Strain identifier

BacDive ID: 24445

Type strain: Yes

Species: Lentzea nigeriaca

Strain Designation: NJ2035

Strain history: <- Nevzat Sahin, Ondokuz Mayis Univ., Turkey

NCBI tax ID(s): 1128665 (species)

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General

@ref: 20625

BacDive-ID: 24445

DSM-Number: 45680

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

description: Lentzea nigeriaca NJ2035 is an aerobe, spore-forming, mesophilic bacterium that was isolated from arid soil.

NCBI tax id

  • NCBI tax id: 1128665
  • Matching level: species

strain history

@refhistory
20625<- N. Sahin, Ondokuz Mayis Univ., Dept. of Biology, Samsun, Turkey; NJ2035 <- M. Camas
67770DSM 45680 <-- N. Sahin; Ondokuz Mayis Univ., Turkey; NJ2035.
67771<- Nevzat Sahin, Ondokuz Mayis Univ., Turkey

doi: 10.13145/bacdive24445.20250331.9.3

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 nigeriaca
  • full scientific name: Lentzea nigeriaca (Camas et al. 2013) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Lechevalieria nigeriaca

@ref: 20625

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Lentzea

species: Lentzea nigeriaca

full scientific name: Lentzea nigeriaca (Camas et al. 2013) Nouioui et al. 2018

strain designation: NJ2035

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31106positiverod-shapedno
67771positive
125439positive99.2

multimedia

  • @ref: 20625
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45680.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 20625
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperature
20625positivegrowth28
31106positivegrowth20-45
31106positiveoptimum29
67770positivegrowth28
67771positivegrowth28

culture pH

@refabilitytypepHPH range
31106positivegrowth5.0-10.0alkaliphile
31106positiveoptimum7.2

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31106aerobe
67771aerobe
125439obligate aerobe98.9

spore formation

  • @ref: 31106
  • spore formation: yes

halophily

  • @ref: 31106
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 1.0-5.0 %

observation

@refobservation
67770quinones: MK-9(H4), MK-9(H2)
67771quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3110616449alanine+carbon source
3110622599arabinose+carbon source
3110629016arginine+carbon source
3110617057cellobiose+carbon source
3110623652dextrin+carbon source
3110628260galactose+carbon source
31106182404-hydroxy-L-proline+carbon source
3110617716lactose+carbon source
3110617306maltose+carbon source
3110629864mannitol+carbon source
3110637684mannose+carbon source
3110628044phenylalanine+carbon source
3110626271proline+carbon source
3110626546rhamnose+carbon source
3110617822serine+carbon source
3110617992sucrose+carbon source
3110626986threonine+carbon source
311064853esculin+hydrolysis

enzymes

  • @ref: 31106
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20625arid soilAbujaNigeriaNGAAfrica
67770Arid soil in AbujaNigeriaNGAAfrica
67771From soilArid estate, Abuja cityNigeriaNGAAfrica

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Xerophilic

Safety information

risk assessment

  • @ref: 20625
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20625
  • description: Lechevalieria nigeriaca strain NJ2035 16S ribosomal RNA gene, partial sequence
  • accession: JN989291
  • length: 1473
  • database: nuccore
  • NCBI tax ID: 1128665

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lentzea nigeriaca DSM 45680GCA_016907955contigncbi1128665
66792Lentzea nigeriaca strain DSM 456801128665.3wgspatric1128665
66792Lentzea nigeriaca DSM 456802901015569draftimg1128665

GC content

@refGC-contentmethod
2062568.4fluorimetric
3110668.4
6777068.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.9
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.2
125439BacteriaNetmotilityAbility to perform movementno84.3
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes63.5
125438gram-positivegram-positivePositive reaction to Gram-stainingyes87.618yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.422no
125438spore-formingspore-formingAbility to form endo- or exosporesyes82.953no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.418yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.5yes
125438motile2+flagellatedAbility to perform flagellated movementno79.333yes

External links

@ref: 20625

culture collection no.: DSM 45680, JCM 31207, KCTC 29057, NRRL B-24881

straininfo link

  • @ref: 88322
  • straininfo: 403146

literature

  • topic: Phylogeny
  • Pubmed-ID: 23645016
  • title: Lechevalieria nigeriaca sp. nov., isolated from arid soil.
  • authors: Camas M, Veyisoglu A, Tatar D, Saygin H, Cetin D, Sazak A, Guven K, Sahin N
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.052266-0
  • year: 2013
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nigeria, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
20625Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45680Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45680)
31106Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172743528776041
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
88322Reimer, 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-ID403146.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG