Strain identifier

BacDive ID: 14136

Type strain: Yes

Species: Parapedobacter composti

Strain Designation: 4M40

Strain history: S.-W. Kwon 4M40.

NCBI tax ID(s): 623281 (species)

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General

@ref: 16611

BacDive-ID: 14136

DSM-Number: 22900

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

description: Parapedobacter composti 4M40 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from cotton waste compost.

NCBI tax id

  • NCBI tax id: 623281
  • Matching level: species

strain history

@refhistory
16611<- S.-W. Kwon, KACC; 4M40 <- H.-Y. Weon
67770S.-W. Kwon 4M40.

doi: 10.13145/bacdive14136.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Parapedobacter
  • species: Parapedobacter composti
  • full scientific name: Parapedobacter composti Kim et al. 2010

@ref: 16611

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Parapedobacter

species: Parapedobacter composti

full scientific name: Parapedobacter composti Kim et al. 2010

strain designation: 4M40

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29451negative1.2-5 µm0.2-0.5 µmrod-shapedno
69480negative99.995

pigmentation

  • @ref: 29451
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16611
  • 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
16611positivegrowth28mesophilic
29451positivegrowth15-45
29451positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
29451positivegrowth06-08
29451positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29451
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29451no
69481no100
69480no99.991

halophily

  • @ref: 29451
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

@refobservation
29451aggregates in chains
67770quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2945122599arabinose+carbon source
2945117234glucose+carbon source
2945128087glycogen+carbon source
2945137684mannose+carbon source
2945128053melibiose+carbon source
2945126546rhamnose+carbon source
2945133942ribose+carbon source
2945117814salicin+carbon source
2945117992sucrose+carbon source

enzymes

@refvalueactivityec
29451catalase+1.11.1.6
29451cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16611cotton waste compostSuwonRepublic of KoreaKORAsia
67770Cotton waste compostRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Engineered#Biodegradation#Composting
#Engineered#Waste#Solid plant waste
#Host#Plants#Shrub (Scrub)

taxonmaps

  • @ref: 69479
  • File name: preview.99_131755.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15793;96_42497;97_54351;98_88151;99_131755&stattab=map
  • Last taxonomy: Parapedobacter composti subclade
  • 16S sequence: FJ754321
  • Sequence Identity:
  • Total samples: 14
  • soil counts: 8
  • animal counts: 5
  • plant counts: 1

Safety information

risk assessment

  • @ref: 16611
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16611
  • description: Parapedobacter composti strain 4M40 16S ribosomal RNA gene, partial sequence
  • accession: FJ754321
  • length: 1463
  • database: ena
  • NCBI tax ID: 623281

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parapedobacter composti strain DSM 22900623281.3wgspatric623281
66792Parapedobacter composti DSM 229002675903219draftimg623281
67770Parapedobacter composti DSM 22900GCA_900112315contigncbi623281

GC content

@refGC-contentmethod
1661148.6high performance liquid chromatography (HPLC)
2945148.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.324yes
anaerobicno98.762no
halophileno86.323no
spore-formingno92.977yes
glucose-utilyes91.016yes
flagellatedno97.535no
aerobicyes82.697yes
thermophileno96.749yes
motileno91.426yes
glucose-fermentno85.645no

External links

@ref: 16611

culture collection no.: DSM 22900, JCM 15978, KACC 10972

straininfo link

  • @ref: 83301
  • straininfo: 402739

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19767359Parapedobacter luteus sp. nov. and Parapedobacter composti sp. nov., isolated from cotton waste compost.Kim SJ, Weon HY, Kim YS, Yoo SH, Kim BY, Anandham R, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.013318-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Gossypium/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sphingobacterium/*classification/genetics/*isolation & purification/metabolism, Waste Products/*analysisMetabolism
Phylogeny33013721Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae.Nagar S, Talwar C, Haider S, Puri A, Ponnusamy K, Gupta M, Sood U, Bajaj A, Lal R, Kumar RFront Microbiol10.3389/fmicb.2020.017252020

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16611Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22900)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22900
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
29451Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2585628776041
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
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
83301Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402739.1StrainInfo: A central database for resolving microbial strain identifiers