Strain identifier

BacDive ID: 22921

Type strain: Yes

Species: Alkalicoccus daliensis

Strain history: L. Zhai DLS13.

NCBI tax ID(s): 745820 (species)

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General

@ref: 19137

BacDive-ID: 22921

DSM-Number: 26767

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

description: Alkalicoccus daliensis DSM 26767 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from Dali soda lake.

NCBI tax id

  • NCBI tax id: 745820
  • Matching level: species

strain history

@refhistory
19137<- JCM; JCM 17097
67770L. Zhai DLS13.

doi: 10.13145/bacdive22921.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Alkalicoccus
  • species: Alkalicoccus daliensis
  • full scientific name: Alkalicoccus daliensis (Zhai et al. 2012) Gupta et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus daliensis

@ref: 19137

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Alkalicoccus

species: Alkalicoccus daliensis

full scientific name: Alkalicoccus daliensis (Zhai et al. 2012) Gupta et al. 2020

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30243positive2.5-3.5 µm0.4-0.5 µmrod-shapedyes
69480yes92.815
69480positive100

pigmentation

  • @ref: 30243
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19137
  • name: CASO AGAR (MERCK 105458) (DSMZ Medium 220)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/220
  • composition: Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: NaCl 50.0 g/l Agar 15.0 g/l Casein peptone 15.0 g/l Soy peptone 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19137positivegrowth30mesophilic
30243positivegrowth10-45
30243positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30243positivegrowth7.5-11alkaliphile
30243positiveoptimum9

Physiology and metabolism

oxygen tolerance

  • @ref: 30243
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
30243yes
69481yes100
69480yes91.346

halophily

@refsaltgrowthtested relationconcentration
30243NaClpositivegrowth0-8 %
30243NaClpositiveoptimum2 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3024317057cellobiose+carbon source
3024328757fructose+carbon source
3024328260galactose+carbon source
3024317234glucose+carbon source
3024317754glycerol+carbon source
3024317716lactose+carbon source
3024317306maltose+carbon source
3024329864mannitol+carbon source
3024337684mannose+carbon source
3024316634raffinose+carbon source
3024326546rhamnose+carbon source
3024333942ribose+carbon source
3024317814salicin+carbon source
3024317992sucrose+carbon source
3024318222xylose+carbon source
302434853esculin+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
3024316136hydrogen sulfideyes
3024335581indoleyes

metabolite tests

  • @ref: 30243
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
30243catalase+1.11.1.6
30243cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19137Dali soda lakeInner Mongolia Autonomous RegionChinaCHNAsia
67770Sediment sample of Dali Lake in Inner Mongolia Autonomous RegionChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Condition#Alkaline

taxonmaps

  • @ref: 69479
  • File name: preview.99_76103.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_7678;97_40833;98_53224;99_76103&stattab=map
  • Last taxonomy: Alkalicoccus daliensis
  • 16S sequence: GU583651
  • Sequence Identity:
  • Total samples: 26
  • soil counts: 8
  • aquatic counts: 12
  • animal counts: 4
  • plant counts: 2

Safety information

risk assessment

  • @ref: 19137
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19137
  • description: Bacillus daliensis strain DLS13 16S ribosomal RNA gene, partial sequence
  • accession: GU583651
  • length: 1467
  • database: ena
  • NCBI tax ID: 745820

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus daliensis strain CGMCC 1.10369745820.3wgspatric745820
66792Alkalicoccus daliensis CGMCC 1.103692617270767draftimg745820
67770Alkalicoccus daliensis CGMCC 1.10369GCA_900103955scaffoldncbi745820

GC content

@refGC-contentmethod
1913743.9thermal denaturation, midpoint method (Tm)
3024343.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes88.833yes
flagellatedyes69.956no
gram-positiveyes87.446no
anaerobicno98.549no
aerobicyes76.885yes
halophileyes94.044no
spore-formingyes73.868no
thermophileno98.35no
glucose-utilyes91.048yes
glucose-fermentno87.409no

External links

@ref: 19137

culture collection no.: DSM 26767, CGMCC 1.10369, DLS 13, JCM 17097, NBRC 107572

straininfo link

  • @ref: 87169
  • straininfo: 407933

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21669916Bacillus daliensis sp. nov., an alkaliphilic, Gram-positive bacterium isolated from a soda lake.Zhai L, Liao T, Xue Y, Ma YInt J Syst Evol Microbiol10.1099/ijs.0.031575-02011Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Water MicrobiologyGenetics
Phylogeny26978771Bacillusurumqiensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a salt lake.Zhang S, Li Z, Yan Y, Zhang C, Li J, Zhao BInt J Syst Evol Microbiol10.1099/ijsem.0.0010282016Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lakes/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19137Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26767)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26767
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
30243Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2658528776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
87169Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407933.1StrainInfo: A central database for resolving microbial strain identifiers