We are hiring!

Strain identifier

BacDive ID: 6194

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 7.1 (current version):
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 7.1 (current version)

General

@ref: 2129

BacDive-ID: 6194

DSM-Number: 162

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Rhodomicrobium vannielii DSM 162 is an anaerobe, mesophilic bacterium of the family Hyphomicrobiaceae.

NCBI tax id

NCBI tax idMatching level
648757strain
1069species

strain history: <- ATCC <- C.B. van Niel, ATH 3.1.1 <- H.C. Douglas

doi: 10.13145/bacdive6194.20221219.7.1

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: 69480
  • gram stain: negative
  • confidence: 99.243

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: 69480
  • spore formation: no
  • confidence: 95.913

compound production

  • @ref: 2129
  • compound: hydrogen

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 98.186

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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218R.vannielii 16S ribosomal RNAM341271484ena1069
2129Rhodomicrobium vannielii partial 16S rRNA gene, strain DSM 162FN6662471470ena1069

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodomicrobium vannielii ATCC 17100 ATCC 17100GCA_000166055completencbi648757
66792Rhodomicrobium vannielii ATCC 17100 ATCC 17100GCA_016461745contigncbi648757
66792Rhodomicrobium udaipurense strain JA6431202716.4wgspatric1202716
66792Rhodomicrobium vannielii ATCC 17100648757.17wgspatric648757
66792Rhodomicrobium vannielii ATCC 17100648757.4completepatric648757
66792Rhodomicrobium vannielii ATCC 17100649633090completeimg648757
66792Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 V15GCA_001215885scaffoldpatric85569
66792Escherichia coli Ec.46391GCA_007558405contigpatric562
66792Staphylococcus aureus M3925GCA_900251895scaffoldpatric1280

GC content

  • @ref: 2129
  • GC-content: 62.8

External links

@ref: 2129

culture collection no.: DSM 162, ATCC 17100, ATH 3.1.1

straininfo link

@refpassport
20218http://www.straininfo.net/strains/21290
20218http://www.straininfo.net/strains/21289

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology6653558Structural studies on the phosphate-free lipid A of Rhodomicrobium vannielii ATCC 17100.Holst O, Borowiak D, Weckesser J, Mayer HEur J Biochem10.1111/j.1432-1033.1983.tb07832.x1983Amides/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/*analysisPhylogeny
Phylogeny23291882Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream.Ramana VV, Raj PS, Tushar L, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.046409-02013Bacterial 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/analysisGenetics
Phylogeny31661050Rhodomicrobium lacus sp. nov., an alkalitolerent bacterium isolated from Umiam lake, Shillong, India.G S, Kumar D, Uppada J, Ch S, Ch V RInt J Syst Evol Microbiol10.1099/ijsem.0.0038132020Bacterial 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 MicrobiologyTranscriptome
Pathogenicity33383833The Lipid A from the Lipopolysaccharide of the Phototrophic Bacterium Rhodomicrobium vannielii ATCC 17100 Revisited.Komaniecka I, Susniak K, Choma A, Heine H, Holst OInt J Mol Sci10.3390/ijms220102582020Chromatography, 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 SpectrometryProteome
Genetics33795336Revised Draft Genome Sequences of Rhodomicrobium vannielii ATCC 17100 and Rhodomicrobium udaipurense JA643.Conners EM, Davenport EJ, Bose AMicrobiol Resour Announc10.1128/MRA.00022-212021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2129Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 162)https://www.dsmz.de/collection/catalogue/details/culture/DSM-162
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
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)