Strain identifier
BacDive ID: 13821
Type strain:
Species: Phaeovulum veldkampii
Strain Designation: 51, BN 714
Strain history: <- ATCC <- J. F. Imhoff; 51 <- T. A. Hansen; CIP 103912
NCBI tax ID(s): 1185920 (strain), 33049 (species)
General
@ref: 4412
BacDive-ID: 13821
DSM-Number: 11550
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Phaeovulum veldkampii 51 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from freshwater pond.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1185920 | strain |
33049 | species |
strain history
- @ref: 4412
- history: <- ATCC <- J. F. Imhoff; 51 <- T. A. Hansen; CIP 103912
doi: 10.13145/bacdive13821.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Phaeovulum
- species: Phaeovulum veldkampii
- full scientific name: Phaeovulum veldkampii (Hansen and Imhoff 1985) Suresh et al. 2020
synonyms
@ref synonym 20215 Bieblia veldkampii 20215 Rhodobacter veldkampii
@ref: 4412
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Rhodobacter
species: Rhodobacter veldkampii
full scientific name: Rhodobacter veldkampii Hansen and Imhoff 1985
strain designation: 51, BN 714
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.998
Culture and growth conditions
culture medium
- @ref: 4412
- name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)
- growth: yes
- link: https://mediadive.dsmz.de/medium/27
- composition: Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l MgSO4 x 7 H2O 0.4 g/l Yeast extract 0.3 g/l L-Cysteine HCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Fe(III) citrate 0.005 g/l Resazurin 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water
culture temp
- @ref: 4412
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 4412
- oxygen tolerance: anaerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.996
Isolation, sampling and environmental information
isolation
- @ref: 4412
- sample type: freshwater pond
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Freshwater |
#Environmental | #Aquatic | #Pond (small) |
taxonmaps
- @ref: 69479
- File name: preview.99_22210.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_11227;97_13598;98_16752;99_22210&stattab=map
- Last taxonomy: Bieblia veldkampii subclade
- 16S sequence: D16421
- Sequence Identity:
- Total samples: 100
- soil counts: 8
- aquatic counts: 79
- animal counts: 12
- plant counts: 1
Safety information
risk assessment
- @ref: 4412
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Rhodobacter veldkampii 16S rRNA | D13477 | 1351 | ena | 1185920 |
20218 | Rhodobacter veldkampii gene for 16S rRNA | D16421 | 1389 | ena | 1185920 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Phaeovulum veldkampii DSM 11550 | GCA_004363195 | scaffold | ncbi | 1185920 |
66792 | Phaeovulum veldkampii DSM 11550 | GCA_003034995 | contig | ncbi | 1185920 |
66792 | Phaeovulum veldkampii DSM 11550 | GCA_016653435 | scaffold | ncbi | 1185920 |
66792 | Rhodobacter veldkampii DSM 11550 | 1185920.8 | wgs | patric | 1185920 |
66792 | Rhodobacter veldkampii DSM 11550 | 1185920.6 | wgs | patric | 1185920 |
66792 | Rhodobacter veldkampii DSM 11550 | 1185920.4 | wgs | patric | 1185920 |
66792 | Rhodobacter veldkampii DSM 11550 | 2795385478 | draft | img | 1185920 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 86 | no |
motile | no | 57.704 | no |
flagellated | no | 86.496 | no |
gram-positive | no | 98.575 | no |
anaerobic | no | 79.7 | no |
aerobic | no | 75.367 | no |
halophile | no | 74.604 | no |
spore-forming | no | 96.091 | no |
glucose-util | yes | 56.634 | no |
thermophile | no | 94.983 | yes |
glucose-ferment | no | 90.103 | no |
External links
@ref: 4412
culture collection no.: DSM 11550, ATCC 35703, CIP 103912, IFO 16458, NBRC 16458
straininfo link
- @ref: 82998
- straininfo: 41237
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4412 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11550) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11550 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
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) | |||
82998 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID41237.1 | StrainInfo: A central database for resolving microbial strain identifiers |