Strain identifier

BacDive ID: 7168

Type strain: Yes

Species: Methylorubrum rhodesianum

Strain history: CIP <- 1993, NCIMB <- 1987, R.I. Mateles, Jerusalem, Israel, Pseudomonas 1 <- J.S. Rock

NCBI tax ID(s): 29427 (species)

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General

@ref: 2284

BacDive-ID: 7168

DSM-Number: 5687

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

description: Methylorubrum rhodesianum DSM 5687 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from fermentor.

NCBI tax id

  • NCBI tax id: 29427
  • Matching level: species

strain history

@refhistory
2284<- NCIMB <- R.I. Mateles <- J.S. Rock
67770NCIMB 12249 <-- R. I. Mateles strain 1 <-- J. S. Rock.
122218CIP <- 1993, NCIMB <- 1987, R.I. Mateles, Jerusalem, Israel, Pseudomonas 1 <- J.S. Rock

doi: 10.13145/bacdive7168.20230509.8.1

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 rhodesianum
  • full scientific name: Methylorubrum rhodesianum (Green et al. 1988) Green and Ardley 2018

  • synonyms

    @refsynonym
    20215Methylobacterium lusitanum
    20215Methylobacterium rhodesianum

@ref: 2284

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Methylorubrum

species: Methylorubrum rhodesianum

full scientific name: Methylorubrum rhodesianum (Green et al. 1988) Green and Ardley 2018

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative100
122218negativerod-shapedno

colony morphology

  • @ref: 53489
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2284COLBY AND ZATHMAN MEDIUM (DSMZ Medium 606)yeshttps://mediadive.dsmz.de/medium/606Name: COLBY AND ZATHMAN MEDIUM (DSMZ Medium 606) Composition: Agar 15.0 g/l Methanol 1.584 g/l K2HPO4 1.2 g/l KH2PO4 0.62 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l NaCl 0.1 g/l CaCl2 x 6 H2O 0.05 g/l FeCl3 x 6 H2O 0.001 g/l ZnSO4 x 7 H2O 7e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l H3BO3 1e-05 g/l MnSO4 x 5 H2O 1e-05 g/l CuSO4 x 5 H2O 5e-06 g/l CoCl2 x 6 H2O 5e-06 g/l Distilled water
34919MEDIUM 53 - for Marinomonas and Methylobacterium (except Methylobacterium organophilum)yesDistilled water make up to (1000.000 ml);Methanol (5.000 ml);Brain heartinfusion (37.000 g)
122218CIP Medium 53yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=53

culture temp

@refgrowthtypetemperaturerange
2284positivegrowth30mesophilic
34919positivegrowth30mesophilic
53489positivegrowth30mesophilic
67770positivegrowth30mesophilic
122218positivegrowth15-30
122218nogrowth10psychrophilic
122218nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
53489aerobe
122218obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12221817632nitrate-reduction
12221816301nitrite-reduction

antibiotic resistance

  • @ref: 122218
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122218
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12221815688acetoin-
12221817234glucose-

enzymes

@refvalueactivityec
122218oxidase+
122218beta-galactosidase-3.2.1.23
122218alcohol dehydrogenase-1.1.1.1
122218gelatinase-
122218DNase-
122218caseinase-3.4.21.50
122218catalase+1.11.1.6
122218lecithinase-
122218lysine decarboxylase-4.1.1.18
122218ornithine decarboxylase-4.1.1.17
122218urease+3.5.1.5

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122218-+-----------------------------+----------------++---------------------+---+---++-+-----++-----+--+

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentisolation date
2284fermentor
53489Fermentor with formaldehyde as sole C-source1976-01-01
67770Fermentor operating with formaldehyde as a sole carbon source
122218Other, FermentorJerusalemIsraelISRAsia1987

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Bioreactor

taxonmaps

  • @ref: 69479
  • File name: preview.99_253.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_177;97_192;98_215;99_253&stattab=map
  • Last taxonomy: Methylorubrum
  • 16S sequence: AB175643
  • Sequence Identity:
  • Total samples: 110728
  • soil counts: 23280
  • aquatic counts: 23711
  • animal counts: 47578
  • plant counts: 16159

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
22841Risk group (German classification)
1222181Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Methylobacterium rhodesianum gene for 16S ribosomal RNA, partial sequence, strain:DSM 5687AB1756421435ena29427
20218Methylobacterium rhodesianum gene for 16S ribosomal RNA, partial sequence, strain:NCIMB 12249AB1756431435ena29427
20218Methylobacterium rhodesianum 16S ribosomal RNA sequenceL208501316ena29427

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylorubrum rhodesianum DSM 5687GCA_014199985scaffoldncbi29427
66792Methylorubrum rhodesianum strain DSM 568729427.3wgspatric29427
66792Methylorubrum rhodesianum DSM 56872829766573draftimg29427

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno74.929no
gram-positiveno97.452no
anaerobicno96.974yes
aerobicyes85.688yes
halophileno93.93no
spore-formingno92.233no
glucose-utilyes88.432no
thermophileno99.044yes
motileyes87.583no
glucose-fermentno88.144no

External links

@ref: 2284

culture collection no.: DSM 5687, ATCC 43882, NCIMB 12249, CCUG 36915, CIP 103771, JCM 10891, IFO 15844, NBRC 15844, VKM B-2142

straininfo link

  • @ref: 76621
  • straininfo: 92884

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16314683Reclassification of Methylobacterium chloromethanicum and Methylobacterium dichloromethanicum as later subjective synonyms of Methylobacterium extorquens and of Methylobacterium lusitanum as a later subjective synonym of Methylobacterium rhodesianum.Kato Y, Asahara M, Arai D, Goto K, Yokota AJ Gen Appl Microbiol10.2323/jgam.51.2872005Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal, Fatty Acids/analysis, Methylobacterium/chemistry/*classification/genetics/metabolism, Methylobacterium extorquens/chemistry/*classification/genetics/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNAMetabolism
Phylogeny30024371Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov.Green PN, Ardley JKInt J Syst Evol Microbiol10.1099/ijsem.0.0028562018Bacterial Typing Techniques, DNA, Bacterial/genetics, Methylobacterium/*classification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2284Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5687)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5687
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
34919Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15605
53489Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 36915)https://www.ccug.se/strain?id=36915
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/
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
76621Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92884.1StrainInfo: A central database for resolving microbial strain identifiers
122218Curators of the CIPCollection of Institut Pasteur (CIP 103771)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103771