Strain identifier

BacDive ID: 1555

Type strain: Yes

Species: Sediminibacillus halophilus

Strain Designation: EN8d

Strain history: <- A. Ventosa; EN8d

NCBI tax ID(s): 482461 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7389

BacDive-ID: 1555

DSM-Number: 18088

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, motile, rod-shaped

description: Sediminibacillus halophilus EN8d is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from sediment, Lake Erliannor.

NCBI tax id

  • NCBI tax id: 482461
  • Matching level: species

strain history

  • @ref: 7389
  • history: <- A. Ventosa; EN8d

doi: 10.13145/bacdive1555.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Sediminibacillus
  • species: Sediminibacillus halophilus
  • full scientific name: Sediminibacillus halophilus Carrasco et al. 2008

@ref: 7389

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Sediminibacillus

species: Sediminibacillus halophilus

full scientific name: Sediminibacillus halophilus Carrasco et al. 2008

strain designation: EN8d

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32621positive1.5-7 µm0.9 µmrod-shapedyes
69480yes96.372
69480positive100

pigmentation

  • @ref: 32621
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7389
  • name: 10% MH MEDIUM (DSMZ Medium 593)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/593
  • composition: Name: 10% MH MEDIUM (DSMZ Medium 593) Composition: NaCl 81.0 g/l Agar 15.0 g/l Yeast extract 10.0 g/l MgSO4 9.6 g/l MgCl2 7.0 g/l Proteose peptone no. 3 5.0 g/l KCl 2.0 g/l Glucose 1.0 g/l CaCl2 0.36 g/l NaHCO3 0.06 g/l NaBr 0.026 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7389positivegrowth30mesophilic
32621positivegrowth15-55
32621positiveoptimum37mesophilic

culture pH

@refabilitytypepHPH range
32621positivegrowth5-9.5alkaliphile
32621positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32621
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
32621no
69481no99
69480yes100

halophily

@refsaltgrowthtested relationconcentration
32621NaClpositivegrowth0-20 %
32621NaClpositiveoptimum5-7.5 %

observation

  • @ref: 32621
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3262122599arabinose+carbon source
3262117057cellobiose+carbon source
3262128260galactose+carbon source
3262117716lactose+carbon source
326214853esculin+hydrolysis
3262117632nitrate+reduction

enzymes

@refvalueactivityec
32621acid phosphatase+3.1.3.2
32621alkaline phosphatase+3.1.3.1
32621catalase+1.11.1.6
32621cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 7389
  • sample type: sediment, Lake Erliannor
  • geographic location: Inner Mongolia
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4329.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2171;97_2627;98_3257;99_4329&stattab=map
  • Last taxonomy: Bacillaceae
  • 16S sequence: AM905297
  • Sequence Identity:
  • Total samples: 181
  • soil counts: 57
  • aquatic counts: 25
  • animal counts: 92
  • plant counts: 7

Safety information

risk assessment

  • @ref: 7389
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7389
  • description: Sediminibacillus halophilus 16S rRNA gene, type strain EN8dT
  • accession: AM905297
  • length: 1453
  • database: ena
  • NCBI tax ID: 482461

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sediminibacillus halophilus CGMCC 1.6199GCA_900103695scaffoldncbi482461
66792Sediminibacillus halophilus strain CGMCC 1.6199482461.3wgspatric482461
66792Sediminibacillus halophilus CGMCC 1.61992675902964draftimg482461

GC content

  • @ref: 7389
  • GC-content: 47.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes93.79yes
flagellatedyes91.705no
gram-positiveyes90.822yes
anaerobicno99.161yes
aerobicyes86.328yes
halophileyes95.541no
spore-formingyes91.118yes
glucose-fermentno84.547no
thermophileno99.155no
glucose-utilyes86.674no

External links

@ref: 7389

culture collection no.: DSM 18088, CCM 7364, CECT 7148, CGMCC 1.6199

straininfo link

  • @ref: 71200
  • straininfo: 312513

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18676487Sediminibacillus halophilus gen. nov., sp. nov., a moderately halophilic, Gram-positive bacterium from a hypersaline lake.Carrasco IJ, Marquez MC, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.65790-02008Bacillaceae/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityGenetics
Phylogeny19542144Sediminibacillus albus sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a hypersaline lake, and emended description of the genus Sediminibacillus Carrasco et al. 2008.Wang X, Xue Y, Ma YInt J Syst Evol Microbiol10.1099/ijs.0.004234-02009Bacillaceae/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Fresh Water/chemistry/microbiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species Specificity, Spores, Bacterial/physiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7389Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18088)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18088
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32621Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2883228776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71200Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312513.1StrainInfo: A central database for resolving microbial strain identifiers