Strain identifier
BacDive ID: 6302
Type strain:
Species: Lapillicoccus jejuensis
Strain Designation: R-AC-013
Strain history: <- SD Lee, Cheju Univ.
NCBI tax ID(s): 402171 (species)
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
@ref | history |
---|---|
7621 | <- Soon Dong Lee, R-Ac013 |
67770 | KCTC 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
@ref | gram stain | cell length | cell shape | motility | confidence |
---|---|---|---|---|---|
32068 | positive | 0.25 µm | coccus-shaped | no | |
67771 | positive | ||||
69480 | positive | 100 |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19767 | Sun yellow (1037) | 10-14 days | ISP 2 |
19767 | Sun yellow (1037) | 10-14 days | ISP 3 |
19767 | Sun yellow (1037) | 10-14 days | ISP 4 |
19767 | Sun yellow (1037) | 10-14 days | ISP 5 |
19767 | Sun yellow (1037) | 10-14 days | ISP 6 |
19767 | Sun yellow (1037) | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
19767 | no | ISP 2 |
19767 | no | ISP 3 |
19767 | no | ISP 4 |
19767 | no | ISP 5 |
19767 | no | ISP 6 |
19767 | no | ISP 7 |
pigmentation
- @ref: 32068
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
19767 | ISP 2 | yes | Name: 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 | |
19767 | ISP 3 | yes | Name: 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: | |
19767 | ISP 4 | yes | Name: 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 | |
19767 | ISP 5 | yes | Name: 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 | |
19767 | ISP 6 | yes | Name: 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 | |
19767 | ISP 7 | yes | Name: 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 | |
7621 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water | https://mediadive.dsmz.de/medium/535 |
7621 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | Name: 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 | https://mediadive.dsmz.de/medium/65 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19767 | positive | optimum | 28 | mesophilic |
32068 | positive | growth | 20-37 | |
32068 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
7621 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32068 | positive | growth | 4.1-11.1 | alkaliphile |
32068 | positive | optimum | 7.1 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
32068 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
32068 | no | |
69481 | no | 100 |
69480 | no | 99.894 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32068 | NaCl | positive | growth | 0-2 % |
32068 | NaCl | positive | optimum | 1 % |
observation
@ref | observation |
---|---|
32068 | aggregates in clumps |
67770 | quinones: MK-8(H4), MK-9, MK-7, MK-8(H2) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32068 | 22599 | arabinose | + | carbon source |
32068 | 25115 | malate | + | carbon source |
32068 | 29864 | mannitol | + | carbon source |
32068 | 4853 | esculin | + | hydrolysis |
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | + | hydrolysis |
68379 | 5291 | gelatin | + | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32068 | acid phosphatase | + | 3.1.3.2 |
32068 | catalase | + | 1.11.1.6 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | + | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68379 | gelatinase | + | |
68379 | urease | + | 3.5.1.5 |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | + | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | - | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19767 | - | - | - | - | - | + | + | - | + | + | + | - | - | - | - | - | - | - | - |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19767 | - | + | + | - | + | - | - | + | - | - | + | + | - | - | + | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7621 | small stone collected from an agricultural field | Jeju | Republic of Korea | KOR | Asia |
67770 | Small stone from an agricultural field | Jeju | Republic of Korea | KOR | Asia |
67771 | From a little stone | Jeju | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
7621 | 1 | Risk group (German classification) |
19767 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lapillicoccus jejuensis strain DSM 18607 | 402171.3 | wgs | patric | 402171 |
66792 | Lapillicoccus jejuensis DSM 18607 | 2806310636 | draft | img | 402171 |
67770 | Lapillicoccus jejuensis DSM 18607 | GCA_006715055 | contig | ncbi | 402171 |
GC content
- @ref: 7621
- GC-content: 74.1
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | yes | 88.911 | yes |
anaerobic | no | 98.971 | no |
halophile | no | 96.59 | yes |
spore-forming | no | 83.092 | yes |
glucose-util | yes | 85.881 | no |
aerobic | yes | 94.211 | no |
flagellated | no | 94.913 | yes |
motile | no | 74.093 | yes |
thermophile | no | 97.984 | yes |
glucose-ferment | no | 90.319 | no |
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7621 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18607) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18607 | ||||
19767 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM18607.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
32068 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28315 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||||
68379 | Automatically annotated from API Coryne | ||||||
68382 | Automatically annotated from API zym | ||||||
69479 | João 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 | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
75777 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402465.1 | StrainInfo: A central database for resolving microbial strain identifiers |