Strain identifier

BacDive ID: 13312

Type strain: Yes

Species: Lentzea flaviverrucosa

Strain Designation: AS4.0578

Strain history: CIP <- 2002, Z. Liu, Chinese Academy Sciences, Beijing, China: strain AS4.0578 <- CGMCC <- JCM <- Z. Liu

NCBI tax ID(s): 200379 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11860

BacDive-ID: 13312

DSM-Number: 44664

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

description: Lentzea flaviverrucosa AS4.0578 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 200379
  • Matching level: species

strain history

@refhistory
11860<- Z. Liu, AS, China
67770Z. Liu AS 4.0578.
119380CIP <- 2002, Z. Liu, Chinese Academy Sciences, Beijing, China: strain AS4.0578 <- CGMCC <- JCM <- Z. Liu

doi: 10.13145/bacdive13312.20230509.8.1

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 flaviverrucosa
  • full scientific name: Lentzea flaviverrucosa (ex Yan and Deng 1966) Xie et al. 2002

@ref: 11860

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Lentzea

species: Lentzea flaviverrucosa

full scientific name: Lentzea flaviverrucosa (ex Yan and Deng 1966) Xie et al. 2002

strain designation: AS4.0578

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.048
69480100positive
119380nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11860GYM 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
39933MEDIUM 275 - for Actinomadura rugatobispora and Actinomadura verrucososporayesDistilled water make up to (1000.000 ml);Sodium chloride (1.000 g);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Ammonium sulphate (2.000 g);Starch maize (10.000 g);Calcium carbonate (2.000 g);Trace salt solution - M00447 (1.000 ml)
119380CIP Medium 275yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=275

culture temp

@refgrowthtypetemperaturerange
11860positivegrowth28mesophilic
39933positivegrowth30mesophilic
67770positivegrowth28mesophilic
119380positivegrowth22-37
119380nogrowth10psychrophilic
119380nogrowth15psychrophilic
119380nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119380
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes94
69480yes100

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11938017632nitrate-reduction
11938016301nitrite-reduction
11938017632nitrate-respiration

antibiotic resistance

  • @ref: 119380
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite tests

  • @ref: 119380
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
119380oxidase-
119380alcohol dehydrogenase-1.1.1.1
119380catalase+1.11.1.6
119380lysine decarboxylase-4.1.1.18
119380ornithine decarboxylase-4.1.1.17
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
119380-+++-+----+-++-+-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11860soilShanxi province, Wutaishan MountainChinaCHNAsia
67770SoilWutaishan Mountain, Shanxi ProvinceChinaCHNAsia
119380Environment, SoilWutaishan mountainChinaCHNAsia1966

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_32369.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_840;97_982;98_3756;99_32369&stattab=map
  • Last taxonomy: Lentzea
  • 16S sequence: AF183957
  • Sequence Identity:
  • Total samples: 289
  • soil counts: 231
  • aquatic counts: 15
  • animal counts: 10
  • plant counts: 33

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118601Risk group (German classification)
1193801Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11860
  • description: Lentzea flavoverrucosus 16S ribosomal RNA gene, partial sequence
  • accession: AF183957
  • length: 1426
  • database: ena
  • NCBI tax ID: 200379

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lentzea flaviverrucosa strain DSM 44664200379.4wgspatric200379
66792Lentzea flaviverrucosa DSM 446642770939509draftimg200379
67770Lentzea flaviverrucosa CGMCC 4.578GCA_900110985scaffoldncbi200379
67770Lentzea flaviverrucosa DSM 44664GCA_003350445scaffoldncbi200379

GC content

  • @ref: 11860
  • GC-content: 64.1
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes94no
motileno91.755no
gram-positiveyes89.845no
anaerobicno99.21no
aerobicyes92.204no
halophileno85.418no
spore-formingyes93.648no
glucose-utilyes88.704no
flagellatedno96.722no
thermophileno98.938yes
glucose-fermentno91.966no

External links

@ref: 11860

culture collection no.: DSM 44664, AS 4.0578, JCM 11373, BCRC 16960, CGMCC 4.0578, CIP 107743, NBRC 100042

straininfo link

  • @ref: 82512
  • straininfo: 100722

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12361291Description of Lentzea flaviverrucosa sp. nov. and transfer of the type strain of Saccharothrix aerocolonigenes subsp. staurosporea to Lentzea albida.Xie Q, Wang Y, Huang Y, Wu Y, Ba F, Liu ZInt J Syst Evol Microbiol10.1099/00207713-52-5-18152002Actinomycetales/*classification/genetics/isolation & purification/metabolism, Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Soil Microbiology, Species Specificity, Terminology as TopicGenetics
35439047Discovery of unusual dimeric piperazyl cyclopeptides encoded by a Lentzea flaviverrucosa DSM 44664 biosynthetic supercluster.Li C, Hu Y, Wu X, Stumpf SD, Qi Y, D'Alessandro JM, Nepal KK, Sarotti AM, Cao S, Blodgett JAVProc Natl Acad Sci U S A10.1073/pnas.21179411192022*Actinobacteria/genetics, *Actinomycetales/genetics, Multigene Family, Peptides, Cyclic/genetics, *Streptomyces/genetics

Reference

@idauthorscataloguedoi/urltitle
11860Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44664)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44664
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
39933Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5212
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
82512Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100722.1StrainInfo: A central database for resolving microbial strain identifiers
119380Curators of the CIPCollection of Institut Pasteur (CIP 107743)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107743