Strain identifier

BacDive ID: 24250

Type strain: Yes

Species: Nocardioides szechwanensis

Strain Designation: RHLT1-17

Strain history: CGMCC 1.11147 <-- Q. Liu et al. RHLT1-17.

NCBI tax ID(s): 1005944 (species)

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General

@ref: 20683

BacDive-ID: 24250

DSM-Number: 27403

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

description: Nocardioides szechwanensis RHLT1-17 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from soil collected at Hailuogou glacier.

NCBI tax id

  • NCBI tax id: 1005944
  • Matching level: species

strain history

@refhistory
20683<- NBRC; NBRC 108562
67770CGMCC 1.11147 <-- Q. Liu et al. RHLT1-17.

doi: 10.13145/bacdive24250.20230509.8.1

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 szechwanensis
  • full scientific name: Nocardioides szechwanensis Liu et al. 2013

@ref: 20683

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides szechwanensis

full scientific name: Nocardioides szechwanensis Liu et al. 2013 emend. Nouioui et al. 2018

strain designation: RHLT1-17

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30526positive1.31 µm0.8 µmrod-shapedno
69480no93.992
69480positive100

colony morphology

  • @ref: 20683
  • incubation period: 3-7 days

pigmentation

  • @ref: 30526
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20683
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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
20683positivegrowth20psychrophilic
30526positivegrowth0-35
30526positiveoptimum17.5psychrophilic
67770positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
30526positivegrowth6.5-11alkaliphile
30526positiveoptimum8.75

Physiology and metabolism

oxygen tolerance

  • @ref: 30526
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30526no
69481no100
69480no99.855

halophily

@refsaltgrowthtested relationconcentration
30526NaClpositivegrowth0-1 %
30526NaClpositiveoptimum0.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3052617057cellobiose+carbon source
3052628757fructose+carbon source
3052617234glucose+carbon source
3052629864mannitol+carbon source
3052637684mannose+carbon source
3052626546rhamnose+carbon source
3052617992sucrose+carbon source
3052627082trehalose+carbon source
3052618222xylose+carbon source
3052617632nitrate+reduction

enzymes

@refvalueactivityec
30526alkaline phosphatase+3.1.3.1
30526gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20683soil collected at Hailuogou glacierSzechwan ProvChinaCHNAsia
67770Soil at Hailuogou glacierSzechwan Province, south-western of ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Glacier
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 20683
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20683
  • description: Nocardioides szechwanensis strain CGMCC 1.11147 16S ribosomal RNA gene, partial sequence
  • accession: JF750424
  • length: 1403
  • database: ena
  • NCBI tax ID: 1005944

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides szechwanensis strain CGMCC 1.111471005944.4wgspatric1005944
66792Nocardioides szechwanensis strain NBRC 1085621005944.5wgspatric1005944
66792Nocardioides szechwanensis CGMCC 1.111472671180088draftimg1005944
67770Nocardioides szechwanensis NBRC 108562GCA_007992395contigncbi1005944
67770Nocardioides szechwanensis CGMCC 1.11147GCA_900103935scaffoldncbi1005944

GC content

@refGC-contentmethod
2068367.9
6777067.9thermal denaturation, midpoint method (Tm)
6777071genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno97.774yes
flagellatedno98.886yes
gram-positiveyes92.923yes
anaerobicno99.109yes
aerobicyes92.088yes
halophileno95.848yes
spore-formingno86.388yes
thermophileno97.43no
glucose-utilyes86.069yes
glucose-fermentno89.23no

External links

@ref: 20683

culture collection no.: DSM 27403, CGMCC 1.11147, NBRC 108562, JCM 19669

straininfo link

  • @ref: 88192
  • straininfo: 398597

literature

  • topic: Phylogeny
  • Pubmed-ID: 22345140
  • title: Nocardioides szechwanensis sp. nov. and Nocardioides psychrotolerans sp. nov., isolated from a glacier.
  • authors: Liu Q, Xin YH, Liu HC, Zhou YG, Wen Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.038091-0
  • year: 2012
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Ice Cover/*microbiology, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
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
20683Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27403Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27403)
30526Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172685828776041
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
88192Reimer, 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-ID398597.1