Strain identifier

BacDive ID: 7170

Type strain: Yes

Species: Methylorubrum zatmanii

Strain Designation: 135

Strain history: CIP <- 1993, NCIMB <- R.I. Mateles, Jerusalem, Israel, Pseudomonas 135 <- J.S. Rock

NCBI tax ID(s): 29429 (species)

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

@ref: 2285

BacDive-ID: 7170

DSM-Number: 5688

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

description: Methylorubrum zatmanii 135 is a mesophilic, Gram-negative, motile bacterium that was isolated from fermentor.

NCBI tax id

  • NCBI tax id: 29429
  • Matching level: species

strain history

@refhistory
2285<- NCIMB <- R.I. Mateles, 135 <- J.S. Rock
67770NCIMB 12243 <-- R. I. Mateles 135 <-- J. S. Rock.
124022CIP <- 1993, NCIMB <- R.I. Mateles, Jerusalem, Israel, Pseudomonas 135 <- J.S. Rock

doi: 10.13145/bacdive7170.20230509.8.1

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

    • @ref: 20215
    • synonym: Methylobacterium zatmanii

@ref: 2285

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Methylorubrum

species: Methylorubrum zatmanii

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

strain designation: 135

type strain: yes

Morphology

cell morphology

  • @ref: 124022
  • gram stain: negative
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2285COLBY 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
40783MEDIUM 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)
124022CIP Medium 53yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=53

culture temp

@refgrowthtypetemperaturerange
2285positivegrowth30mesophilic
40783positivegrowth30mesophilic
67770positivegrowth30mesophilic
124022positivegrowth30mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12402217632nitrate-reduction
12402216301nitrite-reduction

metabolite production

  • @ref: 124022
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12402215688acetoin-
12402217234glucose-

enzymes

@refvalueactivityec
124022oxidase+
124022beta-galactosidase-3.2.1.23
124022alcohol dehydrogenase-1.1.1.1
124022gelatinase-
124022DNase-
124022caseinase-3.4.21.50
124022catalase+1.11.1.6
124022lecithinase-
124022lysine decarboxylase-4.1.1.18
124022ornithine decarboxylase-4.1.1.17
124022urease+3.5.1.5

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
124022-+-----------------------------+-------------+--++-------------------------+---++-+-----+------+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2285fermentor
67770Fermentor operating with formaldehyde as a sole carbon source
124022Other, FermentorJerusalemIsraelISRAsia

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: AB175647
  • 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
22851Risk group (German classification)
1240221Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Methylobacterium zatmanii gene for 16S ribosomal RNA, partial sequence, strain:DSM 5688AB1756471435ena29429
20218Methylobacterium zatmanii (NCIMB 12243) 16S ribosomal RNAL208041316ena29429

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylorubrum zatmanii LMG 6087GCA_014845115contigncbi29429
66792Methylorubrum zatmanii strain LMG 608729429.5wgspatric29429

GC content

  • @ref: 67770
  • GC-content: 70.3
  • method: Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno97.862no
anaerobicno97.319no
halophileno92.656no
spore-formingno92.529no
glucose-utilyes87.366no
motileyes87.554no
flagellatedno73.023no
aerobicyes89.24no
thermophileno99.122yes
glucose-fermentno89.049no

External links

@ref: 2285

culture collection no.: DSM 5688, ATCC 43883, NCIMB 12243, CCUG 36916, CIP 103774, LMG 6087, IFO 15845, VKM B-2161, JCM 10892, CCM 4464, NBRC 15845

straininfo link

  • @ref: 76623
  • straininfo: 13721

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24297603Methylobacterium pseudosasae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the bamboo phyllosphere.Madhaiyan M, Poonguzhali SAntonie Van Leeuwenhoek10.1007/s10482-013-0085-02013Acyl-Butyrolactones/analysis, Alcohol Oxidoreductases/genetics, Bambusa/*microbiology, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Methanol/*metabolism, Methylobacterium/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
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
2285Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5688)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5688
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
40783Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15608
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
76623Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13721.1StrainInfo: A central database for resolving microbial strain identifiers
124022Curators of the CIPCollection of Institut Pasteur (CIP 103774)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103774