Strain identifier

BacDive ID: 23148

Type strain: No

Species: Nakamurella panacisegetis

Strain Designation: P4-7

Strain history: <- JS Lee, KRIBB

NCBI tax ID(s): 1090615 (species)

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General

@ref: 19181

BacDive-ID: 23148

DSM-Number: 26919

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

description: Nakamurella panacisegetis P4-7 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from ginseng field.

NCBI tax id

  • NCBI tax id: 1090615
  • Matching level: species

strain history

@refhistory
19181<- CECT <- K.-C. Lee
67770CECT 7604 <-- J.-S. Lee; KCTC, South Korea; P4-7.
67771<- JS Lee, KRIBB

doi: 10.13145/bacdive23148.20230509.8.1

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 panacisegetis
  • full scientific name: Nakamurella panacisegetis Kim et al. 2012

@ref: 19181

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nakamurellaceae

genus: Nakamurella

species: Nakamurella panacisegetis

full scientific name: Nakamurella panacisegetis Kim et al. 2012

strain designation: P4-7

type strain: no

Morphology

cell morphology

@refgram stainconfidence
67771positive
69480positive100

Culture and growth conditions

culture medium

  • @ref: 19181
  • 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

@refgrowthtypetemperaturerange
19181positivegrowth25mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

observation

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19181ginseng fieldGeumsan CountyRepublic of KoreaKORAsia
67770Soil of a ginseng fieldGeumsan CountyRepublic of KoreaKORAsia
67771From soil of ginseng fieldRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_108077.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_3989;97_9658;98_11866;99_108077&stattab=map
  • Last taxonomy: Nakamurella panacisegetis subclade
  • 16S sequence: HE599560
  • Sequence Identity:
  • Total samples: 5862
  • soil counts: 3935
  • aquatic counts: 751
  • animal counts: 855
  • plant counts: 321

Safety information

risk assessment

  • @ref: 19181
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Humicoccus sp. KCTC 19426 16S ribosomal RNA gene, partial sequenceEU9393101385ena584994
19181Nakamurella panacisegetis partial 16S rRNA gene, type strain P4-7THE5995601443ena1090615

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nakamurella panacisegetis P4-7,KCTC 19426,CECT 7604GCA_900104535chromosomencbi1090615
66792Nakamurella panacisegetis strain P4-7,KCTC 19426,CECT 76041090615.3completepatric1090615
66792Nakamurella panacisegetis DSM 269192636416005draftimg1090615

GC content

@refGC-contentmethod
1918169.9
6777069.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes80no
motileno92.553no
flagellatedno98.571no
gram-positiveyes93.206yes
anaerobicno99.382no
aerobicyes94.027no
halophileno96.264no
spore-formingno76.54no
glucose-utilyes89.273no
glucose-fermentno86.809no
thermophileno98.222yes

External links

@ref: 19181

culture collection no.: DSM 26919, CECT 7604, KCTC 19426, JCM 31706

straininfo link

  • @ref: 87382
  • straininfo: 381616

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22703716Nakamurella panacisegetis sp. nov. and proposal for reclassification of Humicoccus flavidus Yoon et al., 2007 and Saxeibacter lacteus Lee et al., 2008 as Nakamurella flavida comb. nov. and Nakamurella lactea comb. nov.Kim KK, Lee KC, Lee JSSyst Appl Microbiol10.1016/j.syapm.2012.05.0022012Actinomycetales/*classification/genetics/isolation & purification/physiology, Chromatography, Thin Layer, Genes, Fungal, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Soil MicrobiologyGenetics
Phylogeny28820108Nakamurella intestinalis sp. nov., isolated from the faeces of Pseudorhynchus japonicus.Kim SJ, Cho H, Joa JH, Hamada M, Ahn JH, Weon HY, Kwon SWInt J Syst Evol Microbiol10.1099/ijsem.0.0020592017Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/*microbiology, Orthoptera/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
19181Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26919)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26919
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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)
87382Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID381616.1StrainInfo: A central database for resolving microbial strain identifiers