Strain identifier

BacDive ID: 133061

Type strain: Yes

Species: Halodesulfovibrio spirochaetisodalis

Strain Designation: JC271

Strain history: <- Ch Sasikala, JNT Univ, India

NCBI tax ID(s): 1560234 (species)

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General

@ref: 24849

BacDive-ID: 133061

DSM-Number: 100016

keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, mesophilic, Gram-negative, motile, vibrio-shaped

description: Halodesulfovibrio spirochaetisodalis JC271 is an obligate anaerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1560234
  • Matching level: species

strain history

@refhistory
24849<- C. Sasikala, Jawaharlal Nehru Technological Univ., Hyderabad, India; JC271 <- Y. Shivani {2013}
67771<- Ch Sasikala, JNT Univ, India

doi: 10.13145/bacdive133061.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfovibrionales
  • family: Desulfovibrionaceae
  • genus: Halodesulfovibrio
  • species: Halodesulfovibrio spirochaetisodalis
  • full scientific name: Halodesulfovibrio spirochaetisodalis Shivani et al. 2017

@ref: 24849

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfovibrionaceae

genus: Halodesulfovibrio

species: Halodesulfovibrio spirochaetisodalis

full scientific name: Halodesulfovibrio spirochaetisodalis Shivani et al. 2017

strain designation: JC271

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25150negative2.0-5.0 µm0.7-0.9 µmvibrio-shapedyes
67771rod-shapedyes
67771curved-shaped
67771negative
69480yes94.093
69480negative99.988

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
25150positiveoptimum30.0-35.0mesophilic
25150positivegrowth15.0-40.0
67771positivegrowth35mesophilic

culture pH

@refabilitytypepHPH range
25150positivegrowth6.5-9.0alkaliphile
25150positiveoptimum7.5-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
25150obligate anaerobe
67771anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481no100
69480no99.981

halophily

@refsalttested relationconcentration
25150NaClmaximum6 %
25150NaClminimum1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2515035391aspartate-electron donor
2515016150benzoate-electron donor
251505291gelatin-hydrolysis
2515017754glycerol-electron donor
2515017822serine-electron donor
2515017359sulfite-electron acceptor
2515027897tryptophan-energy source
2515030089acetate+electron donor
2515035391aspartate+growth
2515015356cysteine+electron donor
2515029806fumarate+growth
2515017754glycerol+growth
2515029985L-glutamate+growth
2515024996lactate+growth
2515025115malate+growth
2515015361pyruvate+growth
2515030031succinate+growth

metabolite production

  • @ref: 25150
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 25150
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25150catalase-1.11.1.6
25150cytochrome oxidase-1.9.3.1
25150tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24849soilGujaratIndiaINDAsia
67771From soilGujaratIndiaINDAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5213.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15981;96_2533;97_3094;98_3886;99_5213&stattab=map
  • Last taxonomy: Halodesulfovibrio
  • 16S sequence: LN614381
  • Sequence Identity:
  • Total samples: 879
  • soil counts: 30
  • aquatic counts: 424
  • animal counts: 382
  • plant counts: 43

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
25150Desulfovibrio sp. JC271 partial 16S rRNA gene, strain JC271LN614381.11395nuccore1560234
24849Desulfovibrio sp. JC271 partial 16S rRNA gene, strain JC271LN6143811543ena1560234

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halodesulfovibrio spirochaetisodalis JC2712751185719draftimg1560234
67771Halodesulfovibrio spirochaetisodalis JC271GCA_001672295scaffoldncbi1560234

GC content

@refGC-contentmethod
2484946.2sequence analysis
2484947.1high performance liquid chromatography (HPLC)
6777145.2genome sequence analysis

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 100
  • training_data: no

External links

@ref: 24849

culture collection no.: DSM 100016, KCTC 15474

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902290
  • title: Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp.
  • authors: Shivani Y, Subhash Y, Sasikala C, Ramana CV
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001574
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Desulfovibrio/*classification/genetics/isolation & purification, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA
  • topic2: Transcriptome

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
24849Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100016Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100016)
25150Y. S. Shivani, Y.,Sasikala, C.,Ramana, C. V.Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp10.1099/ijsem.0.001574IJSEM 67: 87-93 201727902290
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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