Strain identifier

BacDive ID: 23147

Type strain: Yes

Species: Nakamurella flavida

Strain Designation: DS-52

Strain history: CIP <- 2005, J. H. Yoon, KRIBB, Taejon, Korea: strain DS-52, "Solicoccus flavidus"

NCBI tax ID(s): 363630 (species)

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General

@ref: 19182

BacDive-ID: 23147

DSM-Number: 26917

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

description: Nakamurella flavida DS-52 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 363630
  • Matching level: species

strain history

@refhistory
19182<- JCM <- J. H. Yoon; DS-52
67770CIP 108919 <-- J. H. Yoon DS-52.
67771<- JH Yoon, KRIBB
119376CIP <- 2005, J. H. Yoon, KRIBB, Taejon, Korea: strain DS-52, "Solicoccus flavidus"

doi: 10.13145/bacdive23147.20250331.9.3

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 flavida
  • full scientific name: Nakamurella flavida (Yoon et al. 2007) Kim et al. 2012

  • synonyms

    • @ref: 20215
    • synonym: Humicoccus flavidus

@ref: 19182

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nakamurellaceae

genus: Nakamurella

species: Nakamurella flavida

full scientific name: Nakamurella flavida (Yoon et al. 2007) Kim et al. 2012

strain designation: DS-52

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31775positive0.9 µm0.9 µmcoccus-shapedno
67771positive
125438no90.5
125438positive91.554
125439positive99.5
119376positivecoccus-shapedno

colony morphology

  • @ref: 119376

pigmentation

  • @ref: 31775
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19182GYM 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
38365MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
119376CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperature
19182positivegrowth25
31775positivegrowth04-32
31775positiveoptimum25
38365positivegrowth25
67770positivegrowth25
67771positivegrowth25
119376positivegrowth5-30
119376nogrowth37
119376nogrowth41

culture pH

@refabilitytypepHPH range
31775positivegrowth5.0-8.5alkaliphile
31775positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31775aerobe
67771aerobe
119376obligate aerobe
125439obligate aerobe99.4

spore formation

  • @ref: 31775
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31775NaClpositivegrowth<4 %
119376NaClpositivegrowth0-2 %
119376NaClnogrowth4 %
119376NaClnogrowth6 %
119376NaClnogrowth8 %
119376NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3177522599arabinose+carbon source
3177517057cellobiose+carbon source
3177528757fructose+carbon source
3177528260galactose+carbon source
3177517234glucose+carbon source
3177525115malate+carbon source
3177517306maltose+carbon source
3177537684mannose+carbon source
3177517814salicin+carbon source
3177530031succinate+carbon source
3177517992sucrose+carbon source
3177527082trehalose+carbon source
3177518222xylose+carbon source
317754853esculin+hydrolysis
11937616947citrate-carbon source
1193764853esculin+hydrolysis
119376606565hippurate+hydrolysis
11937617632nitrate-reduction
11937616301nitrite-reduction
11937615792malonate-assimilation
11937617632nitrate-respiration

metabolite production

  • @ref: 119376
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11937615688acetoin-
11937617234glucose-

enzymes

@refvalueactivityec
31775acid phosphatase+3.1.3.2
31775catalase+1.11.1.6
31775gelatinase+
31775urease+3.5.1.5
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382alkaline phosphatase-3.1.3.1
119376oxidase-
119376beta-galactosidase+3.2.1.23
119376alcohol dehydrogenase-1.1.1.1
119376gelatinase-
119376amylase+
119376DNase+
119376caseinase-3.4.21.50
119376catalase+1.11.1.6
119376tween esterase-
119376gamma-glutamyltransferase-2.3.2.2
119376lecithinase-
119376lipase-
119376lysine decarboxylase-4.1.1.18
119376ornithine decarboxylase-4.1.1.17
119376phenylalanine ammonia-lyase-4.3.1.24
119376protease-
119376tryptophan deaminase-
119376urease+3.5.1.5
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119376--++-++---+----++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
19182soilDokdoRepublic of KoreaKORAsia
67770Soil
67771From soilDokdoRepublic of KoreaKORAsia
119376Environment, SoilDokdo IslandRepublic of KoreaKORAsia2004

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_32752.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_3989;97_9658;98_24236;99_32752&stattab=map
  • Last taxonomy: Nakamurella flavida subclade
  • 16S sequence: DQ321750
  • Sequence Identity:
  • Total samples: 145
  • soil counts: 71
  • aquatic counts: 14
  • animal counts: 26
  • plant counts: 34

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
191821Risk group (German classification)
1193761Risk group (French classification)

Sequence information

16S sequences

  • @ref: 19182
  • description: Humicoccus flavidus strain DS-52 16S ribosomal RNA gene, partial sequence
  • accession: DQ321750
  • length: 1475
  • database: nuccore
  • NCBI tax ID: 363630

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nakamurella flavida KCTC 19127GCA_016918095contigncbi363630
66792Nakamurella flavida strain KCTC 19127363630.3wgspatric363630
66792Nakamurella flavida DSM 269172923639079draftimg363630

GC content

@refGC-contentmethod
1918272.6high performance liquid chromatography (HPLC)
1918274.3high performance liquid chromatography (HPLC)
3177572.6

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.554yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.7yes
125438spore-formingspore-formingAbility to form endo- or exosporesno66.251yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.696yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95yes
125438motile2+flagellatedAbility to perform flagellated movementno90.5yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes66.1
125439BacteriaNetmotilityAbility to perform movementno75.4
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.4

External links

@ref: 19182

culture collection no.: DSM 26917, CIP 108919, JCM 15652, KCTC 19127, NBRC 105867

straininfo link

  • @ref: 87381
  • straininfo: 365189

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17220441Humicoccus flavidus gen. nov., sp. nov., isolated from soil.Yoon JH, Kang SJ, Jung SY, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64246-02007Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Gram-Positive Cocci/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny26813967Nakamurella endophytica sp. nov., a novel endophytic actinobacterium isolated from the bark of Kandelia candel.Tuo L, Li FN, Pan Z, Lou I, Guo M, Ming-Yuen Lee S, Chen L, Hu L, Sun CHInt J Syst Evol Microbiol10.1099/ijsem.0.0009232016Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peptidoglycan/chemistry, *Phylogeny, Plant Bark/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny27707433Nakamurella silvestris sp. nov., an actinobacterium isolated from alpine forest soil.Franca L, Albuquerque L, Zhang DC, Nouioui I, Klenk HP, da Costa MS, Margesin RInt J Syst Evol Microbiol10.1099/ijsem.0.0015412016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Forests, Italy, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31710581Nakamurella flava sp. nov., a novel endophytic actinobacterium isolated from Mentha haplocalyx Briq.Yan XR, Chen MS, Yang C, An MB, Li HY, Shi HC, Tuo LInt J Syst Evol Microbiol10.1099/ijsem.0.0038312020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Endophytes/classification/isolation & purification, Fatty Acids/chemistry, Mentha/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryEnzymology
Phylogeny34910249Nakamurella leprariae sp. nov., isolated from a lichen sample.An DF, Yang SJ, Jiang LQ, Wang XY, Huang XY, Lang L, Chen XM, Fan MQ, Li GD, Jiang MG, Wang LS, Jiang CL, Jiang YArch Microbiol10.1007/s00203-021-02626-72021Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids, *Lichens, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19182Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26917)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26917
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
31775Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2804828776041
38365Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6602
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
87381Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID365189.1StrainInfo: A central database for resolving microbial strain identifiers
119376Curators of the CIPCollection of Institut Pasteur (CIP 108919)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108919
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1