Strain identifier

BacDive ID: 24446

Type strain: Yes

Species: Pseudonocardia sediminis

Strain history: S.-K. Tang YIM M13141.

NCBI tax ID(s): 1397368 (species)

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General

@ref: 20748

BacDive-ID: 24446

DSM-Number: 45779

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic

description: Pseudonocardia sediminis DSM 45779 is a spore-forming, mesophilic bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 1397368
  • Matching level: species

strain history

@refhistory
20748<- S.-K. Tang, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; YIM M13141 <- D.-F. Zhang, YIM
67770S.-K. Tang YIM M13141.

doi: 10.13145/bacdive24446.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Pseudonocardia
  • species: Pseudonocardia sediminis
  • full scientific name: Pseudonocardia sediminis Zhang et al. 2014

@ref: 20748

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia sediminis

full scientific name: Pseudonocardia sediminis Zhang et al. 2014

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.667
69480100positive

Culture and growth conditions

culture medium

  • @ref: 20748
  • name: GPHF-MEDIUM (DSMZ Medium 553)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/553
  • composition: Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20748positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 99

observation

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
20748marine sedimentSouth China Sea (21° 23.2029 N 117° 37.2089 E) at a depth of 652 mChinaCHNAsia21.3867117.62
67770Marine sediment from the South China Sea

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_122167.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1626;97_61724;98_82188;99_122167&stattab=map
  • Last taxonomy: Pseudonocardia sediminis subclade
  • 16S sequence: KF564279
  • Sequence Identity:
  • Total samples: 942
  • soil counts: 90
  • aquatic counts: 32
  • animal counts: 278
  • plant counts: 542

Safety information

risk assessment

  • @ref: 20748
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20748
  • description: Pseudonocardia sediminis strain YIM M13141 16S ribosomal RNA gene, complete sequence
  • accession: KF564279
  • length: 1541
  • database: ena
  • NCBI tax ID: 1397368

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia sediminis strain DSM 457791397368.3wgspatric1397368
66792Pseudonocardia sediminis DSM 457792806310546draftimg1397368
67770Pseudonocardia sediminis DSM 45779GCA_004217185contigncbi1397368

GC content

  • @ref: 20748
  • GC-content: 73.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
motileno92.069no
gram-positiveyes91.441no
anaerobicno99.177no
halophileno84.46no
spore-formingyes69.5no
thermophileno99.565yes
glucose-utilyes88.798no
aerobicyes93.846no
flagellatedno97.534no
glucose-fermentno90.8no

External links

@ref: 20748

culture collection no.: DSM 45779, JCM 18540, YIM M13141

straininfo link

  • @ref: 88323
  • straininfo: 404135

literature

  • topic: Phylogeny
  • Pubmed-ID: 24198055
  • title: Pseudonocardia sediminis sp. nov., isolated from marine sediment.
  • authors: Zhang DF, Jiang Z, Li L, Liu BB, Zhang XM, Tian XP, Zhang S, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.057844-0
  • year: 2013
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
20748Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45779Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45779)
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/gkaa1025Nucleic 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.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
88323Reimer, 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-ID404135.1