Strain identifier

BacDive ID: 17530

Type strain: Yes

Species: Silanimonas lenta

Strain Designation: 25-4

Strain history: <- C.-J. Kim, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; 25-4 <- E. M. Lee

NCBI tax ID(s): 1123253 (strain), 265429 (species)

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General

@ref: 6272

BacDive-ID: 17530

DSM-Number: 16282

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Silanimonas lenta 25-4 is a mesophilic, Gram-negative bacterium that was isolated from hot spring water.

NCBI tax id

NCBI tax idMatching level
1123253strain
265429species

strain history

  • @ref: 6272
  • history: <- C.-J. Kim, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; 25-4 <- E. M. Lee

doi: 10.13145/bacdive17530.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Silanimonas
  • species: Silanimonas lenta
  • full scientific name: Silanimonas lenta Lee et al. 2005

@ref: 6272

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Silanimonas

species: Silanimonas lenta

full scientific name: Silanimonas lenta Lee et al. 2005

strain designation: 25-4

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.967

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_16282_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16282_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16282_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16282_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16282_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6272NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
6272R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

  • @ref: 6272
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

Isolation, sampling and environmental information

isolation

  • @ref: 6272
  • sample type: hot spring water
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Thermal spring
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6486.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_3067;97_3767;98_4783;99_6486&stattab=map
  • Last taxonomy: Silanimonas lenta subclade
  • 16S sequence: AY557615
  • Sequence Identity:
  • Total samples: 1396
  • soil counts: 333
  • aquatic counts: 877
  • animal counts: 110
  • plant counts: 76

Safety information

risk assessment

  • @ref: 6272
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6272
  • description: Silanimonas lenta strain 25-4 16S ribosomal RNA gene, partial sequence
  • accession: AY557615
  • length: 1382
  • database: ena
  • NCBI tax ID: 265429

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Silanimonas lenta DSM 16282GCA_000429065scaffoldncbi1123253
66792Silanimonas lenta DSM 162821123253.3wgspatric1123253
66792Silanimonas lenta DSM 162822524614862draftimg1123253

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes78.02no
flagellatedno74.386no
gram-positiveno98.917no
anaerobicno95.668no
aerobicyes82.07no
halophileno93.868no
spore-formingno96.395no
glucose-utilyes79.327no
thermophileno83.815yes
glucose-fermentno86.049no

External links

@ref: 6272

culture collection no.: DSM 16282

straininfo link

  • @ref: 86525
  • straininfo: 135135

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653905Silanimonas lenta gen. nov., sp. nov., a slightly thermophilic and alkaliphilic gammaproteobacterium isolated from a hot spring.Lee EM, Jeon CO, Choi I, Chang KS, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.63328-02005Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Hot Springs/*microbiology, Hot Temperature, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Xanthomonadaceae/chemistry/*classification/genetics/isolation & purificationStress
Phylogeny28829021Silanimonas algicola sp. nov., isolated from laboratory culture of a bloom-forming cyanobacterium, Microcystis.Chun SJ, Cui Y, Ko SR, Lee HG, Oh HM, Ahn CYInt J Syst Evol Microbiol10.1099/ijsem.0.0021022017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Eutrophication, Fatty Acids/chemistry, Lakes/*microbiology, *Microcystis, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6272Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16282)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16282
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
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
86525Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135135.1StrainInfo: A central database for resolving microbial strain identifiers