Strain identifier

BacDive ID: 1548

Type strain: Yes

Species: Salsuginibacillus kocurii

Strain Designation: CH9d

Strain history: <- A. Ventosa <- I.J. Carrasco, CH9d

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

@ref: 7388

BacDive-ID: 1548

DSM-Number: 18087

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive, motile, rod-shaped

description: Salsuginibacillus kocurii CH9d is an aerobe, spore-forming, Gram-positive bacterium that was isolated from sediment.

NCBI tax id

NCBI tax idMatching level
427078species
1123239strain

strain history

  • @ref: 7388
  • history: <- A. Ventosa <- I.J. Carrasco, CH9d

doi: 10.13145/bacdive1548.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Salsuginibacillus
  • species: Salsuginibacillus kocurii
  • full scientific name: Salsuginibacillus kocurii Carrasco et al. 2007

@ref: 7388

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Salsuginibacillus

species: Salsuginibacillus kocurii

full scientific name: Salsuginibacillus kocurii Carrasco et al. 2007

strain designation: CH9d

type strain: yes

Morphology

cell morphology

  • @ref: 32212
  • gram stain: positive
  • cell length: 3.25 µm
  • cell width: 0.75 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 32212
  • production: no

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_18087_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18087_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18087_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18087_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18087_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 7388
  • name: HALOMONAS MAGADIENSIS MEDIUM (DSMZ Medium 971)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/971
  • composition: Name: HALOMONAS MAGADIENSIS MEDIUM (DSMZ Medium 971; with strain-specific modifications) Composition: NaCl 80.0 g/l Agar 20.0 g/l Na2CO3 10.0 g/l Glucose 10.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.2 g/l Distilled water

culture temp

@refgrowthtypetemperature
7388positivegrowth30
32212positivegrowth37
32212positiveoptimum20-50

culture pH

@refabilitytypepHPH range
32212positivegrowth5.8-10.0alkaliphile
32212positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32212
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32212yes
69481yes100

halophily

@refsaltgrowthtested relationconcentration
32212NaClpositivegrowth03-20 %
32212NaClpositiveoptimum10 %

observation

  • @ref: 32212
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3221230089acetate+carbon source
3221217057cellobiose+carbon source
3221216947citrate+carbon source
3221216236ethanol+carbon source
3221215740formate+carbon source
3221217234glucose+carbon source
3221229864mannitol+carbon source
3221215361pyruvate+carbon source
3221233942ribose+carbon source
3221217992sucrose+carbon source
3221217632nitrate+reduction

enzymes

  • @ref: 32212
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 7388
  • sample type: sediment
  • geographic location: Lake Chagannor, Inner Mongolia
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_175510.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_4889;96_22575;97_28218;98_114817;99_175510&stattab=map
  • Last taxonomy: Salsuginibacillus kocurii subclade
  • 16S sequence: AM492160
  • Sequence Identity:
  • Total samples: 99
  • soil counts: 10
  • aquatic counts: 53
  • animal counts: 35
  • plant counts: 1

Safety information

risk assessment

  • @ref: 7388
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7388
  • description: Salsuginibacillus kocurii 16S rRNA gene, type strain CH9dT
  • accession: AM492160
  • length: 1502
  • database: nuccore
  • NCBI tax ID: 427078

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salsuginibacillus kocurii DSM 18087GCA_000377705scaffoldncbi1123239
66792Salsuginibacillus kocurii DSM 180871123239.3wgspatric1123239
66792Salsuginibacillus kocurii DSM 180872517572235draftimg1123239

GC content

  • @ref: 7388
  • GC-content: 44.7

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes84.321yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.218no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes81.631no
69480spore-formingspore-formingAbility to form endo- or exosporesyes81.02no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno91.773yes
69480flagellatedmotile2+Ability to perform flagellated movementyes80.972no

External links

@ref: 7388

culture collection no.: DSM 18087, CCM 7365, CECT 7154, CGMCC 1.6287

straininfo link

  • @ref: 71193
  • straininfo: 310985

literature

  • topic: Phylogeny
  • Pubmed-ID: 17911315
  • title: Salsuginibacillus kocurii gen. nov., sp. nov., a moderately halophilic bacterium from soda-lake sediment.
  • authors: Carrasco IJ, Marquez MC, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65136-0
  • year: 2007
  • mesh: Bacillaceae/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids, Genes, rRNA, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Locomotion/physiology, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Spores, Bacterial/cytology, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7388Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18087)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18087
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
32212Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2845428776041
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
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
71193Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310985.1StrainInfo: A central database for resolving microbial strain identifiers