Strain identifier

BacDive ID: 132246

Type strain: Yes

Species: Microbacterium rhizomatis

Strain history: <- DC Yang, KyungHee Univ.

NCBI tax ID(s): 1631477 (species)

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General

@ref: 24035

BacDive-ID: 132246

DSM-Number: 103406

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

description: Microbacterium rhizomatis DSM 103406 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from rhizome, ginseng root.

NCBI tax id

  • NCBI tax id: 1631477
  • Matching level: species

strain history

@refhistory
24035<- JCM, Riken BioResource Center, Tsukuba, Japan; JCM 30598 <-D.C. Yang and Y.J. Kim, Kyung Hee Univerity, Korea; DCY100
67770D.-C. Yang and Y.-J. Kim; Kyung Hee Univ., South Korea; DCY100.
67771<- DC Yang, KyungHee Univ.

doi: 10.13145/bacdive132246.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium rhizomatis
  • full scientific name: Microbacterium rhizomatis Hoang et al. 2015

@ref: 24035

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium rhizomatis

full scientific name: Microbacterium rhizomatis Hoang et al. 2015

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
67771positive
69480positive100

Culture and growth conditions

culture medium

  • @ref: 24035
  • 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
24035positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no91
69480no99.951

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12

enzymes

  • @ref: 67770
  • value: beta-glucosidase
  • ec: 3.2.1.21

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24035rhizome, ginseng rootHwacheon mountainRepublic of KoreaKORAsia
67770Rhizome of mountain ginseng root in Hwacheon mountainGangwon ProvinceRepublic of KoreaKORAsia
67771From rhizome of mountain ginseng root in Hwacheon mountainGangwon provinceRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

Safety information

risk assessment

  • @ref: 24035
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24035
  • description: Microbacterium rhizomatis strain DCY100 16S ribosomal RNA gene, partial sequence
  • accession: KP161851
  • length: 1408
  • database: ena
  • NCBI tax ID: 1631477

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium rhizomatis strain JCM 305981631477.3wgspatric1631477
66792Microbacterium rhizomatis JCM 305982922489777draftimg1631477
67770Microbacterium rhizomatis JCM 30598GCA_008710745contigncbi1631477

GC content

@refGC-contentmethod
2403563.6
6777063.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno91no
motileno92.908no
gram-positiveyes91.876yes
anaerobicno99.595yes
aerobicyes93.734yes
halophileno93.355no
spore-formingno91.298no
glucose-utilyes85.809no
flagellatedno98.316no
thermophileno99.349no
glucose-fermentno93.125no

External links

@ref: 24035

culture collection no.: DSM 103406, JCM 30598, KCTC 39529, DCY 100

straininfo link

  • @ref: 90596
  • straininfo: 401350

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26296337Microbacterium rhizomatis sp. nov., a beta-glucosidase-producing bacterium isolated from rhizome of Korean mountain ginseng.Hoang VA, Kim YJ, Nguyen NL, Kang CH, Kang JP, Singh P, Farh ME, Yang DU, Yang DCInt J Syst Evol Microbiol10.1099/ijsem.0.0003992015*Actinomycetales/classification, Bacterial Typing Techniques, Base Composition, Cellulases/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genotype, Glucosidases, Glycolipids/chemistry, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization/genetics, Panax/microbiology, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizome, Sequence Analysis, DNA, Soil MicrobiologyGenetics
Phylogeny33502309Microbacterium caowuchunii sp. nov. and Microbacterium lushaniae sp. nov., isolated from plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau of PR China.Tian Z, Yang J, Lai XH, Pu J, Jin D, Luo X, Huang Y, Li J, Zhang G, Wang S, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0046622021Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Contents/microbiology, Lagomorpha/*microbiology, Microbacterium/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
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
24035Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103406Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103406)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
90596Reimer, 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-ID401350.1