Strain identifier

BacDive ID: 11129

Type strain: Yes

Species: Nocardioides exalbidus

Strain Designation: RC825

Strain history: IAM 15416 <-- B. Li et al. RC825.

NCBI tax ID(s): 402596 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16105

BacDive-ID: 11129

DSM-Number: 22017

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

description: Nocardioides exalbidus RC825 is a mesophilic, Gram-positive bacterium that was isolated from Lichen.

NCBI tax id

  • NCBI tax id: 402596
  • Matching level: species

strain history

@refhistory
16105<- JCM/RIKEN <- B. Li et al., Inst. Molecular and Cellular Biosci., Univ. Tokyo, Japan; RC825
67770IAM 15416 <-- B. Li et al. RC825.

doi: 10.13145/bacdive11129.20230509.8.1

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 exalbidus
  • full scientific name: Nocardioides exalbidus Li et al. 2007

@ref: 16105

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides exalbidus

full scientific name: Nocardioides exalbidus Li et al. 2007 emend. Nouioui et al. 2018

strain designation: RC825

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16105TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
16105GYM 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
16105R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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 water

culture temp

@refgrowthtypetemperaturerange
67770positivegrowth28mesophilic
16105positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no91
69480no99.502

observation

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16105LichenIzu-Oshima IslandJapanJPNAsia
67770LichenIzu-Oshima IslandJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Other
  • Cat3: #Lichen

taxonmaps

  • @ref: 69479
  • File name: preview.99_17362.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_2445;97_2980;98_13150;99_17362&stattab=map
  • Last taxonomy: Nocardioides exalbidus
  • 16S sequence: AB273624
  • Sequence Identity:
  • Total samples: 321
  • soil counts: 163
  • aquatic counts: 29
  • animal counts: 82
  • plant counts: 47

Safety information

risk assessment

  • @ref: 16105
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16105
  • description: Nocardioides exalbidus gene for 16S rRNA, partial sequence, strain: RC825
  • accession: AB273624
  • length: 1453
  • database: ena
  • NCBI tax ID: 402596

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides exalbidus strain DSM 22017402596.4wgspatric402596
66792Nocardioides exalbidus DSM 220172639762616draftimg402596
67770Nocardioides exalbidus DSM 22017GCA_900105585contigncbi402596

GC content

@refGC-contentmethod
1610574.0high performance liquid chromatography (HPLC)
6777071.8genome sequence analysis
6777074high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno91no
gram-positiveyes90.901no
anaerobicno98.941no
halophileno96.066no
spore-formingno82.042no
glucose-utilyes89.506no
aerobicyes92.443no
flagellatedno94.113no
thermophileno99.468yes
motileno78.558no
glucose-fermentno88.795no

External links

@ref: 16105

culture collection no.: DSM 22017, CCTCC AA 206016, IAM 15416, JCM 23199

straininfo link

  • @ref: 80378
  • straininfo: 319384

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27654931Nocardioides flavus sp. nov., isolated from marine sediment.Wang S, Zhou Y, Zhang GInt J Syst Evol Microbiol10.1099/ijsem.0.0015072016Actinomycetales/*classification/genetics/isolation & purification, Bacteria, Aerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryEnzymology
Phylogeny27902315Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave.Han MX, Fang BZ, Tian Y, Zhang WQ, Jiao JY, Liu L, Zhang ZT, Xiao M, Wei DQ, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0016762017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32141810Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil.Roh SG, Lee C, Kim MK, Kang HJ, Kim YS, Kim MJ, Malik A, Kim SBInt J Syst Evol Microbiol10.1099/ijsem.0.0040952020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sand/microbiology, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34542392Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula.Chhetri G, Kim I, Kang M, Kim J, So Y, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0050122021*Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nocardioides, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *TagetesTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16105Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22017)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22017
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
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/
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
80378Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID319384.1StrainInfo: A central database for resolving microbial strain identifiers