Strain identifier

BacDive ID: 140254

Type strain: Yes

Species: Flexivirga oryzae

Strain Designation: R1

Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; R1.

NCBI tax ID(s): 1794944 (species)

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General

@ref: 42861

BacDive-ID: 140254

DSM-Number: 105369

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, Gram-positive, coccus-shaped, colony-forming

description: Flexivirga oryzae R1 is an obligate aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from rice paddy.

NCBI tax id

  • NCBI tax id: 1794944
  • Matching level: species

strain history

@refhistory
42861<- KACC, Jeonju, Jeollabuk-do; KACC 18597 <- Ch.-O. Jeon, Chung-Ang Univ., Seoul, Republic of Korea; R1
67770C. O. Jeon; Chung-Ang Univ., South Korea; R1.

doi: 10.13145/bacdive140254.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermacoccaceae
  • genus: Flexivirga
  • species: Flexivirga oryzae
  • full scientific name: Flexivirga oryzae Hyeon et al. 2017

@ref: 42861

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermacoccaceae

genus: Flexivirga

species: Flexivirga oryzae

full scientific name: Flexivirga oryzae Hyeon et al. 2017

strain designation: R1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
25184positive0.5-0.6 µmcoccus-shapedno
69480positive100

colony morphology

  • @ref: 25184
  • colony color: creamy white
  • colony shape: circular
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25184Reasoner's 2A agar (R2A)yes
42861R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
25184positivegrowth10.0-37.0
25184positiveoptimum30mesophilic
42861positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25184positivegrowth5.0-9.0alkaliphile
25184positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25184
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
25184no
69480no99.9

halophily

@refsaltgrowthtested relationconcentration
25184NaClpositivegrowth0.0-3.0 %(w/v)
25184NaCloptimum0 %(w/v)

murein

  • @ref: 25184
  • murein short key: A11.39
  • type: A4alpha L-Lys-L-Ser2-D-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4), MK-8(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25184168082-dehydro-D-gluconate-builds acid from
2518417128adipate-assimilation
2518427613amygdalin-builds acid from
2518415963ribitol-builds acid from
2518418333D-arabitol-builds acid from
2518428847D-fucose-builds acid from
2518417716lactose-builds acid from
2518416899D-mannitol-builds acid from
251846731melezitose-builds acid from
2518428053melibiose-builds acid from
2518416634raffinose-builds acid from
2518416988D-ribose-builds acid from
2518417992sucrose-builds acid from
2518417924D-sorbitol-builds acid from
2518416443D-tagatose-builds acid from
2518427689decanoate-assimilation
2518417113erythritol-builds acid from
2518416813galactitol-builds acid from
251845291gelatin-hydrolysis
2518428066gentiobiose-builds acid from
2518424265gluconate-builds acid from
2518417754glycerol-builds acid from
2518415443inulin-builds acid from
2518430849L-arabinose-assimilation
2518430849L-arabinose-builds acid from
2518418403L-arabitol-builds acid from
2518462345L-rhamnose-builds acid from
2518417266L-sorbose-builds acid from
2518465328L-xylose-builds acid from
2518474863methyl beta-D-xylopyranoside-builds acid from
25184506227N-acetylglucosamine-assimilation
25184506227N-acetylglucosamine-builds acid from
2518432032potassium gluconate-assimilation
2518453258sodium citrate-assimilation
2518428017starch-builds acid from
2518427897tryptophan-energy source
2518453424tween 20-hydrolysis
2518453426tween 80-hydrolysis
2518418186tyrosine-hydrolysis
2518416199urea-hydrolysis
2518417151xylitol-builds acid from
25184581435-dehydro-D-gluconate+builds acid from
2518418305arbutin+builds acid from
25184casein+hydrolysis
2518417057cellobiose+builds acid from
2518417108D-arabinose+builds acid from
2518415824D-fructose+builds acid from
2518412936D-galactose+builds acid from
2518417634D-glucose+assimilation
2518417634D-glucose+builds acid from
2518462318D-lyxose+builds acid from
2518416899D-mannitol+assimilation
2518416024D-mannose+assimilation
2518416024D-mannose+builds acid from
2518465327D-xylose+builds acid from
251844853esculin+hydrolysis
251844853esculin+builds acid from
2518417754glycerol+builds acid from
2518428087glycogen+builds acid from
2518417268myo-inositol+builds acid from
2518418287L-fucose+builds acid from
2518425115malate+assimilation
2518417306maltose+assimilation
2518417306maltose+builds acid from
25184320061methyl alpha-D-glucopyranoside+builds acid from
2518443943methyl alpha-D-mannoside+builds acid from
2518417632nitrate+reduction
2518418401phenylacetate+assimilation
2518417814salicin+builds acid from
2518428017starch+hydrolysis
2518417992sucrose+builds acid from
2518427082trehalose+builds acid from
2518432528turanose+builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
2518435581indoleno
2518472813exopolysaccharideyes

metabolite tests

  • @ref: 25184
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25184acid phosphatase+3.1.3.2
25184alkaline phosphatase+3.1.3.1
25184alpha-chymotrypsin-3.4.21.1
25184alpha-fucosidase-3.2.1.51
25184alpha-galactosidase-3.2.1.22
25184alpha-glucosidase+3.2.1.20
25184alpha-mannosidase-3.2.1.24
25184arginine dihydrolase-3.5.3.6
25184beta-galactosidase+3.2.1.23
25184beta-glucosidase+3.2.1.21
25184beta-glucuronidase-3.2.1.31
25184catalase+1.11.1.6
25184cystine arylamidase-3.4.11.3
25184cytochrome oxidase-1.9.3.1
25184esterase (C 4)+
25184esterase Lipase (C 8)+
25184leucine arylamidase+3.4.11.1
25184lipase (C 14)-
25184N-acetyl-beta-glucosaminidase-3.2.1.52
25184naphthol-AS-BI-phosphohydrolase+
25184trypsin-3.4.21.4
25184tryptophan deaminase-4.1.99.1
25184valine arylamidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    2518410-Methyl C17:03.8
    2518410-Methyl C18:01.5
    25184C17:0 anteiso10.5
    25184C17:1 anteiso ω9c5
    25184C16:01.2
    25184C16:1 2OH2.9
    25184C16:1ω7c / C16:1ω6c2.8
    25184C17:1ω6c1.9
    25184C18:1ω9c1
    25184C15:0 iso4.5
    25184C16:0 iso28.5
    25184C16:1 iso H3.3
    25184C17:0 iso9.2
    25184C17:1 iso ω9c / C16:0 10-methyl17.4
    25184C18:0 iso1.6
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: liquid
  • incubation temperature: 30
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA 6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
25184rice paddySacheonRepublic of KoreaKORAsia35128R2A agar (BD)3 days25
42861rice paddySacheonRepublic of KoreaKORAsia
67770Rice paddyRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_168642.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_20999;97_35147;98_45372;99_168642&stattab=map
  • Last taxonomy: Flexivirga oryzae subclade
  • 16S sequence: KR025522
  • Sequence Identity:
  • Total samples: 42
  • soil counts: 4
  • aquatic counts: 20
  • animal counts: 18

Safety information

risk assessment

  • @ref: 42861
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42861
  • description: Flexivirga oryzae strain R1 16S ribosomal RNA gene, partial sequence
  • accession: KR025522
  • length: 1445
  • database: ena
  • NCBI tax ID: 1794944

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flexivirga oryzae DSM 105369GCA_014190805contigncbi1794944
66792Flexivirga oryzae strain DSM 1053691794944.3wgspatric1794944
66792Flexivirga oryzae DSM 1053692821263656draftimg1794944

GC content

@refGC-contentmethod
2518464.5fluorimetric
4286164.5
6777064.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno88no
motileno96.617yes
gram-positiveyes89.607yes
anaerobicno99.113no
aerobicyes93.093no
halophileno93.283no
spore-formingno81.985yes
glucose-utilyes90.78yes
flagellatedno98.695yes
thermophileno98.199yes
glucose-fermentno86.938no

External links

@ref: 42861

culture collection no.: DSM 105369, JCM 31060, KACC 18597

straininfo link

  • @ref: 96562
  • straininfo: 408276

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27902309Flexivirga oryzae sp. nov., isolated from soil of a rice paddy, and emended description of the genus Flexivirga Anzai et al. 2012.Hyeon JW, Kim HR, Lee HJ, Jeong SE, Choi SH, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0016572017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Oryza/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31800390Flexivirga caeni sp. nov., isolated from activated sludge.Keum DH, Lee YJ, Lee SY, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0039102020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
25184J. W. K. Hyeon, H. R.,Lee, H. J.,Jeong, S. E.,Choi, S. H.,Jeon, C. O.Flexivirga oryzae sp. nov., isolated from soil of a rice paddy, and emended description of the genus Flexivirga Anzai et al. 201210.1099/ijsem.0.001657IJSEM 67: 479-484 201727902309
42861Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105369Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105369)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
96562Reimer, 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-ID408276.1