Strain identifier

BacDive ID: 13303

Type strain: Yes

Species: Lentzea xinjiangensis

Strain Designation: R24

Strain history: CGMCC 4.3525 <-- W. Wang et al. R24.

NCBI tax ID(s): 402600 (species)

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General

@ref: 12324

BacDive-ID: 13303

DSM-Number: 45081

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

description: Lentzea xinjiangensis R24 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 402600
  • Matching level: species

strain history

@refhistory
12324<- Y. Huang; CGMCC 4.3525 <- J. Mao
67770CGMCC 4.3525 <-- W. Wang et al. R24.

doi: 10.13145/bacdive13303.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Lentzea
  • species: Lentzea xinjiangensis
  • full scientific name: Lentzea xinjiangensis (Wang et al. 2007) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Lechevalieria xinjiangensis

@ref: 12324

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Lentzea

species: Lentzea xinjiangensis

full scientific name: Lentzea xinjiangensis (Wang et al. 2007) Nouioui et al. 2018

strain designation: R24

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32210positiverod-shapedno
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19913Pastel yellow10-14 daysISP 2
19913Pastel yellow10-14 daysISP 3
19913Golden yellow10-14 daysISP 4
19913Signal yellow10-14 daysISP 5
19913Signal yellow10-14 daysISP 6
19913Signal yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19913noISP 2
19913yesISP 3Aerial MyceliumCream
19913yesISP 4Aerial MyceliumCream
19913noISP 5
19913noISP 6
19913noISP 7

pigmentation

  • @ref: 32210
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12324GYM 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
12324ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
19913ISP 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
19913ISP 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:
19913ISP 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
19913ISP 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
19913ISP 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
19913ISP 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

culture temp

@refgrowthtypetemperaturerange
12324positivegrowth28mesophilic
19913positiveoptimum28mesophilic
32210positivegrowth10-45
32210positiveoptimum27.5mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32210positivegrowth5.0-12.0alkaliphile
32210positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32210
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481yes96
69480yes100

halophily

@refsaltgrowthtested relationconcentration
32210NaClpositivegrowth04-05 %
32210NaClpositiveoptimum4.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1991317234glucose+
1991322599arabinose+
1991317992sucrose+
1991318222xylose-
1991317268myo-inositol+
1991329864mannitol+
1991328757fructose+
1991326546rhamnose-
1991316634raffinose-
1991362968cellulose-
3221030089acetate+carbon source
3221016449alanine+carbon source
3221022599arabinose+carbon source
3221017057cellobiose+carbon source
3221016947citrate+carbon source
3221033984fucose+carbon source
3221028260galactose+carbon source
3221017234glucose+carbon source
3221029987glutamate+carbon source
3221017754glycerol+carbon source
32210182404-hydroxy-L-proline+carbon source
3221017716lactose+carbon source
3221025017leucine+carbon source
3221015792malonate+carbon source
3221017306maltose+carbon source
3221029864mannitol+carbon source
3221017268myo-inositol+carbon source
3221028044phenylalanine+carbon source
3221017272propionate+carbon source
3221026546rhamnose+carbon source
322109300suberic acid+carbon source
3221030031succinate+carbon source
3221017992sucrose+carbon source
3221018222xylose+carbon source
3221017632nitrate+reduction

enzymes

@refvalueactivityec
32210catalase+1.11.1.6
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19913+++++++-++++--++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12324soilXinjiangChinaCHNAsia
67770Radiation-polluted soilXinjiang Uygur Autonomous Region of ChinaChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_48426.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_840;97_982;98_2059;99_48426&stattab=map
  • Last taxonomy: Lentzea
  • 16S sequence: DQ898283
  • Sequence Identity:
  • Total samples: 223
  • soil counts: 145
  • aquatic counts: 2
  • animal counts: 11
  • plant counts: 65

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
123241Risk group (German classification)
199131Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12324
  • description: Lechevalieria xinjiangensis strain R24 16S ribosomal RNA gene, partial sequence
  • accession: DQ898283
  • length: 1402
  • database: ena
  • NCBI tax ID: 402600

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lechevalieria xinjiangensis strain CGMCC 4.3525402600.4wgspatric402600
66792Lechevalieria xinjiangensis CGMCC 4.35252667527444draftimg402600
67770Lentzea xinjiangensis CGMCC 4.3525GCA_900110955scaffoldncbi402600

GC content

@refGC-contentmethod
1232468.6
6777068.6thermal denaturation, midpoint method (Tm)
6777070.7genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes96no
gram-positiveyes93.253no
anaerobicno99.127yes
halophileno82.672no
spore-formingyes97.581no
glucose-utilyes90.475yes
aerobicyes92.557yes
flagellatedno97.006yes
thermophileno98.196no
motileno92.787yes
glucose-fermentno90.884no

External links

@ref: 12324

culture collection no.: DSM 45081, CGMCC 4.3525, JCM 15473, NBRC 106319

straininfo link

  • @ref: 82504
  • straininfo: 406437

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18048731Lechevalieria xinjiangensis sp. nov., a novel actinomycete isolated from radiation-polluted soil in China.Wang W, Zhang Z, Tang Q, Mao J, Wei D, Huang Y, Liu Z, Shi Y, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.65134-02007Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Soil Pollutants, RadioactiveGenetics
Phylogeny19651742Lechevalieria atacamensis sp. nov., Lechevalieria deserti sp. nov. and Lechevalieria roselyniae sp. nov., isolated from hyperarid soils.Okoro CK, Bull AT, Mutreja A, Rong X, Huang Y, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.009985-02009Actinomycetales/*classification/genetics/physiology, Base Sequence, Chile, Desert Climate, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12324Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45081)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45081
19913Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45081.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
32210Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2845228776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
82504Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406437.1StrainInfo: A central database for resolving microbial strain identifiers