Strain identifier

BacDive ID: 7343

Type strain: Yes

Species: Leifsonia bigeumensis

Strain Designation: MSL-27

Strain history: CIP <- 2009, KCTC <- C.-J. Kim, Functional Metabolomics Research Center, KRIBB, Daejeon 305-806, Republic of Korea: strain MSL-27

NCBI tax ID(s): 433643 (species)

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General

@ref: 8037

BacDive-ID: 7343

DSM-Number: 19322

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

description: Leifsonia bigeumensis MSL-27 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil, farming field.

NCBI tax id

  • NCBI tax id: 433643
  • Matching level: species

strain history

@refhistory
8037<- Chang-Jin Kim; MSL 27
67770KCTC 19268 <-- C.-J. Kim MSL-27.
67771<- CJ Kim, KRIBB
116815CIP <- 2009, KCTC <- C.-J. Kim, Functional Metabolomics Research Center, KRIBB, Daejeon 305-806, Republic of Korea: strain MSL-27

doi: 10.13145/bacdive7343.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Leifsonia
  • species: Leifsonia bigeumensis
  • full scientific name: Leifsonia bigeumensis Dastager et al. 2008

@ref: 8037

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Leifsonia

species: Leifsonia bigeumensis

full scientific name: Leifsonia bigeumensis Dastager et al. 2008

strain designation: MSL-27

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
32489positiveovoid-shapedyes
67771positive
116815positiverod-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
19781Rapeseed yellow (1021)10-14 daysISP 2
19781Rapeseed yellow (1021)10-14 daysISP 3
1978110-14 daysISP 4
1978110-14 daysISP 5
19781Rapeseed yellow (1021)10-14 daysISP 6
19781Rapeseed yellow (1021)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19781noISP 2
19781noISP 3
19781noISP 4
19781noISP 5
19781noISP 6
19781noISP 7

pigmentation

  • @ref: 32489
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8037R2A 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
19781ISP 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
19781ISP 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:
19781ISP 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
19781ISP 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
19781ISP 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
19781ISP 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
116815CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperature
8037positivegrowth28
19781positiveoptimum28
32489positivegrowth20-37
32489positiveoptimum28
67770positivegrowth28
67771positivegrowth30

culture pH

@refabilitytypepHPH range
32489positivegrowth06-12alkaliphile
32489positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32489aerobe
67771aerobe

spore formation

  • @ref: 32489
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32489NaClpositivegrowth01-03 %
32489NaClpositiveoptimum01-03 %

observation

@refobservation
32489aggregates in chains
67770quinones: MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3248917057cellobiose+carbon source
3248929864mannitol+carbon source
3248928053melibiose+carbon source
3248916634raffinose+carbon source
3248926546rhamnose+carbon source
3248927082trehalose+carbon source
3248917632nitrate+reduction
6837928087glycogen-fermentation
6837917306maltose-fermentation
6837916988D-ribose-fermentation
683794853esculin-hydrolysis
6837916199urea+hydrolysis
6837917632nitrate-reduction
11681517632nitrate+reduction
11681516301nitrite-reduction
6837917992sucrose+fermentation
6837917716lactose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837917634D-glucose-fermentation
683795291gelatin+hydrolysis

metabolite production

  • @ref: 116815
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase-3.2.1.23
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
116815oxidase-
116815catalase-1.11.1.6
116815urease-3.5.1.5
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alkaline phosphatase+3.1.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19781-+++--+--++------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19781+++-++---+----+-+--
116815----+----++---+-+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8037soil, farming fieldBigeum IslandRepublic of KoreaKORAsia
67770Soil from Bigeum IslandRepublic of KoreaKORAsia
67771From farming fieldBikeum islandRepublic of KoreaKORAsia
116815Environment, Soil, farming fieldBigeum IslandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80371Risk group (German classification)
197811Risk group (German classification)
1168151Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8037
  • description: Leifsonia bigeumensis strain MSL-27 16S ribosomal RNA gene, partial sequence
  • accession: EF466124
  • length: 1491
  • database: nuccore
  • NCBI tax ID: 433643

GC content

@refGC-contentmethod
803769
6777069thermal denaturation, midpoint method (Tm)

External links

@ref: 8037

culture collection no.: DSM 19322, KCTC 19268, MSL 27, JCM 16949, CIP 109937

straininfo link

  • @ref: 76793
  • straininfo: 396569

literature

  • topic: Phylogeny
  • Pubmed-ID: 18676484
  • title: Leifsonia bigeumensis sp. nov., isolated from soil on Bigeum Island, Korea.
  • authors: Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65572-0
  • year: 2008
  • mesh: Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8037Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19322)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19322
19781Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19322.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
32489Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2870928776041
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
76793Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396569.1StrainInfo: A central database for resolving microbial strain identifiers
116815Curators of the CIPCollection of Institut Pasteur (CIP 109937)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109937