Strain identifier

BacDive ID: 10174

Type strain: Yes

Species: Nakamurella lactea

Strain Designation: DLS-10

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 1123241 (strain), 459515 (species)

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General

@ref: 8076

BacDive-ID: 10174

DSM-Number: 19367

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

description: Nakamurella lactea DLS-10 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from rock sample.

NCBI tax id

NCBI tax idMatching level
1123241strain
459515species

strain history

@refhistory
8076<- Soon Dong Lee; DLS-10
67770KCTC 19285 <-- S. D. Lee DLS-10.
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive10174.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Nakamurellales
  • family: Nakamurellaceae
  • genus: Nakamurella
  • species: Nakamurella lactea
  • full scientific name: Nakamurella lactea (Lee et al. 2008) Kim et al. 2012

  • synonyms

    • @ref: 20215
    • synonym: Saxeibacter lacteus

@ref: 8076

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nakamurellaceae

genus: Nakamurella

species: Nakamurella lactea

full scientific name: Nakamurella lactea (Lee et al. 2008) Kim et al. 2012 emend. Nouioui et al. 2017

strain designation: DLS-10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32480positive0.95 µm0.55 µmrod-shapedno
67771positive
69480no94.511
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
18347Ivory (1014)10-14 daysISP 2
18347Ivory (1014)10-14 daysISP 3
18347Ivory (1014)10-14 daysISP 4
18347Ivory (1014)10-14 daysISP 5
18347Ivory (1014)10-14 daysISP 6
18347Ivory (1014)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18347noISP 2
18347noISP 3
18347noISP 4
18347noISP 5
18347noISP 6
18347noISP 7

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_19367_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19367_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19367_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19367_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19367_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8076GYM 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
18347ISP 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
18347ISP 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:
18347ISP 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
18347ISP 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
18347ISP 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
18347ISP 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

@refgrowthtypetemperaturerange
8076positivegrowth28mesophilic
18347positiveoptimum28mesophilic
32480positivegrowth04-37
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

  • @ref: 32480
  • ability: positive
  • type: growth
  • pH: 5.1-9.1
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32480aerobe
67771aerobe

spore formation

@refspore formationconfidence
32480no
69481no90
69480no99.759

halophily

  • @ref: 32480
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <3 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4), MK-9(H0), MK-7(H0), MK-8(H2), MK-8(H4), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3248022599arabinose+carbon source
3248017268myo-inositol+carbon source
3248017632nitrate+reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
32480acid phosphatase+3.1.3.2
32480catalase+1.11.1.6
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379pyrazinamidase-3.5.1.B15
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18347--+/-+/---++---+----++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18347-++++----++++-+-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8076rock sampleJejuRepublic of KoreaKORAsia
67770Rock from the peak of Darangshi OreumJejuRepublic of KoreaKORAsia
67771From rockJejuRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4951.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2430;97_2960;98_3704;99_4951&stattab=map
  • Last taxonomy: Nakamurella lactea subclade
  • 16S sequence: AM778124
  • Sequence Identity:
  • Total samples: 695
  • soil counts: 304
  • aquatic counts: 116
  • animal counts: 218
  • plant counts: 57

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183471German classification
80761Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8076Saxeibacter lacteus partial 16S rRNA gene, type strain DLS-10TAM7781241399ena1123241
8076Saxeibacter lacteus partial 16S rRNA gene, strain KCTC 19285HE5995611440ena1123241

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saxeibacter lacteus DSM 193671123241.3wgspatric1123241
66792Nakamurella lactea DSM 193672524614512draftimg1123241
67770Nakamurella lactea DSM 19367GCA_000426645scaffoldncbi1123241

GC content

@refGC-contentmethod
807670.4high performance liquid chromatography (HPLC)
807674.3
807668.9sequence analysis
6777068.9genome sequence analysis
6777074.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno90no
motileno91.467yes
flagellatedno98.964no
gram-positiveyes88.709yes
anaerobicno99.191no
aerobicyes91.724no
halophileno93.81no
spore-formingno83.853yes
thermophileno97.15yes
glucose-utilyes85.953no
glucose-fermentno78.13yes

External links

@ref: 8076

culture collection no.: DSM 19367, JCM 16024, KCTC 19285, DLS 10, NBRC 106258

straininfo link

  • @ref: 79552
  • straininfo: 404452

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18398192Saxeibacter lacteus gen. nov., sp. nov., an actinobacterium isolated from rock.Lee SD, Park SK, Yun YW, Lee DWInt J Syst Evol Microbiol10.1099/ijs.0.65558-02008Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/chemistry/genetics, Fatty Acids/metabolism, Genes, Bacterial, Geologic Sediments/microbiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as TopicMetabolism
28074122High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea.Nouioui I, Goker M, Carro L, Montero-Calasanz MD, Rohde M, Woyke T, Kyrpides NC, Klenk HPStand Genomic Sci10.1186/s40793-016-0216-02017
Phylogeny33146743Nakamurella aerolata sp. Nov., Isolated from an Automobile Air Conditioning System.Chaudhary DK, Lee H, Dahal RH, Kim DY, Cha IT, Lee KE, Kim DUCurr Microbiol10.1007/s00284-020-02274-y2020Actinobacteria, *Air Conditioning, *Automobiles, Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid, Fatty Acids, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8076Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19367)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19367
18347Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19367.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
32480Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2870028776041
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
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
79552Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404452.1StrainInfo: A central database for resolving microbial strain identifiers