Strain identifier

BacDive ID: 6302

Type strain: Yes

Species: Lapillicoccus jejuensis

Strain Designation: R-AC-013

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 402171 (species)

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

@ref: 7621

BacDive-ID: 6302

DSM-Number: 18607

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

description: Lapillicoccus jejuensis R-AC-013 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from small stone collected from an agricultural field.

NCBI tax id

  • NCBI tax id: 402171
  • Matching level: species

strain history

@refhistory
7621<- Soon Dong Lee, R-Ac013
67770KCTC 19200 <-- S. D. Lee R-Ac013.
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive6302.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Lapillicoccus
  • species: Lapillicoccus jejuensis
  • full scientific name: Lapillicoccus jejuensis Lee and Lee 2007

@ref: 7621

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Lapillicoccus

species: Lapillicoccus jejuensis

full scientific name: Lapillicoccus jejuensis Lee and Lee 2007

strain designation: R-AC-013

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
32068positive0.25 µmcoccus-shapedno
67771positive
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19767Sun yellow (1037)10-14 daysISP 2
19767Sun yellow (1037)10-14 daysISP 3
19767Sun yellow (1037)10-14 daysISP 4
19767Sun yellow (1037)10-14 daysISP 5
19767Sun yellow (1037)10-14 daysISP 6
19767Sun yellow (1037)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19767noISP 2
19767noISP 3
19767noISP 4
19767noISP 5
19767noISP 6
19767noISP 7

pigmentation

  • @ref: 32068
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19767ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19767ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19767ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19767ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19767ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19767ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
7621TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yesName: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535
7621GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yesName: 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 waterhttps://mediadive.dsmz.de/medium/65

culture temp

@refgrowthtypetemperaturerange
19767positiveoptimum28mesophilic
32068positivegrowth20-37
32068positiveoptimum30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
7621positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32068positivegrowth4.1-11.1alkaliphile
32068positiveoptimum7.1

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32068aerobe
67771aerobe

spore formation

@refspore formationconfidence
32068no
69481no100
69480no99.894

halophily

@refsaltgrowthtested relationconcentration
32068NaClpositivegrowth0-2 %
32068NaClpositiveoptimum1 %

observation

@refobservation
32068aggregates in clumps
67770quinones: MK-8(H4), MK-9, MK-7, MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3206822599arabinose+carbon source
3206825115malate+carbon source
3206829864mannitol+carbon source
320684853esculin+hydrolysis
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
32068acid phosphatase+3.1.3.2
32068catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19767-----++-+++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19767-++-+--+--++--+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7621small stone collected from an agricultural fieldJejuRepublic of KoreaKORAsia
67770Small stone from an agricultural fieldJejuRepublic of KoreaKORAsia
67771From a little stoneJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial

taxonmaps

  • @ref: 69479
  • File name: preview.99_48404.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1391;97_3482;98_13161;99_48404&stattab=map
  • Last taxonomy: Lapillicoccus jejuensis
  • 16S sequence: AM398397
  • Sequence Identity:
  • Total samples: 673
  • soil counts: 283
  • aquatic counts: 43
  • animal counts: 324
  • plant counts: 23

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76211Risk group (German classification)
197671Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7621
  • description: Lapillicoccus jejuensis partial 16S rRNA gene, type strain R-Ac013T
  • accession: AM398397
  • length: 1412
  • database: ena
  • NCBI tax ID: 402171

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lapillicoccus jejuensis strain DSM 18607402171.3wgspatric402171
66792Lapillicoccus jejuensis DSM 186072806310636draftimg402171
67770Lapillicoccus jejuensis DSM 18607GCA_006715055contigncbi402171

GC content

  • @ref: 7621
  • GC-content: 74.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes88.911yes
anaerobicno98.971no
halophileno96.59yes
spore-formingno83.092yes
glucose-utilyes85.881no
aerobicyes94.211no
flagellatedno94.913yes
motileno74.093yes
thermophileno97.984yes
glucose-fermentno90.319no

External links

@ref: 7621

culture collection no.: DSM 18607, KCTC 19200, JCM 15623, NBRC 106263, NCIMB 14544

straininfo link

  • @ref: 75777
  • straininfo: 402465

literature

  • topic: Phylogeny
  • Pubmed-ID: 18048726
  • title: Lapillicoccus jejuensis gen. nov., sp. nov., a novel actinobacterium of the family Intrasporangiaceae, isolated from stone.
  • authors: Lee SD, Lee DW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64911-0
  • year: 2007
  • mesh: Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Aerobiosis/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Korea, Locomotion/physiology, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7621Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18607)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18607
19767Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18607.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
32068Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2831528776041
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
75777Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402465.1StrainInfo: A central database for resolving microbial strain identifiers