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BacDive ID 13310
Type strain
Culture col. no. DSM 43393 IMRU 550 NRRL B-16137 KCTC 19912 CGMCC 4.2094 BCRC 16972 JCM 11305 2 more
NCBI tax ID(s) 438851
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 10 (current version):
version 10 (current version)

General

@ref: 11008

BacDive-ID: 13310

DSM-Number: 43393

keywords: genome sequence, 16S sequence, mesophilic

description: Lentzea californiensis DSM 43393 is a mesophilic prokaryote that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 438851
  • Matching level: species

strain history

@refhistory
11008<- R. E. Gordon, IMRU, (Nocardia aerocolonigenes) <- E. N. Azarowicz, Univ. of California, 30, (Nocardia sp.)
67770NRRL B-16137 <-- IMRU 550 <-- E. N. Azarowicz.

doi: 10.13145/bacdive13310.20251217.10

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: kingdom/bacillati
  • keyword: phylum/actinomycetota
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Lentzea
  • species: Lentzea californiensis
  • full scientific name: Lentzea californiensis Labeda et al. 2001

@ref: 11008

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Lentzea

species: Lentzea californiensis

full scientific name: Lentzea californiensis Labeda et al. 2001 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

  • @ref: 125439
  • gram stain: positive
  • confidence: 98.8

colony morphology

@refcolony colorincubation periodmedium used
19571sun yellow10-14 daysISP 2
19571sun yellow10-14 daysISP 3
19571beige10-14 daysISP 4
19571beige10-14 daysISP 5
19571sun yellow10-14 daysISP 6
19571beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19571yesAerial MyceliumWhiteISP 2
19571yesAerial MyceliumWhiteISP 3
19571yesAerial MyceliumWhiteISP 4
19571noISP 5
19571noISP 6
19571noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11008GYM 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
19571ISP 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
19571ISP 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:
19571ISP 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
19571ISP 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
19571ISP 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
19571ISP 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

@refgrowthtypetemperature
11008positivegrowth28
19571positiveoptimum28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 99

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1957117234glucose+
1957122599arabinose+
1957117992sucrose+
1957118222xylose-
1957117268myo-inositol+
1957129864mannitol+
1957128757fructose+
1957126546rhamnose+/-
1957116634raffinose+
1957162968cellulose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
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
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
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368arginine dihydrolase+3.5.3.6
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368lysine decarboxylase+4.1.1.18
68368beta-galactosidase+3.2.1.23

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19571+-+++++++++++-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19571+++++-+--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11008soilCaliforniaUSAUSANorth America
67770SoilCAUSAUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5023.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_840;97_982;98_3756;99_5023&stattab=map
  • Last taxonomy: Lentzea albidocapillata
  • 16S sequence: LC214996
  • Sequence Identity:
  • Total samples: 810
  • soil counts: 500
  • aquatic counts: 19
  • animal counts: 45
  • plant counts: 246

Interaction and safety

risk assessment

@refbiosafety levelbiosafety level comment
110081Risk group (German classification)
195711Risk group (German classification)

Sequence information

Genome sequences

  • @ref: 66792
  • description: ASM2464882v1 assembly for Lentzea californiensis DSM 43393
  • assembly level: contig
  • INSDC accession: GCA_024648825
  • BV-BRC accession: 438851.3
  • IMG accession: 2596583533
  • NCBI tax ID: 438851
  • score: 72.32

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lentzea californiensis strain NRRL B-16137 16S ribosomal RNA gene, partial sequenceAF1744351451nuccore438851
67770Lentzea californiensis gene for 16S ribosomal RNA, partial sequence, culture_collection: JCM:11305LC2149961455nuccore438851

GC content

  • @ref: 67770
  • GC-content: 69.3
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidence
125439BacteriaNetspore_formationAbility to form endo- or exosporesno51.7
125439BacteriaNetmotilityAbility to perform movementno75.3
125439BacteriaNetgram_stainReaction to gram-stainingpositive98.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99

Literature

@ref: 11008

culture collection no.: DSM 43393, IMRU 550, NRRL B-16137, JCM 11305, BCRC 16972, CGMCC 4.2094, KCTC 19912

straininfo link

  • @ref: 126262
  • straininfo: 50267

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11411672Revival of the genus Lentzea and proposal for Lechevalieria gen. nov.Labeda DP, Hatano K, Kroppenstedt RM, Tamura TInt J Syst Evol Microbiol10.1099/00207713-51-3-10452001Actinomycetales/*classification/genetics/physiology, Carbohydrate Metabolism, Carboxylic Acids/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Genetics30186281Genome-Based Taxonomic Classification of the Phylum Actinobacteria.Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.Front Microbiol10.3389/fmicb.2018.020072018Morphology, Chemotaxonomy, G+C content, Genome size, Phylogenetic systematics, Phylogenomics, Genome Blast Distance PhylogenyPhylogeny
Phylogeny32699968Lentzea indica sp. nov., a novel actinobacteria isolated from Indian Himalayan-soil.Maiti PK, Mandal SAntonie Van Leeuwenhoek10.1007/s10482-020-01449-82020Actinobacteria/*classification/growth & development/*isolation & purification, *Bacterial Typing Techniques, Genotyping Techniques, India, Mycelium, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyPhenotype
38630118Lentzea sokolovensis sp. nov., Lentzea kristufekii sp. nov. and Lentzea miocenica sp. nov., rare actinobacteria from Miocene lacustrine sediment of the Sokolov Coal Basin, Czech Republic.Lara AC, Kotrbova L, Keller M, Nouioui I, Neumann-Schaal M, Mast Y, Chronakova A.Int J Syst Evol Microbiol10.1099/ijsem.0.0063352024polyphasic taxonomy, actinomycetes, Lentzea, Post-mining Sites, Actinobacteria, Actinomycetales

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11008Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43393)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43393
19571Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43393.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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/
68368Automatically annotated from API 20E
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
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1
126262A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer10.1093/database/baaf059StrainInfo—the central database for linked microbial strain identifiers

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