Strain identifier

BacDive ID: 24254

Type strain: Yes

Species: Nocardioides zeae

Strain Designation: JM-1068

Strain history: CIP <- 2013, P. Kämpfer, Justus Liebig Giessen Univ., Giessen, Germany: strain JM-1068

NCBI tax ID(s): 1457234 (species)

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General

@ref: 20687

BacDive-ID: 24254

DSM-Number: 28163

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

description: Nocardioides zeae JM-1068 is a mesophilic, Gram-positive bacterium that was isolated from internal stem tissue of field grown healthy corn, Zea mays cultivar 'Sweet Belle'.

NCBI tax id

  • NCBI tax id: 1457234
  • Matching level: species

strain history

@refhistory
20687<- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; JM-1068 <- J. Mcinroy
67770CIP 110696 <-- P. Kämpfer; Justus-Liebig-Univ. Giessen, Germany; JM-1068.
124028CIP <- 2013, P. Kämpfer, Justus Liebig Giessen Univ., Giessen, Germany: strain JM-1068

doi: 10.13145/bacdive24254.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides zeae
  • full scientific name: Nocardioides zeae Glaeser et al. 2014

@ref: 20687

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides zeae

full scientific name: Nocardioides zeae Glaeser et al. 2014

strain designation: JM-1068

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
124028positiverod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
36247MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
20687R2A MEDIUM (DSMZ Medium 830)yesName: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled waterhttps://mediadive.dsmz.de/medium/830
20687TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yesName: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/92
124028CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20687positivegrowth28mesophilic
36247positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no90
69480no99.973

observation

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

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
20687internal stem tissue of field grown healthy corn, Zea mays cultivar 'Sweet Belle'Zea maysE.V. Smith Research Center, Alabama, TallasseeUSAUSANorth America
67770Healthy stem of a Zea mays plantZea mays
124028Plant, Field grown corn root tissueTallassee, Alabama, USAUnited States of AmericaUSANorth America2005

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Stem (Branch)

taxonmaps

  • @ref: 69479
  • File name: preview.99_16215.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_2830;97_9948;98_12231;99_16215&stattab=map
  • Last taxonomy: Nocardioides zeae subclade
  • 16S sequence: KF900163
  • Sequence Identity:
  • Total samples: 15558
  • soil counts: 5821
  • aquatic counts: 2245
  • animal counts: 5517
  • plant counts: 1975

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
206871Risk group (German classification)
1240281Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20687
  • description: Nocardioides zeae strain JM-1068 16S ribosomal RNA gene, partial sequence
  • accession: KF900163
  • length: 1438
  • database: ena
  • NCBI tax ID: 1457234

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides zeae strain JCM 307281457234.3wgspatric1457234
66792Nocardioides zeae JCM 307282902192801draftimg1457234
67770Nocardioides zeae JCM 30728GCA_010686755scaffoldncbi1457234

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno90no
motileno95.99no
gram-positiveyes88.379no
anaerobicno99.122no
halophileno92.387no
spore-formingno83.124no
glucose-utilyes89.902no
thermophileno98.887yes
aerobicyes94.87no
flagellatedno97.709no
glucose-fermentno91.987no

External links

@ref: 20687

culture collection no.: DSM 28163, CIP 110696, LMG 28079, JCM 30728

straininfo link

  • @ref: 88196
  • straininfo: 404056

literature

  • topic: Phylogeny
  • Pubmed-ID: 24801154
  • title: Nocardioides zeae sp. nov., isolated from the stem of Zea mays.
  • authors: Glaeser SP, McInroy JA, Busse HJ, Kampfer P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.061481-0
  • year: 2014
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Stems/microbiology, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
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
20687Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28163Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28163)
36247Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30503
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/
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
88196Reimer, 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-ID404056.1
124028Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110696Collection of Institut Pasteur (CIP 110696)