Strain identifier

BacDive ID: 158291

Type strain: Yes

Species: Lentzea pudingi

Strain history: <- chengliang Cao, Jiangsu Normal Univ.

NCBI tax ID(s): 1789439 (species)

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General

@ref: 64951

BacDive-ID: 158291

DSM-Number: 108672

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

description: Lentzea pudingi DSM 108672 is an aerobe, spore-forming, mesophilic bacterium that builds a substrate mycelium and was isolated from From a weathered limestone sample in a karst area.

NCBI tax id

  • NCBI tax id: 1789439
  • Matching level: species

strain history

@refhistory
64951<- J.-S. Lee, KCTC; KCTC 39694 <- C. Cao, Jiangsu Normal Univ., China; DHS C021
67771<- chengliang Cao, Jiangsu Normal Univ.

doi: 10.13145/bacdive158291.20230509.8.1

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 pudingi
  • full scientific name: Lentzea pudingi Cao et al. 2017

@ref: 64951

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Lentzea

species: Lentzea pudingi

full scientific name: Lentzea pudingi Cao et al. 2017

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
65501positiveno
69480no93.843
69480positive100

colony morphology

  • @ref: 65501
  • medium used: ISP 2

multicellular morphology

@refforms multicellular complexcomplex namecomplex color
65501yessubstrate myceliumslightly yellow
65501yesaerial myceliumlight grey

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64951ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
65501ISP 3yes
65501ISP 4yes
65501ISP 5yes
65501Czapek's agaryes
65501Nutrient agar (NA)yes
65501ISP 2yes
65501PDAyes

culture temp

@refgrowthtypetemperaturerange
64951positivegrowth28mesophilic
65501positivegrowth15-37
65501positiveoptimum28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
65501positivegrowth6-10alkaliphile
65501positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65501aerobe
67771aerobe

spore formation

@refspore descriptionspore formationconfidence
65501mature aerial mycelium develops into rod-shaped spore chainsyes
69480yes100
69481yes92

halophily

@refsaltgrowthtested relationconcentrationhalophily level
65501NaClpositivegrowth5 %(w/v)
65501NaClpositiveoptimum0 %(w/v)non-halophilic

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
65501casein+hydrolysis
65501D-arabinose+carbon source17108
65501D-galactose-carbon source12936
65501D-mannose-carbon source16024
65501D-rhamnose+carbon source63150
65501D-ribose-carbon source16988
65501D-sorbitol-carbon source17924
65501L-glutamate+nitrogen source29985
65501L-histidine+nitrogen source15971
65501L-lysine-nitrogen source18019
65501L-valine+nitrogen source16414
65501lactose+carbon source17716
65501nitrate+reduction17632
65501raffinose+carbon source16634
65501starch+hydrolysis28017
65501tween 80+hydrolysis53426
65501urea+/-degradation16199
65501xylitol+carbon source17151
68369malate+assimilation25115
68369adipate+assimilation17128
68369decanoate-assimilation27689
68369gluconate+assimilation24265
68369maltose+assimilation17306
68369N-acetylglucosamine+assimilation59640
68369D-mannitol+assimilation16899
68369D-mannose+assimilation16024
68369L-arabinose+assimilation30849
68369D-glucose+assimilation17634
68369gelatin+hydrolysis5291
68369esculin+hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate+reduction17632

metabolite production

@refChebi-IDmetaboliteproduction
6550116136hydrogen sulfideno
6836935581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
65501catalase+1.11.1.6
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382acid phosphatase-3.1.3.2
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
64951-++/---++/---+/--+/--+-+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
64951+----++++++++++-+++/--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationlatitudelongitudeenrichment culture compositionenrichment culture durationenrichment culture temperature
67771From a weathered limestone sample in a karst areaChinaCHNAsia
64951a weathered limestone sample in a karst areaChinaCHNAsiaGuizhou Province, Puding Karst Ecosystem Research Station (26° 09'–26° 31' N, 105° 27'–105° 58' E)26.15105.45
65501limestone sampleChinaCHNAsiaPuding Karst Ecosystem Research Station, Guizhou Province26.15105.45culture medium consisting (per litre): 1.0 g sodium humate, 0.5 g Na2HPO4 , 1.5 g KCl, 0.05 g MgSO4 . 7H2O, 0.01 g FeSO4 . 7H2O and 0.02 g CaCO3. The pH was adjusted at 7.2 ± 0.1. After sterilizing, following antibiotics were added (per litre): 20 mg nalidixic acid, 40 mg cycloheximide and 40 mg nystatin.21 days28

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_27719.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_840;97_982;98_2059;99_27719&stattab=map
  • Last taxonomy: Lentzea
  • 16S sequence: KU564532
  • Sequence Identity:
  • Total samples: 367
  • soil counts: 287
  • aquatic counts: 22
  • animal counts: 13
  • plant counts: 45

Safety information

risk assessment

  • @ref: 64951
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64951
  • description: Lentzea pudingi strain DHS C021 16S ribosomal RNA gene, partial sequence
  • accession: KU564532
  • length: 1466
  • database: ena
  • NCBI tax ID: 1789439

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lentzea pudingi CGMCC 4.7319GCA_014646255scaffoldncbi1789439
66792Lentzea pudingi strain CGMCC 4.73191789439.3wgspatric1789439

GC content

  • @ref: 65501
  • GC-content: 69.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes92no
flagellatedno96.805yes
gram-positiveyes89.359yes
anaerobicno99.002yes
aerobicyes92.853yes
halophileno84.996no
spore-formingyes94.716no
thermophileno99.011yes
glucose-utilyes89.382yes
motileno91.123yes
glucose-fermentno91.597no

External links

@ref: 64951

culture collection no.: DSM 108672, CGMCC 4.7319, KCTC 39694, DHS C021

straininfo link

  • @ref: 111108
  • straininfo: 404036

literature

  • topic: Phylogeny
  • Pubmed-ID: 29022551
  • title: Lentzea pudingi sp. nov., isolated from a weathered limestone sample in a karst area.
  • authors: Cao C, Yuan B, Qin S, Jiang J, Tao F, Lian B
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002400
  • year: 2017
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, *Calcium Carbonate, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
64951Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-108672Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108672)
65501Chengliang Cao, Bo Yuan, Sheng Qin, Jihong Jiang, Faxiang Tao and Bin LianLentzea pudingi sp. nov., isolated from a weathered limestone sample in a karst area10.1099/ijsem.0.002400IJSEM 67: 4873-4878 201729022551
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111108Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID404036.1