Strain identifier

BacDive ID: 18120

Type strain: Yes

Species: Exiguobacterium soli

Strain history: S. Shivaji DVS 3Y.

NCBI tax ID(s): 309483 (species)

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General

@ref: 16103

BacDive-ID: 18120

DSM-Number: 22015

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, coccus-shaped

description: Exiguobacterium soli DSM 22015 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Moraine sample.

NCBI tax id

  • NCBI tax id: 309483
  • Matching level: species

strain history

@refhistory
16103<- JCM/RIKEN <- S. Shivaji, Centre for Cellular and Molecular Biology, Hyderabad, India; DVS 3Y
67770S. Shivaji DVS 3Y.

doi: 10.13145/bacdive18120.20230509.8.1

Name and taxonomic classification

LPSN

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

@ref: 16103

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacilli, not assigned to family

genus: Exiguobacterium

species: Exiguobacterium soli

full scientific name: Exiguobacterium soli Chaturvedi et al. 2008

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31180positive1.5 µm1.15 µmcoccus-shapedyes
69480yes93.419
69480positive100

pigmentation

  • @ref: 31180
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16103
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16103positivegrowth25mesophilic
31180positivegrowth2.5-30
31180positiveoptimum25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
31180positivegrowth06-10alkaliphile
31180positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31180
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31180no
69481yes95
69480no93.87

halophily

@refsaltgrowthtested relationconcentration
31180NaClpositivegrowth0-5.8 %
31180NaClpositiveoptimum0-5.8 %

murein

  • @ref: 16103
  • murein short key: A11.01
  • type: A3alpha L-Lys-Gly

observation

@refobservation
31180aggregates in chains
67770quinones: MK-6, MK-7, MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31180581435-dehydro-D-gluconate+carbon source
3118016449alanine+carbon source
3118022599arabinose+carbon source
3118029016arginine+carbon source
3118022653asparagine+carbon source
3118017057cellobiose+carbon source
3118023652dextrin+carbon source
3118028757fructose+carbon source
3118028260galactose+carbon source
3118017234glucose+carbon source
3118029987glutamate+carbon source
3118015428glycine+carbon source
3118028087glycogen+carbon source
3118027570histidine+carbon source
3118024996lactate+carbon source
3118017716lactose+carbon source
3118025017leucine+carbon source
3118017306maltose+carbon source
3118037684mannose+carbon source
3118028053melibiose+carbon source
3118018257ornithine+carbon source
3118026271proline+carbon source
3118015361pyruvate+carbon source
3118016634raffinose+carbon source
3118026546rhamnose+carbon source
3118033942ribose+carbon source
3118030911sorbitol+carbon source
3118017992sucrose+carbon source
3118027082trehalose+carbon source
3118018222xylose+carbon source
311804853esculin+hydrolysis

enzymes

@refvalueactivityec
31180acid phosphatase+3.1.3.2
31180alkaline phosphatase+3.1.3.1
31180catalase+1.11.1.6
31180gelatinase+
31180cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
16103Moraine sampleMcMurdo Dry ValleysAustralia and Oceania
67770Moraine sample from the McMurdo Dry ValleysAntarcticaAntarcticaATA

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1295.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_130;96_390;97_439;98_501;99_1295&stattab=map
  • Last taxonomy: Exiguobacterium
  • 16S sequence: AY864633
  • Sequence Identity:
  • Total samples: 17203
  • soil counts: 2271
  • aquatic counts: 7226
  • animal counts: 5645
  • plant counts: 2061

Safety information

risk assessment

  • @ref: 16103
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16103
  • description: Exiguobacterium sp. DVS3y 16S ribosomal RNA gene, partial sequence
  • accession: AY864633
  • length: 1518
  • database: ena
  • NCBI tax ID: 309483

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Exiguobacterium soli strain DSM 22015309483.3wgspatric309483
66792Exiguobacterium soli DSM 220152913394191draftimg309483

GC content

  • @ref: 16103
  • GC-content: 48.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes95no
gram-positiveyes89.138yes
anaerobicno98.489yes
halophileyes69.637no
spore-formingno82.33yes
glucose-utilyes89.309yes
motileyes90.378yes
flagellatedyes81.988no
thermophileno99.694yes
aerobicyes90.079yes
glucose-fermentno77.978no

External links

@ref: 16103

culture collection no.: DSM 22015, JCM 14376, MTCC 4816, DVS 3Y

straininfo link

  • @ref: 87108
  • straininfo: 401707

literature

  • topic: Phylogeny
  • Pubmed-ID: 18842873
  • title: Exiguobacterium soli sp. nov., a psychrophilic bacterium from the McMurdo Dry Valleys, Antarctica.
  • authors: Chaturvedi P, Prabahar V, Manorama R, Pindi PK, Bhadra B, Begum Z, Shivaji S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.2008/000067-0
  • year: 2008
  • mesh: Antarctic Regions, Bacillaceae/chemistry/*classification/*genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16103Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22015)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22015
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
31180Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2750728776041
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)
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
87108Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401707.1StrainInfo: A central database for resolving microbial strain identifiers