Strain identifier

BacDive ID: 158539

Type strain: Yes

Species: Ravibacter arvi

Strain Designation: J77-1

Strain history: J. Kim; Kyonggi Univ., South Korea; J77-1.

NCBI tax ID(s): 2051041 (species)

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General

@ref: 65230

BacDive-ID: 158539

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

description: Ravibacter arvi J77-1 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from farmland soil.

NCBI tax id

  • NCBI tax id: 2051041
  • Matching level: species

strain history

  • @ref: 67770
  • history: J. Kim; Kyonggi Univ., South Korea; J77-1.

doi: 10.13145/bacdive158539.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Ravibacter
  • species: Ravibacter arvi
  • full scientific name: Ravibacter arvi Chaudhary et al. 2017

@ref: 65230

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cytophagaceae

genus: Ravibacter

species: Ravibacter arvi

strain designation: J77-1

type strain: yes

Morphology

cell morphology

  • @ref: 65230
  • gram stain: negative
  • cell length: 1.5-2.0 µm
  • cell width: 0.7-0.9 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 65230
  • colony size: 0.5-1.0 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: R2A agar

pigmentation

  • @ref: 65230
  • production: yes
  • name: flexirubin-type pigments

Culture and growth conditions

culture medium

@refnamegrowth
65230Reasoner's 2A agar (R2A)yes
65230Nutrient agar (NA)yes
65230tryptone soy agaryes
65230sorbitol MacConkey agarno
65230Marine agar (MA)no
65230LB (Luria-Bertani) MEDIUMyes
65230brain-heart infusion agaryes
65230veal infusion agaryes

culture temp

@refgrowthtypetemperaturerange
65230positivegrowth15-40
65230positiveoptimum25-37mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
65230positivegrowth5-10alkaliphile
65230positiveoptimum6-8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 65230
  • oxygen tolerance: aerobe

spore formation

  • @ref: 65230
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
65230NaClpositiveoptimum0 %
65230NaClpositivegrowth0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65230168082-dehydro-D-gluconate-builds acid from
652302-oxogluconate-builds acid from
65230161933-hydroxybenzoate-builds acid from
65230370543-hydroxybutyrate-builds acid from
65230178794-hydroxybenzoate-builds acid from
652305468404-nitrophenyl alpha-D-galactoside+builds acid from
6523017128adipate-assimilation
6523027689decanoate-assimilation
6523085146carboxymethylcellulose-hydrolysis
65230casein-hydrolysis
65230crab shell chitin-hydrolysis
6523017634D-glucose+assimilation
6523016899D-mannitol+assimilation
6523016899D-mannitol+builds acid from
6523016024D-mannose+assimilation
6523016988D-ribose+builds acid from
6523017924D-sorbitol-builds acid from
6523016991dna-hydrolysis
652304853esculin+hydrolysis
65230esculin ferric citrate+builds acid from
652305291gelatin-fermentation
652305291gelatin-hydrolysis
6523017234glucose-fermentation
6523028087glycogen-builds acid from
6523017268myo-inositol+builds acid from
6523017240itaconate+builds acid from
65230L-alanine 4-nitroanilide-builds acid from
6523030849L-arabinose-builds acid from
6523016467L-arginine-fermentation
6523018287L-fucose+builds acid from
6523015971L-histidine-builds acid from
6523017203L-proline+builds acid from
6523062345L-rhamnose+builds acid from
6523017115L-serine+builds acid from
6523016828L-tryptophan-builds acid from
6523024996lactate-builds acid from
6523025115malate-assimilation
6523017306maltose+assimilation
6523017306maltose+builds acid from
6523028053melibiose+builds acid from
65230506227N-acetylglucosamine+assimilation
6523017632nitrate-reduction
6523018401phenylacetate-assimilation
6523032032potassium gluconate-assimilation
6523017272propionate-builds acid from
6523017814salicin+builds acid from
6523032954sodium acetate-builds acid from
6523053258sodium citrate-assimilation
6523062983sodium malonate-builds acid from
6523028017starch-hydrolysis
652309300suberic acid-builds acid from
6523017992sucrose+builds acid from
6523027897tryptophan-energy source
6523053423tween 40+hydrolysis
6523053426tween 80-hydrolysis
6523018186tyrosine-hydrolysis
6523016199urea+builds acid from
6523031011valerate-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6523015688acetoinno
6523016136hydrogen sulfideno
6523035581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
6523017234glucose-
6523015688acetoin-
6523035581indole-

enzymes

@refvalueactivityec
65230catalase+1.11.1.6
65230cytochrome oxidase-1.9.3.1
65230tryptophan deaminase-4.1.99.1
65230alkaline phosphatase+3.1.3.1
65230esterase (C 4)+
65230esterase Lipase (C 8)+
65230lipase (C 14)+
65230leucine arylamidase+3.4.11.1
65230valine arylamidase+
65230cystine arylamidase+3.4.11.3
65230trypsin+3.4.21.4
65230acid phosphatase+3.1.3.2
65230naphthol-AS-BI-phosphohydrolase+
65230alpha-galactosidase+3.2.1.22
65230beta-galactosidase+3.2.1.23
65230alpha-glucosidase+3.2.1.20
65230beta-glucosidase+3.2.1.21
65230N-acetyl-beta-glucosaminidase+3.2.1.52
65230alpha-mannosidase+3.2.1.24
65230alpha-chymotrypsin-3.4.21.1
65230beta-glucuronidase-3.2.1.31
65230alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65230C12:00.2
    65230C14:00.6
    65230C16:010.1
    65230C15:0 anteiso0.5
    65230C11:0 iso0.5
    65230C13:0 iso0.5
    65230C14:0 iso0.3
    65230C15:0 iso9.9
    65230C17:0 iso0.4
    65230C16:1ω5c6.9
    65230C14:0 2OH0.2
    65230C15:0 iso 3OH2.5
    65230C16:0 2OH1.1
    65230C16:0 3OH4.6
    65230C16:0 iso 3OH0.2
    65230C17:0 iso 3OH8.5
    65230C18:0 2OH0.6
    65230C16:1ω7c and/or C16:1ω6c52.1
    65230C17:1 iso I and/or C17:1 anteiso B0.4
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
65230farmland soilSuwonRepublic of KoreaKORAsiaR2A broth300 ml of R2A broth containing cyclo-heximide (50.0 mg l^-1) and chloramphenicol (0.1 g l^-1)5 weeksroom temperature
67770Farmland soil at SuwonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Field

taxonmaps

  • @ref: 69479
  • File name: preview.99_80735.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_4133;96_33899;97_42988;98_56183;99_80735&stattab=map
  • Last taxonomy: Ravibacter arvi subclade
  • 16S sequence: KY233196
  • Sequence Identity:
  • Total samples: 3203
  • soil counts: 1235
  • aquatic counts: 1053
  • animal counts: 715
  • plant counts: 200

Sequence information

16S sequences

  • @ref: 65230
  • description: 16S rRNA gene sequence
  • accession: KY233196
  • database: nuccore

GC content

  • @ref: 67770
  • GC-content: 50.1
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 65230

culture collection no.: KEMB 9005-548, KACC 19172, JCM 31920

literature

  • topic: Phylogeny
  • Pubmed-ID: 29087270
  • title: Ravibacter arvi gen. nov., sp. nov., isolated from farmland soil during development of new culture techniques.
  • authors: Chaudhary DK, Dahal RH, Altankhuu K, Kim J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002456
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, *Farms, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • 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
65230Dhiraj Kumar Chaudhary, Ram Hari Dahal, Khulan Altankhuu, Jaisoo KimRavibacter arvi gen. nov., sp. nov., isolated from farmland soil during development of new culture techniques10.1099/ijsem.0.002456IJSEM 67: 5252-5260 201729087270
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/