Strain identifier

BacDive ID: 158421

Type strain: Yes

Species: Acidipropionibacterium virtanenii

Strain Designation: JS278

Strain history: <- E. Storgards, VTT Technical Research Centre, Finland; VTT E-113202 <- H. Hakuli

NCBI tax ID(s): 2057246 (species)

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General

@ref: 65097

BacDive-ID: 158421

DSM-Number: 106790

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped, colony-forming

description: Acidipropionibacterium virtanenii JS278 is an anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from malted barley.

NCBI tax id

  • NCBI tax id: 2057246
  • Matching level: species

strain history

  • @ref: 65097
  • history: <- E. Storgards, VTT Technical Research Centre, Finland; VTT E-113202 <- H. Hakuli

doi: 10.13145/bacdive158421.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Acidipropionibacterium
  • species: Acidipropionibacterium virtanenii
  • full scientific name: Acidipropionibacterium virtanenii Deptula et al. 2018

@ref: 65097

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Acidipropionibacterium

species: Acidipropionibacterium virtanenii

full scientific name: Acidipropionibacterium virtanenii Deptula et al. 2018

strain designation: JS278

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
66688positive1-5 µm0.7 µmrod-shaped
69480no90.68
69480positive100

colony morphology

  • @ref: 66688
  • colony size: 2-3 mm
  • colony color: cream-beige and change after 3 days to orange-brown
  • colony shape: circular
  • medium used: yeast-extract lactate agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65097PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
66688yeast-extract lactate agaryes

culture temp

@refgrowthtypetemperaturerange
65097positivegrowth30mesophilic
66688positiveoptimum30mesophilic
66688nogrowth42thermophilic
66688positivegrowth12-37

culture pH

@refabilitytypepHPH range
66688nogrowth4
66688nogrowth4.5
66688positivegrowth5-9alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66688anaerobe
66688aerobe

spore formation

@refspore formationconfidence
69480no99.989
69481no100

halophily

@refsaltgrowthtested relationconcentration
66688NaClpositivegrowth0-1.1 M
66688NaClpositivemaximum6.5 %(w/v)
66688NaClpositiveoptimum0 M

observation

@refobservation
66688Cells are pleomorphic.
66688In liquid cultures, pigmentation is observed when grown on lactic acid or turanose as a carbon source.
66688The main fermentation end products are propionic and acetic acids in molar ratio 2.5, which is unaffected by the presence of oxygen.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
666886731melezitose-builds acid from
6668815443inulin-builds acid from
6668816443D-tagatose-builds acid from
6668816813galactitol-builds acid from
6668817266L-sorbose-builds acid from
6668817268myo-inositol-builds acid from
6668818287L-fucose-builds acid from
6668828087glycogen-builds acid from
6668828847D-fucose-builds acid from
6668843943methyl alpha-D-mannoside-builds acid from
6668862318D-lyxose-builds acid from
6668862345L-rhamnose-builds acid from
6668865327D-xylose-builds acid from
6668865328L-xylose-builds acid from
6668874863methyl beta-D-xylopyranoside-builds acid from
66688potassium 2-dehydro-D-gluconate-builds acid from
66688potassium 5-dehydro-D-gluconate-builds acid from
6668812936D-galactose+builds acid from
6668815824D-fructose+builds acid from
6668815963ribitol+builds acid from
6668816024D-mannose+builds acid from
6668816634raffinose+builds acid from
6668816899D-mannitol+builds acid from
6668816988D-ribose+builds acid from
6668817057cellobiose+builds acid from
6668817108D-arabinose+builds acid from
6668817113erythritol+builds acid from
6668817151xylitol+builds acid from
6668817306maltose+builds acid from
6668817634D-glucose+builds acid from
6668817716lactose+builds acid from
6668817754glycerol+builds acid from
6668817814salicin+builds acid from
6668817924D-sorbitol+builds acid from
6668817992sucrose+builds acid from
6668818305arbutin+builds acid from
6668818333D-arabitol+builds acid from
6668818403L-arabitol+builds acid from
6668827082trehalose+builds acid from
6668828017starch+builds acid from
6668828053melibiose+builds acid from
6668828066gentiobiose+builds acid from
6668830849L-arabinose+builds acid from
6668832032potassium gluconate+builds acid from
6668832528turanose+builds acid from
6668859640N-acetylglucosamine+builds acid from
66688320061methyl alpha-D-glucopyranoside+builds acid from
66688esculin ferric citrate+builds acid from
6668827613amygdalin+/-builds acid from

enzymes

  • @ref: 66688
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
65097malted barleyLathiFinlandFINEurope
66688finnish malted barleyFinlandFINEuropeyeast extract-sodium lactate medium7 days30mixing 10 g barley with 90 ml Ringer's solution, incubated at 4°C for 30 min, and homogenized in Stomacher for 10 min. Serially diluted samples were plated on YEL agar (yeast extract-sodium lactate medium) and incubated anaerobically (O2 0 %, CO2 10 %, H2 10 %, N2 80 %; Anoxomat, Mart Microbiology) at 30°C for 7 days.

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Engineered#Treatment
#Engineered#Food production#Beverage
#Engineered#Food production#Fermented

Sequence information

16S sequences

  • @ref: 66688
  • description: Acidipropionibacterium sp. JS278 16S ribosomal RNA gene, partial sequence
  • accession: MG596783
  • length: 1527
  • database: ena
  • NCBI tax ID: 2057246

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidipropionibacterium virtanenii JS278GCA_003325455completencbi2057246
66792Acidipropionibacterium virtanenii JS2782834914592completeimg2057246

GC content

@refGC-contentmethod
6509768.4
6668868.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno98.467no
gram-positiveyes91.686yes
anaerobicno68.988no
aerobicno81.692no
halophileno95.387yes
spore-formingno87.85no
glucose-utilyes90.133no
thermophileno91.384no
motileno93.483no
glucose-fermentyes69.362no

External links

@ref: 65097

culture collection no.: DSM 106790, VTT E-113202

straininfo link

  • @ref: 111224
  • straininfo: 403114

literature

  • topic: Phylogeny
  • Pubmed-ID: 30156530
  • title: Acidipropionibacterium virtanenii sp. nov., isolated from malted barley.
  • authors: Deptula P, Smolander OP, Laine P, Roberts RJ, Edelmann M, Peltola P, Piironen V, Paulin L, Storgards E, Savijoki K, Laitila A, Auvinen P, Varmanen P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002965
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fermentation, Finland, Hordeum/*microbiology, *Phylogeny, Propionibacterium/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
65097Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-106790Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106790)
66688Paulina Deptula, Olli-Pekka Smolander, Pia Laine, Richard J. Roberts, Minnamari Edelmann, Petri Peltola, Vieno Piironen, Lars Paulin, Erna Storgards, Kirsi Savijoki, Arja Laitila, Petri Auvinen, Pekka VarmanenAcidipropionibacterium virtanenii sp. nov., isolated from malted barley10.1099/ijsem.0.002965IJSEM 68: 3175-3183 201830156530
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
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
111224Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID403114.1