Strain identifier

BacDive ID: 24803

Type strain: Yes

Species: Motilibacter rhizosphaerae

Strain Designation: RS-16

Strain history: KACC 16209 <-- S. D. Lee; Jeju Natl. Univ., South Korea; RS-16.

NCBI tax ID(s): 598652 (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: 21229

BacDive-ID: 24803

DSM-Number: 45622

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

description: Motilibacter rhizosphaerae RS-16 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil of the rhizosphere of Peucedanum japonicum Thunb..

NCBI tax id

  • NCBI tax id: 598652
  • Matching level: species

strain history

@refhistory
21229<- S. D. Lee, Jeju National Univ., Rep. of Korea; RS-16
67770KACC 16209 <-- S. D. Lee; Jeju Natl. Univ., South Korea; RS-16.

doi: 10.13145/bacdive24803.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Motilibacterales
  • family: Motilibacteraceae
  • genus: Motilibacter
  • species: Motilibacter rhizosphaerae
  • full scientific name: Motilibacter rhizosphaerae Lee 2013

@ref: 21229

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Motilibacteraceae

genus: Motilibacter

species: Motilibacter rhizosphaerae

full scientific name: Motilibacter rhizosphaerae Lee 2013

strain designation: RS-16

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31110positive1.45 µm0.79 µmrod-shapedno
69480positive99.999

pigmentation

  • @ref: 31110
  • production: yes

multimedia

  • @ref: 21229
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45622.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21229ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
21229GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: 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
21229positivegrowth28mesophilic
31110positivegrowth20-37
31110positiveoptimum37mesophilic
67770positivegrowth28mesophilic

culture pH

  • @ref: 31110
  • ability: positive
  • type: growth
  • pH: 6.0-7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 31110
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31110no
69480no99.798

observation

@refobservation
31110aggregates in clumps
67770quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3111015963ribitol+carbon source
3111023652dextrin+carbon source
3111017306maltose+carbon source
3111028053melibiose+carbon source
3111016634raffinose+carbon source
3111017151xylitol+carbon source
311104853esculin+hydrolysis

enzymes

@refvalueactivityec
31110acid phosphatase+3.1.3.2
31110alkaline phosphatase+3.1.3.1
31110catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
21229soil of the rhizosphere of Peucedanum japonicum Thunb.Peucedanum japonicumJeju, Mara IslandRepublic of KoreaKORAsia
67770Rhizosphere soil of a wild plant (Peucedanum japonicum Thunb.) on Mara Island in JejuPeucedanum japonicumRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_58446.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_25869;97_32451;98_41614;99_58446&stattab=map
  • Last taxonomy: Motilibacter rhizosphaerae subclade
  • 16S sequence: FM998018
  • Sequence Identity:
  • Total samples: 153
  • soil counts: 131
  • aquatic counts: 9
  • animal counts: 9
  • plant counts: 4

Safety information

risk assessment

  • @ref: 21229
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21229
  • description: Motilibacter rhizosphaerae strain RS-16 16S ribosomal RNA gene, partial sequence
  • accession: FM998018
  • length: 1423
  • database: ena
  • NCBI tax ID: 598652

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Motilibacter rhizosphaerae strain DSM 45622598652.3wgspatric598652
66792Motilibacter rhizosphaerae DSM 456222799112218draftimg598652
67770Motilibacter rhizosphaerae DSM 45622GCA_004216915scaffoldncbi598652

GC content

@refGC-contentmethod
2122973.1
6777073.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno82no
gram-positiveyes90.005yes
anaerobicno99.064yes
halophileno96.803no
spore-formingno84.749yes
glucose-utilyes89.995no
flagellatedno93.799yes
aerobicyes87.827yes
thermophileno94.212yes
motileno55.752yes
glucose-fermentno77.497no

External links

@ref: 21229

culture collection no.: DSM 45622, KACC 16209, JCM 32087

straininfo link

  • @ref: 88625
  • straininfo: 400016

literature

  • topic: Phylogeny
  • Pubmed-ID: 23667142
  • title: Proposal of Motilibacteraceae fam. nov., with the description of Motilibacter rhizosphaerae sp. nov.
  • authors: Lee SD
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.052357-0
  • year: 2013
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Apiaceae/microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, *Soil Microbiology, 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
21229Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45622Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45622)
31110Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172743928776041
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/
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
88625Reimer, 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-ID400016.1