Strain identifier

BacDive ID: 133326

Type strain: Yes

Species: Microvirga ossetica

Strain Designation: V5/3M

NCBI tax ID(s): 1882682 (species)

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General

@ref: 25156

BacDive-ID: 133326

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, rod-shaped, colony-forming

description: Microvirga ossetica V5/3M is a Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from root nodules of Vicia alpestris plants.

NCBI tax id

  • NCBI tax id: 1882682
  • Matching level: species

doi: 10.13145/bacdive133326.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Methylobacteriaceae
  • genus: Microvirga
  • species: Microvirga ossetica
  • full scientific name: Microvirga ossetica Safronova et al. 2017

@ref: 25156

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Methylobacteriaceae

genus: Microvirga

species: Microvirga ossetica

strain designation: V5/3M

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25156negative1.0-1.7 µm0.6-1.0 µmrod-shapedno
69480negative99.985

colony morphology

  • @ref: 25156
  • colony size: 1 mm
  • colony color: transparent
  • colony shape: circular
  • medium used: modified yeast extract mannitol agar

Culture and growth conditions

culture medium

  • @ref: 25156
  • name: modified yeast extract mannitol agar
  • growth: yes
  • composition: supplemented with 0.5 % succinate

culture pH

@refabilitytypepH
25156positivegrowth6
25156nogrowth5

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.96

halophily

@refsaltgrowthtested relationconcentration
25156NaClpositivegrowth1 %(w/v)
25156NaClpositivegrowth2 %(w/v)
25156NaClpositivegrowth4 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2515617521(-)-quinic acid-assimilation
2515615588D-malate-assimilation
2515616651(S)-lactate-assimilation
25156167632-oxobutanoate-assimilation
25156309162-oxoglutarate-assimilation
2515636219alpha-lactose-assimilation
2515635391aspartate-assimilation
2515616947citrate-assimilation
2515618333D-arabitol-assimilation
2515630612D-glucarate-assimilation
251568391D-gluconate-assimilation
2515616899D-mannitol-assimilation
2515623652dextrin-assimilation
2515615740formate-assimilation
2515616537galactarate-assimilation
251565291gelatin-assimilation
2515617754glycerol-assimilation
2515616977L-alanine-assimilation
2515616467L-arginine-assimilation
2515629985L-glutamate-assimilation
2515615971L-histidine-assimilation
2515617306maltose-assimilation
2515617309pectin-assimilation
2515617272propionate-assimilation
2515616634raffinose-assimilation
2515617822serine-assimilation
2515617992sucrose-assimilation
2515615589L-malate+assimilation
25156370543-hydroxybutyrate+assimilation
25156739183-O-methyl-D-glucose+assimilation
2515630089acetate+assimilation
2515613705acetoacetate+assimilation
2515673706bromosuccinate+assimilation
2515617057cellobiose+assimilation
2515615824D-fructose+assimilation
2515678697D-fructose 6-phosphate+assimilation
2515628847D-fucose+assimilation
2515612936D-galactose+assimilation
2515618024D-galacturonic acid+assimilation
2515617634D-glucose+assimilation
2515615748D-glucuronate+assimilation
2515616024D-mannose+assimilation
2515617924D-sorbitol+assimilation
2515632528turanose+assimilation
2515628066gentiobiose+assimilation
2515632323glucuronamide+assimilation
2515617596inosine+assimilation
2515617464L-galactonic acid gamma-lactone+assimilation
2515662345L-rhamnose+assimilation
2515628053melibiose+assimilation
2515617632nitrate+reduction
2515617164stachyose+assimilation
2515627082trehalose+assimilation
2515616199urea+hydrolysis

enzymes

@refvalueactivityec
25156catalase+1.11.1.6
25156urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    2515610-Methyl C19:01.6
    25156C16:07.1
    25156C16:1ω7c / C15:0 iso 2OH3.7
    25156C17:01.1
    25156C18:01.9
    25156C18:0 3OH1.1
    25156C18:1ω7c63
    25156Cyclo C19:0ω8c4.2
    25156C16:1 iso I / C14:0 3OH12.411
  • type of FA analysis: whole cell analysis
  • incubation medium: LMG medium 115
  • incubation temperature: 28
  • incubation time: 3
  • library/peak naming table: TSBA 5
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 25156
  • sample type: root nodules of Vicia alpestris plants
  • geographic location: North Ossetia region (Caucasus)
  • country: Russia
  • origin.country: RUS
  • continent: Europe
  • enrichment culture: yeast extract mannitol agar
  • enrichment culture composition: supplemented with 0.5 % succinate
  • enrichment culture duration: 4-5 days
  • enrichment culture temperature: 28
  • isolation procedure: surface-sterilized in 96 % ethanol for 1 min,rinsed, individually crushed in 100 µl sterile water

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root nodule

taxonmaps

  • @ref: 69479
  • File name: preview.99_28730.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_1174;97_1377;98_21461;99_28730&stattab=map
  • Last taxonomy: Microvirga
  • 16S sequence: KX576552
  • Sequence Identity:
  • Total samples: 778
  • soil counts: 579
  • aquatic counts: 30
  • animal counts: 32
  • plant counts: 137

Sequence information

16S sequences

  • @ref: 25156
  • description: Microvirga sp. strain V5/3M 16S ribosomal RNA gene, partial sequence
  • accession: KX576552
  • length: 1394
  • database: nuccore
  • NCBI tax ID: 1873136

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microvirga ossetica V5/3mGCA_002741015completencbi1882682
66792Microvirga ossetica V5/3m2775506901completeimg1882682

GC content

  • @ref: 25156
  • GC-content: 61.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno80.494no
gram-positiveno97.482yes
anaerobicno97.134no
aerobicyes90.753no
halophileno93.163no
spore-formingno93.714no
glucose-utilyes89.009yes
thermophileno98.631no
motileyes78.965no
glucose-fermentno90.906no

External links

@ref: 25156

culture collection no.: LMG 29787, RCAM 02728

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902217
  • title: Microvirga ossetica sp. nov., a species of rhizobia isolated from root nodules of the legume species Vicia alpestris Steven.
  • authors: Safronova VI, Kuznetsova IG, Sazanova AL, Belimov AA, Andronov EE, Chirak ER, Osledkin YS, Onishchuk OP, Kurchak ON, Shaposhnikov AI, Willems A, Tikhonovich IA
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001577
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Methylobacteriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Russia, Sequence Analysis, DNA, Vicia/*microbiology
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
25156V. I. K. Safronova, I. G.,Sazanova, A. L.,Belimov, A. A.,Andronov, E. E.,Chirak, E. R.,Osledkin, Y. S.,Onishchuk, O. P.,Kurchak, O. N.,Shaposhnikov, A. I.,Willems, A.,Tikhonovich, I. A.Microvirga ossetica sp. nov., a species of rhizobia isolated from root nodules of the legume species Vicia alpestris Steven10.1099/ijsem.0.001577IJSEM 67: 94-100 201727902217
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic 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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1