress33214980The 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 S3 Biotech10.1007/s13205-020-02512-x2020Biotechnology
Metabolism34549358Genome 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 SWorld J Microbiol Biotechnol10.1007/s11274-021-03147-72021Amino Acids, Diamino/*metabolism, *Bacillales/genetics/metabolism, Computational Biology, Genome, Bacterial, High-Throughput Nucleotide Sequencing, Salinity, Salt Stress, Secondary Metabolism/*geneticsGenetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
23824Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102817Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102817)
25075D. 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 saltern10.1099/ijsem.0.001523IJSEM 66: 5371-5378 201627671055
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90401Reimer, 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 identifiers10.60712/SI-ID404520.1