Strain identifier

BacDive ID: 11157

Type strain: Yes

Species: Nocardioides lianchengensis

Strain Designation: D94-1

Strain history: CGMCC 4.6858 <-- J. Zhang et al. D94-1.

NCBI tax ID(s): 1045774 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 17725

BacDive-ID: 11157

DSM-Number: 24663

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

description: Nocardioides lianchengensis D94-1 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1045774
  • Matching level: species

strain history

@refhistory
17725<- Y. Ma, Beijing Forestry Univ., College Biological Scs. and Biotechnol., China; D94-1 <- Y. Ma and J. Zhang
67770CGMCC 4.6858 <-- J. Zhang et al. D94-1.

doi: 10.13145/bacdive11157.20230509.8.1

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 lianchengensis
  • full scientific name: Nocardioides lianchengensis Zhang et al. 2012

@ref: 17725

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides lianchengensis

full scientific name: Nocardioides lianchengensis Zhang et al. 2012

strain designation: D94-1

type strain: yes

Morphology

cell morphology

  • @ref: 30466
  • gram stain: positive
  • cell length: 1.8 µm
  • cell width: 0.4 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 30466
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17725
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: 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 water

culture temp

@refgrowthtypetemperaturerange
17725positivegrowth28mesophilic
30466positivegrowth10-40
30466positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30466positivegrowth06-09alkaliphile
30466positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30466
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30466
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30466NaClpositivegrowth0-4 %
30466NaClpositiveoptimum1 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3046630089acetate+carbon source
30466286442-oxopentanoate+carbon source
3046623652dextrin+carbon source
3046628757fructose+carbon source
3046628260galactose+carbon source
3046624265gluconate+carbon source
3046617234glucose+carbon source
3046617754glycerol+carbon source
3046617596inosine+carbon source
3046624996lactate+carbon source
3046629864mannitol+carbon source
3046637684mannose+carbon source
3046617272propionate+carbon source
3046615361pyruvate+carbon source
3046651850methyl pyruvate+carbon source
3046626546rhamnose+carbon source
3046633942ribose+carbon source
3046617814salicin+carbon source
3046630911sorbitol+carbon source
3046617992sucrose+carbon source
3046617748thymidine+carbon source
3046627082trehalose+carbon source
3046653423tween 40+carbon source
3046653426tween 80+carbon source
3046616704uridine+carbon source
304664853esculin+hydrolysis

enzymes

@refvalueactivityec
30466acid phosphatase+3.1.3.2
30466alkaline phosphatase+3.1.3.1
30466catalase+1.11.1.6
30466gelatinase+
30466urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17725soilFujian province, Liancheng countyChinaCHNAsia
67770Soil from Liancheng CountyFujian ProvinceChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_17878.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_1021;97_10978;98_13495;99_17878&stattab=map
  • Last taxonomy: Nocardioides lianchengensis subclade
  • 16S sequence: HQ657322
  • Sequence Identity:
  • Total samples: 716
  • soil counts: 80
  • aquatic counts: 144
  • animal counts: 81
  • plant counts: 411

Safety information

risk assessment

  • @ref: 17725
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17725
  • description: Nocardioides lianchengensis strain D94-1 16S ribosomal RNA gene, partial sequence
  • accession: HQ657322
  • length: 1487
  • database: ena
  • NCBI tax ID: 1045774

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides lianchengensis strain CGMCC 4.68581045774.4wgspatric1045774
66792Nocardioides lianchengensis strain CGMCC 4.68581045774.5wgspatric1045774
66792Nocardioides lianchengensis CGMCC 4.68582675903056draftimg1045774
66792Nocardioides lianchengensis DSM 246632844625742draftimg1045774
67770Nocardioides lianchengensis CGMCC 4.6858GCA_900101465scaffoldncbi1045774
67770Nocardioides lianchengensis CGMCC 4.6858GCA_013409225contigncbi1045774

GC content

@refGC-contentmethod
1772571.8thermal denaturation, midpoint method (Tm)
3046671.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno70.606no
flagellatedno93.378yes
gram-positiveyes89.479yes
anaerobicno99.034yes
aerobicyes92.77yes
halophileno94.858no
spore-formingno79.341yes
thermophileno99.628yes
glucose-utilyes88.913no
glucose-fermentno89.106no

External links

@ref: 17725

culture collection no.: DSM 24663, CGMCC 4.6858, JCM 19667

straininfo link

  • @ref: 80406
  • straininfo: 401141

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22228655Nocardioides lianchengensis sp. nov., an actinomycete isolated from soil.Zhang J, Ma Y, Yu HInt J Syst Evol Microbiol10.1099/ijs.0.036723-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny25951861Nocardioides antarcticus sp. nov., isolated from marine sediment.Deng S, Chang X, Zhang Y, Ren L, Jiang F, Qu Z, Peng FInt J Syst Evol Microbiol10.1099/ijs.0.0003092015Actinomycetales/*classification/genetics/isolation & purification, Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17725Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24663)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24663
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
30466Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2680128776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
80406Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401141.1StrainInfo: A central database for resolving microbial strain identifiers