Strain identifier

BacDive ID: 13304

Type strain: Yes

Species: Lentzea fradiae

Strain Designation: Z6

Strain history: CIP <- 2007, JCM <- 2006, J. Zhang, Beijing Inst. Technol., Beijing, China: strain Z6

NCBI tax ID(s): 200378 (species)

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General

@ref: 12341

BacDive-ID: 13304

DSM-Number: 45099

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

description: Lentzea fradiae Z6 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 200378
  • Matching level: species

strain history

@refhistory
12341<- JCM <- J. Zhang; Z6
67770J. Zhang Z6.
119442CIP <- 2007, JCM <- 2006, J. Zhang, Beijing Inst. Technol., Beijing, China: strain Z6

doi: 10.13145/bacdive13304.20230509.8.1

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 fradiae
  • full scientific name: Lentzea fradiae (Zhang et al. 2007) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Lechevalieria fradiae

@ref: 12341

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Lentzea

species: Lentzea fradiae

full scientific name: Lentzea fradiae (Zhang et al. 2007) Nouioui et al. 2018

strain designation: Z6

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
31994positiveno
69480positive100
119442positivenorod-shaped

pigmentation

  • @ref: 31994
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12341GYM 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
12341ORGANIC MEDIUM 79 (DSMZ Medium 426)yeshttps://mediadive.dsmz.de/medium/426Name: ORGANIC MEDIUM 79 (DSMZ Medium 426) Composition: Agar 15.0 g/l Peptone 10.0 g/l Dextrose 10.0 g/l NaCl 6.0 g/l Yeast extract 2.0 g/l Casein peptone 2.0 g/l Distilled water
37770MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
119442CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
12341positivegrowth28mesophilic
31994positivegrowth15-45
31994positiveoptimum30mesophilic
37770positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31994positivegrowth05-10alkaliphile
31994positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31994aerobe
119442obligate aerobe

spore formation

@refspore formationconfidence
31994yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
31994NaClpositivegrowth05-06 %
31994NaClpositiveoptimum5.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3199422599arabinose+carbon source
3199416634raffinose+carbon source
3199430911sorbitol+carbon source
3199427082trehalose+carbon source
3199418222xylose+carbon source
319944853esculin+hydrolysis
3199417632nitrate+reduction
11944217632nitrate+reduction
11944216301nitrite-reduction

metabolite production

  • @ref: 119442
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119442oxidase-
119442catalase+1.11.1.6
119442urease+3.5.1.5
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119442-+++-+---+-+++-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12341soilShanxi province, Wutaishan MountainChinaCHNAsia
67770Soil from Wutaishan MountainShanxi ProvinceChinaCHNAsia
119442Environment, SoilChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_27718.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_840;97_982;98_2059;99_27718&stattab=map
  • Last taxonomy: Lentzea
  • 16S sequence: AY114175
  • Sequence Identity:
  • Total samples: 52
  • soil counts: 7
  • plant counts: 45

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
123411Risk group (German classification)
1194421Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12341
  • description: Lechevalieria fradiae strain AS 4.3506 16S ribosomal RNA gene, partial sequence
  • accession: AY114175
  • length: 1407
  • database: ena
  • NCBI tax ID: 200378

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lechevalieria fradiae strain CGMCC 4.3506200378.4wgspatric200378
66792Lechevalieria fradiae CGMCC 4.35062663762758draftimg200378
67770Lentzea fradiae CGMCC 4.3506GCA_900100955scaffoldncbi200378

GC content

@refGC-contentmethod
1234168
6777070.5genome sequence analysis
6777068thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.689no
gram-positiveyes90.885yes
anaerobicno98.996no
aerobicyes90.565no
halophileno74.62yes
spore-formingyes96.027no
glucose-utilyes87.141no
flagellatedno97.466no
thermophileno98.277yes
glucose-fermentno91.476no

External links

@ref: 12341

culture collection no.: DSM 45099, CGMCC 4.3506, JCM 14205, NBRC 106318, CIP 109572

straininfo link

  • @ref: 82505
  • straininfo: 302764

literature

  • topic: Phylogeny
  • Pubmed-ID: 17392215
  • title: Lechevalieria fradiae sp. nov., a novel actinomycete isolated from soil in China.
  • authors: Zhang J, Xie Q, Liu Z, Goodfellow M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64777-0
  • year: 2007
  • mesh: Actinomycetaceae/*classification/genetics/isolation & purification, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12341Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45099)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45099
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
31994Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2824828776041
37770Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7330
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
82505Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302764.1StrainInfo: A central database for resolving microbial strain identifiers
119442Curators of the CIPCollection of Institut Pasteur (CIP 109572)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109572