Strain identifier
BacDive ID: 6194
Type strain:
Species: Rhodomicrobium vannielii
Strain history: <- ATCC <- C.B. van Niel, ATH 3.1.1 <- H.C. Douglas
NCBI tax ID(s): 648757 (strain), 1069 (species)
General
@ref: 2129
BacDive-ID: 6194
DSM-Number: 162
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Rhodomicrobium vannielii DSM 162 is an anaerobe, mesophilic, motile bacterium of the family Hyphomicrobiaceae.
NCBI tax id
NCBI tax id | Matching level |
---|---|
648757 | strain |
1069 | species |
strain history
- @ref: 2129
- history: <- ATCC <- C.B. van Niel, ATH 3.1.1 <- H.C. Douglas
doi: 10.13145/bacdive6194.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Hyphomicrobiaceae
- genus: Rhodomicrobium
- species: Rhodomicrobium vannielii
- full scientific name: Rhodomicrobium vannielii Duchow and Douglas 1949 (Approved Lists 1980)
@ref: 2129
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Hyphomicrobiaceae
genus: Rhodomicrobium
species: Rhodomicrobium vannielii
full scientific name: Rhodomicrobium vannielii Duchow and Douglas 1949
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 92.611 | |
69480 | 99.991 | negative |
Culture and growth conditions
culture medium
- @ref: 2129
- name: ACID RHODOSPIRILLACEAE MEDIUM (DSMZ Medium 26)
- growth: yes
- link: https://mediadive.dsmz.de/medium/26
- composition: Name: ACID RHODOSPIRILLACEAE MEDIUM (DSMZ Medium 26) Composition: Disodium succinate 1.0 g/l Ammonium acetate 0.5 g/l KH2PO4 0.5 g/l MgSO4 x 7 H2O 0.4 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l L-Cysteine HCl 0.3 g/l Yeast extract 0.2 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: 2129
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 2129
- oxygen tolerance: anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.96 |
compound production
- @ref: 2129
- compound: hydrogen
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_3623.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_244;96_1880;97_2258;98_2771;99_3623&stattab=map
- Last taxonomy: Rhodomicrobium
- 16S sequence: FN666247
- Sequence Identity:
- Total samples: 4835
- soil counts: 2659
- aquatic counts: 1719
- animal counts: 222
- plant counts: 235
Safety information
risk assessment
- @ref: 2129
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | R.vannielii 16S ribosomal RNA | M34127 | 1484 | ena | 1069 |
2129 | Rhodomicrobium vannielii partial 16S rRNA gene, strain DSM 162 | FN666247 | 1470 | ena | 1069 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhodomicrobium vannielii ATCC 17100 | GCA_000166055 | complete | ncbi | 648757 |
66792 | Rhodomicrobium vannielii ATCC 17100 | GCA_016461745 | contig | ncbi | 648757 |
66792 | Rhodomicrobium udaipurense strain JA643 | 1202716.4 | wgs | patric | 1202716 |
66792 | Rhodomicrobium vannielii ATCC 17100 | 648757.17 | wgs | patric | 648757 |
66792 | Rhodomicrobium vannielii ATCC 17100 | 648757.4 | complete | patric | 648757 |
66792 | Rhodomicrobium vannielii ATCC 17100 | 649633090 | complete | img | 648757 |
GC content
- @ref: 2129
- GC-content: 62.8
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 90.14 | no |
flagellated | no | 65.179 | no |
gram-positive | no | 99.057 | no |
anaerobic | yes | 82.305 | yes |
aerobic | no | 86.804 | no |
halophile | no | 94.038 | no |
spore-forming | no | 88.072 | no |
thermophile | no | 89.786 | no |
glucose-util | yes | 66.984 | no |
glucose-ferment | no | 91.144 | no |
External links
@ref: 2129
culture collection no.: DSM 162, ATCC 17100, ATH 3.1.1
straininfo link
- @ref: 75674
- straininfo: 4898
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Enzymology | 6653558 | Structural studies on the phosphate-free lipid A of Rhodomicrobium vannielii ATCC 17100. | Holst O, Borowiak D, Weckesser J, Mayer H | Eur J Biochem | 10.1111/j.1432-1033.1983.tb07832.x | 1983 | Amides/analysis, Chemical Phenomena, Chemistry, Concanavalin A, Dansyl Compounds, Fatty Acids/analysis, Gas Chromatography-Mass Spectrometry, Glucosamine/analysis, *Lipid A/isolation & purification, Magnetic Resonance Spectroscopy, Methylation, Oxidation-Reduction, Rhodospirillaceae/*analysis | Phylogeny |
Phylogeny | 23291882 | Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream. | Ramana VV, Raj PS, Tushar L, Sasikala C, Ramana CV | Int J Syst Evol Microbiol | 10.1099/ijs.0.046409-0 | 2013 | Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodomicrobium/*classification/genetics/isolation & purification, Rivers/*microbiology, Sequence Analysis, DNA, Triterpenes/analysis | Genetics |
Phylogeny | 31661050 | Rhodomicrobium lacus sp. nov., an alkalitolerent bacterium isolated from Umiam lake, Shillong, India. | G S, Kumar D, Uppada J, Ch S, Ch V R | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003813 | 2020 | Bacterial Typing Techniques, Bacteriochlorophyll A/chemistry, Base Composition, Carotenoids/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Lakes/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Rhodomicrobium/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry, Water Microbiology | Transcriptome |
Pathogenicity | 33383833 | The Lipid A from the Lipopolysaccharide of the Phototrophic Bacterium Rhodomicrobium vannielii ATCC 17100 Revisited. | Komaniecka I, Susniak K, Choma A, Heine H, Holst O | Int J Mol Sci | 10.3390/ijms22010258 | 2020 | Chromatography, Liquid, Humans, Lipid A/*chemistry, Lipopolysaccharides/chemistry, Magnetic Resonance Spectroscopy, Mass Spectrometry, Molecular Structure, Phototrophic Processes, Rhodomicrobium/*chemistry/metabolism, Spectrometry, Mass, Electrospray Ionization, Tandem Mass Spectrometry | Proteome |
Genetics | 33795336 | Revised Draft Genome Sequences of Rhodomicrobium vannielii ATCC 17100 and Rhodomicrobium udaipurense JA643. | Conners EM, Davenport EJ, Bose A | Microbiol Resour Announc | 10.1128/MRA.00022-21 | 2021 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2129 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 162) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-162 | |||
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) | |||
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 | |||
75674 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID4898.1 | StrainInfo: A central database for resolving microbial strain identifiers |