Strain identifier

BacDive ID: 16785

Type strain: Yes

Species: Shimazuella kribbensis

Strain Designation: A9500

Strain history: C.-J. Kim A 9500.

NCBI tax ID(s): 1123252 (strain), 139808 (species)

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General

@ref: 12332

BacDive-ID: 16785

DSM-Number: 45090

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive

description: Shimazuella kribbensis A9500 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from forest soil.

NCBI tax id

NCBI tax idMatching level
1123252strain
139808species

strain history

@refhistory
12332<- C.-J. Kim, KRIBB; A9500 <- D.-J. Park
67770C.-J. Kim A 9500.

doi: 10.13145/bacdive16785.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Thermoactinomycetaceae
  • genus: Shimazuella
  • species: Shimazuella kribbensis
  • full scientific name: Shimazuella kribbensis Park et al. 2007

@ref: 12332

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Thermoactinomycetaceae

genus: Shimazuella

species: Shimazuella kribbensis

full scientific name: Shimazuella kribbensis Park et al. 2007

strain designation: A9500

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

multimedia

@refmultimedia contentcaptionintellectual property rights
12332https://www.dsmz.de/microorganisms/photos/DSM_45090.jpgMedium 65 28°C© Leibniz-Institut DSMZ
66793EM_DSM_45090_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45090_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45090_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45090_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45090_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12332GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
12332GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
12332positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

observation

  • @ref: 67770
  • observation: quinones: MK-9, MK-10

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12332forest soilSobaek MountainRepublic of KoreaKORAsia
67770Soil from Sobaek mountainRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_35775.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_284;96_17154;97_21071;98_26389;99_35775&stattab=map
  • Last taxonomy: Shimazuella kribbensis subclade
  • 16S sequence: AB049939
  • Sequence Identity:
  • Total samples: 138
  • soil counts: 119
  • aquatic counts: 7
  • animal counts: 7
  • plant counts: 5

Safety information

risk assessment

  • @ref: 12332
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12332
  • description: Shimazuella kribbensis gene for 16S rRNA, partial sequence
  • accession: AB049939
  • length: 1459
  • database: ena
  • NCBI tax ID: 139808

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shimazuella kribbensis DSM 450901123252.3wgspatric1123252
66792Shimazuella kribbensis DSM 450902515154144draftimg1123252
67770Shimazuella kribbensis DSM 45090GCA_000428065scaffoldncbi1123252

GC content

  • @ref: 67770
  • GC-content: 39.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno80.818no
flagellatedno86.478no
gram-positiveyes91.567no
anaerobicno98.791no
aerobicyes92.97no
halophileno91.679no
spore-formingyes90.559no
thermophileno95.412yes
glucose-utilyes84.766no
glucose-fermentno91.786no

External links

@ref: 12332

culture collection no.: DSM 45090, JCM 14729, KCCM 41585, KCTC 9933

straininfo link

  • @ref: 85801
  • straininfo: 107666

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978236Shimazuella kribbensis gen. nov., sp. nov., a mesophilic representative of the family Thermoactinomycetaceae.Park DJ, Dastager SG, Lee JC, Yeo SH, Yoon JH, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.65194-02007Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Gram-Positive Bacteria/*classification/genetics/isolation & purification/physiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny32447434Shimazuella alba sp. nov. isolated from desert soil and emended description of the genus Shimazuella Park et al. 2007.Saygin H, Ay H, Sahin NArch Microbiol10.1007/s00203-020-01894-z2020Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Desert Climate, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Peptidoglycan/genetics, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, TurkmenistanTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12332Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45090)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45090
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
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 life 35: 676-683 201728604660
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
85801Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID107666.1StrainInfo: A central database for resolving microbial strain identifiers