Strain identifier
BacDive ID: 6181
Type strain: 
Species: Hyphomicrobium facile
Strain Designation: H-526
Strain history: <- P. Hirsch, H-526
NCBI tax ID(s): 51670 (species)
version 9.1 (current version)
General
@ref: 823
BacDive-ID: 6181
DSM-Number: 1565
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Hyphomicrobium facile H-526 is a 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/bacdive6181.20240916.9.1
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: 97.833
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
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
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: nuccore
- NCBI tax ID: 582841
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Hyphomicrobium facile DSM 1565 | GCA_900116175 | contig | ncbi | 51670 |
| 66792 | Hyphomicrobium facile strain DSM 1565 | 51670.3 | wgs | patric | 51670 |
| 66792 | Hyphomicrobium facile facile DSM 1565 | 2636416034 | draft | img | 51670 |
GC content
- @ref: 823
- GC-content: 60.2
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.833 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 88.228 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 85.297 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 85.182 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.029 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 70.115 | no |
External links
@ref: 823
culture collection no.: DSM 1565, ATCC 27485, NCIB 10342
straininfo link
- @ref: 75664
- straininfo: 39026
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 823 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1565) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1565 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 69479 | João 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 75664 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39026.1 | StrainInfo: A central database for resolving microbial strain identifiers |