Strain identifier

BacDive ID: 6181

Type strain: Yes

Species: Hyphomicrobium facile

Strain Designation: H-526

Strain history: <- P. Hirsch, H-526

NCBI tax ID(s): 51670 (species)

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General

@ref: 823

BacDive-ID: 6181

DSM-Number: 1565

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

description: Hyphomicrobium facile H-526 is a mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 51670
  • Matching level: species

strain history

  • @ref: 823
  • history: <- P. Hirsch, H-526

doi: 10.13145/bacdive6181.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Hyphomicrobiaceae
  • genus: Hyphomicrobium
  • species: Hyphomicrobium facile
  • full scientific name: Hyphomicrobium facile corrig. Hirsch 1989

  • synonyms

    • @ref: 20215
    • synonym: Hyphomicrobium facilis

@ref: 823

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Hyphomicrobiaceae

genus: Hyphomicrobium

species: Hyphomicrobium facile

full scientific name: Hyphomicrobium facile Hirsch 1989

strain designation: H-526

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.999

Culture and growth conditions

culture medium

  • @ref: 823
  • name: HYPHOMICROBIUM MEDIUM (DSMZ Medium 162)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/162
  • composition: Name: HYPHOMICROBIUM MEDIUM (DSMZ Medium 162) Composition: Methylamine hydrochloride 3.38 g/l Na2HPO4 2.13 g/l KH2PO4 1.36 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Yeast extract 0.1 g/l CaCl2 x 2 H2O 0.006 g/l FeSO4 x 7 H2O 0.003 g/l Na2MoO4 x 2 H2O 0.0015 g/l MnSO4 x H2O 0.001 g/l Distilled water

culture temp

  • @ref: 823
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.966

Isolation, sampling and environmental information

isolation

  • @ref: 823
  • sample type: soil
  • geographic location: New Hampshire
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2611.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_244;96_928;97_1080;98_1289;99_2611&stattab=map
  • Last taxonomy: Hyphomicrobium
  • 16S sequence: Y14309
  • Sequence Identity:
  • Total samples: 550
  • soil counts: 239
  • aquatic counts: 115
  • animal counts: 98
  • plant counts: 98

Safety information

risk assessment

  • @ref: 823
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 823
  • description: Hyphomicrobium facile subsp. facile partial 16S rRNA gene, type strain IFAM H-526T
  • accession: Y14309
  • length: 1423
  • database: ena
  • NCBI tax ID: 582841

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hyphomicrobium facile DSM 1565GCA_900116175contigncbi51670
66792Hyphomicrobium facile strain DSM 156551670.3wgspatric51670
66792Hyphomicrobium facile facile DSM 15652636416034draftimg51670

GC content

  • @ref: 823
  • GC-content: 60.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.113no
anaerobicno98.532no
halophileno89.31no
spore-formingno94.436no
glucose-utilyes73.641no
aerobicyes92.166no
thermophileno94.918no
flagellatedno79.267no
motileyes69.093no
glucose-fermentno92.311no

External links

@ref: 823

culture collection no.: DSM 1565, ATCC 27485, NCIB 10342

straininfo link

  • @ref: 75664
  • straininfo: 39026

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
823Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1565)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1565
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
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
75664Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39026.1StrainInfo: A central database for resolving microbial strain identifiers