Strain identifier

BacDive ID: 7153

Type strain: Yes

Species: Methylorubrum rhodinum

Strain history: T. Urakami TK 0010 <-- ATCC 14821 <-- W. Heumann.

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 988

BacDive-ID: 7153

DSM-Number: 2163

keywords: mesophilic, Bacteria, 16S sequence, genome sequence

description: Methylorubrum rhodinum DSM 2163 is a mesophilic bacterium that was isolated from Alnus rhizosphere.

NCBI tax id

NCBI tax idMatching level
29428species
1236969strain

strain history

doi: 10.13145/bacdive7153.20220920.7

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Methylobacteriaceae
  • genus: Methylorubrum
  • species: Methylorubrum rhodinum
  • full scientific name: Methylorubrum rhodinum (Heumann 1962) Green and Ardley 2018
  • synonyms

    @refsynonym
    20215Pseudomonas rhodos
    20215Methylobacterium rhodos
    20215Methylobacterium rhodinum

@ref: 988

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Methylorubrum

species: Methylorubrum rhodinum

full scientific name: Methylorubrum rhodinum (Heumann 1962) Green and Ardley 2018

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
988NUTRIENT AGAR (DSMZ Medium 1)yeshttps://bacmedia.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Methanol 10.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
40314MEDIUM 54 - for Methylobacterium organophilum and M. rhodinumyesDistilled water make up to (995.000 ml);Iron (II) sulphate heptahydrate (4.000 mg);Zinc sulphate heptahydrate (0.100 mg);ManganeseII chloride tetrahydrate (0.030 mg);Boric acid (0.300 mg);Magnesium sulphate heptahydrate (1.000 g);Calcium chloride dihydrat

culture temp

@refgrowthtypetemperaturerange
988positivegrowth30mesophilic
40314positivegrowth25mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: Q-10

Isolation, sampling and environmental information

isolation

@refsample typehost species
988Alnus rhizosphereAlnus
67770Alnus rhizosphereAlnus rhizosphere

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

  • @ref: 988
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Methylobacterium rhodinum 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF3381791118ena29428
988Methylobacterium rhodinum gene for 16S ribosomal RNA, partial sequence, strain:DSM 2163AB1756441435ena29428

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylorubrum rhodinum DSM 2163GCA_014199935scaffoldncbi29428
66792Methylorubrum rhodinum JCM 2811 JCM 2811GCA_001310855contigncbi1236969
66792Methylorubrum rhodinum JCM 28111236969.4wgspatric1236969
66792Methylorubrum rhodinum strain DSM 216329428.5wgspatric29428
66792Methylorubrum rhodinum DSM 21632829745981draftimg29428
66792Methylorubrum rhodinum JCM 28112728369659draftimg1236969

GC content

  • @ref: 67770
  • GC-content: 65.8
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 988

culture collection no.: DSM 2163, ATCC 14821, NCIB 9421, JCM 2811, CCM 4463, CCUG 36917, CCUG 51501, CIP 101127, IFO 15691, LMG 2275, NBRC 15691, NCIMB 9421, VKM B-2065

straininfo link

@refpassport
20218http://www.straininfo.net/strains/15069
20218http://www.straininfo.net/strains/15068
20218http://www.straininfo.net/strains/15072

literature

  • topic: Phylogeny
  • Pubmed-ID: 30024371
  • title: Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov.
  • authors: Green PN, Ardley JK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002856
  • year: 2018
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/genetics, Methylobacterium/*classification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
988Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2163)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2163
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40314Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12669
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/