Strain identifier

BacDive ID: 7171

Type strain: Yes

Species: Methylorubrum aminovorans

Strain Designation: TH-15

Strain history: CIP <- 1997, JCM <- T. Urakami, Mitsubishi Gas Chemical Co, Tokyo, Japan: strain TH-15

NCBI tax ID(s): 269069 (species)

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General

@ref: 3422

BacDive-ID: 7171

DSM-Number: 8832

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

description: Methylorubrum aminovorans TH-15 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 269069
  • Matching level: species

strain history

@refhistory
3422<- JCM <- T. Urakami; TH-15
67770T. Urakami TH-15.
116337CIP <- 1997, JCM <- T. Urakami, Mitsubishi Gas Chemical Co, Tokyo, Japan: strain TH-15

doi: 10.13145/bacdive7171.20230509.8.1

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 aminovorans
  • full scientific name: Methylorubrum aminovorans (Urakami et al. 1993) Green and Ardley 2018

  • synonyms

    • @ref: 20215
    • synonym: Methylobacterium aminovorans

@ref: 3422

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Methylorubrum

species: Methylorubrum aminovorans

full scientific name: Methylorubrum aminovorans (Urakami et al. 1993) Green and Ardley 2018

strain designation: TH-15

type strain: yes

Morphology

cell morphology

  • @ref: 116337
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 116337
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3422NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.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
40296MEDIUM 229 - for Methylobacterium aminovoransyesDistilled water make up to (990.000 ml);Zinc sulphate heptahydrate (5.000 mg);ManganeseII chloride tetrahydrate (5.000 mg);Magnesium sulphate heptahydrate (0.200 g);Calcium chloride dihydrate (30.000 mg);Agar (18.000 g);Yeast extract (0.200 g);Ammoniumsul
3422R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
116337CIP Medium 229yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=229

culture temp

@refgrowthtypetemperaturerange
3422positivegrowth28mesophilic
40296positivegrowth30mesophilic
67770positivegrowth30mesophilic
116337positivegrowth25-41
116337nogrowth5psychrophilic
116337nogrowth10psychrophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
116337NaClpositivegrowth0-4 %
116337NaClnogrowth6 %
116337NaClnogrowth8 %
116337NaClnogrowth10 %

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose+builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose+builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose+builds acid from65328
68371D-arabinose+builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
116337citrate-carbon source16947
116337esculin-hydrolysis4853
116337nitrate+reduction17632
116337nitrite-reduction16301
116337phenol-degradation15882
116337nitrate-respiration17632

antibiotic resistance

  • @ref: 116337
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116337
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
116337oxidase+
116337beta-galactosidase-3.2.1.23
116337alcohol dehydrogenase-1.1.1.1
116337gelatinase-
116337amylase-
116337DNase-
116337caseinase-3.4.21.50
116337catalase+1.11.1.6
116337tween esterase-
116337lecithinase-
116337lipase-
116337lysine decarboxylase-4.1.1.18
116337ornithine decarboxylase-4.1.1.17
116337phenylalanine ammonia-lyase-4.3.1.24
116337tryptophan deaminase-
116337urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116337--++-+--+--+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116337+-++/-+/-+/-+----+----------------------------+--+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116337-+-----------------------------+----------------++---------------------+---+---++-------++-----+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3422soil
67770SoilNiigata Pref.JapanJPNAsia
116337Environment, SoilNiigataJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

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: AJ851086
  • 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
34221Risk group (German classification)
1163371Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Methylobacterium aminovorans 16S rRNA gene, strain CCM 4612TAJ8510861392ena269069
20218Methylobacterium aminovorans gene for 16S ribosomal RNA, partial sequence, strain:JCM 8240AB1756291435ena269069

Genome sequences

  • @ref: 66792
  • description: Methylorubrum aminovorans NBRC 15686
  • accession: GCA_022179725
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 269069

GC content

@refGC-contentmethod
342268high performance liquid chromatography (HPLC)
6777067.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno77.42no
gram-positiveno97.627no
anaerobicno98.011no
aerobicyes89.364no
halophileno91.183no
spore-formingno92.6no
motileyes86.082no
glucose-fermentno87.681no
thermophileno98.759yes
glucose-utilyes88.884no

External links

@ref: 3422

culture collection no.: DSM 8832, ATCC 51358, JCM 8240, CCM 4612, CIP 105328, IFO 15686, LMG 21752, NBRC 15686, NCIMB 13343, VKM B-2145

straininfo link

  • @ref: 76624
  • straininfo: 42947

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
3422Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8832)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8832
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
40296Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17336
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/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
76624Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42947.1StrainInfo: A central database for resolving microbial strain identifiers
116337Curators of the CIPCollection of Institut Pasteur (CIP 105328)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105328